suiming47
2010-Nov-24 02:05 UTC
[R] 4. Rexcel (Luis Felipe Parra)-how to run a code from excel
Hi Louis,
It's simple to run a r script from the excel spreadsheet.
Just write your code, source("C:\\Quantil
Aplicativos\\Genercauca\\BackwardSelectionNC.r"), into a cell of a
workingsheet. Then right-click the cell and select "run code" in the
pop-up
menu.
Hope this will help you.
Best,
Bernard
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Today's Topics:
1. Re: "unexpected numeric constant" while reading tab delimited
csv file (Mike Marchywka)
2. how to sample lowess/loess into matrix ? (madr)
3. Re: "unexpected numeric constant" while reading tab delimited
csv file (Duncan Murdoch)
4. Rexcel (Luis Felipe Parra)
5. how to change number of characters per line for print() to
sink()? (Nevil Amos)
6. Invitation ? se connecter sur LinkedIn
(Aline Uwimana via LinkedIn)
7. Re: How to combine Date and time in one column
(Gabor Grothendieck)
8. Tinn-R 2.3.7.0 released (Jose Claudio Faria)
9. Rexcel (Luis Felipe Parra)
10. Re: how to change number of characters per line for print()
to sink()? (jim holtman)
11. Re: boxplot: reverse y-axis order (S Ellison)
12. plot inside function does not work (Alaios)
13. Re: how to sample lowess/loess into matrix ? (madr)
14. Re: plot inside function does not work (Claudia Beleites)
15. Re: Rexcel (Stephen Liu)
16. Re: plot inside function does not work (Alaios)
17. Invitation ? se connecter sur LinkedIn (Yann Lancien via LinkedIn)
18. Prob with merge (Joel)
19. Re: Making a line in a legend shorter (Peter Ehlers)
20. Re: Prob with merge (ONKELINX, Thierry)
21. Re: calculating martingale residual on new data using
"predict.coxph" (Terry Therneau)
22. Re: Prob with merge (Joel)
23. What if geoRglm results showed that a non-spacial model fits?
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24. Help with plotting kohonen maps (Stella Pachidi)
25. Re: ?summaryRprof running at 100% cpu for one hour ...
(Kjetil Halvorsen)
26. Re: ?summaryRprof running at 100% cpu for one hour ...
(Mike Marchywka)
27. hierarchical mixture modelling (Mike Lawrence)
28. Check for is.object (Santosh Srinivas)
29. Fast Two-Dimensional Optimization (Wonsang You)
30. Re: plotting a timeline (?ukasz R?c?awowicz)
31. Re: memory profiling (Patrick Leyshock)
32. Re: ?summaryRprof running at 100% cpu for one hour ...
(Kjetil Halvorsen)
33. Re: An empty grey diagram (Martin Maechler)
34. Re: ?summaryRprof running at 100% cpu for one hour ...
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35. Re: Check for is.object (Jonathan P Daily)
36. Re: solve nonlinear equation using BBsolve (Berend Hasselman)
37. Re: Alternatives to image(...) and filled.contour(...) for
2-D filled Plots (Ista Zahn)
38. Re: statistical test for comparison of two classifications
(nominal) (Matt Shotwell)
39. Re: Check for is.object (Phil Spector)
40. Re: "negative alpha" or custom gradient colors of data dots
in scatterplot ? (Ista Zahn)
41. Problem setting the number of digits in xtable (wphantomfr)
42. RCurl : All connection are used ? (omerle)
43. sm.ancova graphic (Lucia Ca?as)
44. Plotting a cloud/fog of variable density in rgl (JiHO)
45. Re: RCurl : All connection are used ? (Mike Marchywka)
46. Re: Ordeing Zoo object (Manta)
47. Re: Plotting a cloud/fog of variable density in rgl
(Duncan Murdoch)
48. Re: How to produce a graph of glms in R? (Greg Snow)
49. Re: Plotting a cloud/fog of variable density in rgl
(Mike Marchywka)
50. Re: data acquisition with R? (B.-Markus Schuller)
51. Is it possible to make a matrix to start at row 0? (bogdanno)
52. Re: Rexcel (csrabak)
53. Re: question about constraint minimization (dhacademic at gmail.com)
54. Re: Lost in POSIX (Dimitri Shvorob)
55. Re: Find in R and R books (Georg Otto)
56. Re: using rpart with a tree misclassification condition (meytar)
57. Re: memory profiling (Patrick Leyshock)
58. Some questione about plot (romzero)
59. how do remove those predictor which have p value greater than
0.05 in GLM? (shubha)
60. Re: how to apply sample function to each row of a data frame?
(wangwallace)
61. Re: arima (tomreilly)
62. Wait for user input with readline() (Nathan Miller)
63. Re: txtProgressBar strange behavior in R 2.12.0
(Viechtbauer Wolfgang (STAT))
64. How to call web service in R (??)
65. save a regression model that can be used later
(Ni, Melody Zhifang)
66. Re: question about constraint minimization (Ravi Varadhan)
67. Re: Is it possible to make a matrix to start at row 0?
(Joshua Wiley)
68. Re: Is it possible to make a matrix to start at row 0?
(Bert Gunter)
69. Re: RGoogleDocs stopped working (Harlan Harris)
70. Re: sm.ancova graphic (Peter Ehlers)
71. Re: Wait for user input with readline() (Joshua Wiley)
72. Re: Ordeing Zoo object (Gabor Grothendieck)
73. Re: Is it possible to make a matrix to start at row 0?
(Ben Bolker)
74. Re: save a regression model that can be used later
(David Winsemius)
75. how to round only one column of a matrix ? (madr)
76. Re: Is it possible to make a matrix to start at row 0?
(baptiste auguie)
77. Re: how to round only one column of a matrix ? (Phil Spector)
78. Re: How to call web service in R (Steve Lianoglou)
79. aggregate a Date column does not work? (Tan, Richard)
80. R2WinBUGS help (bmiddle)
81. Re: FW: help with time Series regression please (tomreilly)
82. Re: Is it possible to make a matrix to start at row 0?
(Mike Marchywka)
83. Re: aggregate a Date column does not work? (David Winsemius)
84. I need a very specific unique like function and I don't know
even how to properly call this (madr)
85. Re: aggregate a Date column does not work? (Tan, Richard)
86. R package "kernlab" can not be properly loaded (Xiaoqi Cui)
87. Re: Rexcel (Erich Neuwirth)
88. Re: aggregate a Date column does not work? (David Winsemius)
89. Re: aggregate a Date column does not work? (Tan, Richard)
90. Re: aggregate a Date column does not work? (Gabor Grothendieck)
91. Re: "negative alpha" or custom gradient colors of data dots
in... (madr)
92. Re: how do remove those predictor which have p value greater
than 0.05 in GLM? (Frank Harrell)
93. Help: Standard errors arima (lucia)
94. Re: Help: Standard errors arima (David Winsemius)
95. Re: R2WinBUGS help (Uwe Ligges)
96. Re: R package "kernlab" can not be properly loaded
(David Winsemius)
97. Re: R package "kernlab" can not be properly loaded (Uwe Ligges)
98. Re: I need a very specific unique like function and I don't
know even how to properly call this (Ista Zahn)
99. Re: R2WinBUGS help (bmiddle)
100. Re: how do remove those predictor which have p value greater
than 0.05 in GLM? (shubha)
101. Re: Help: Standard errors arima (Dennis Murphy)
102. Probit Analysis: Confidence Interval for the LD50 using
Fieller's and Heterogeneity (UNCLASSIFIED)
(Kenney, Colleen T CTR USA AMC)
103. how to calculate derivative (Yogesh Tiwari)
104. Re: cpgram: access data, confidence bands (David Scott)
105. Re: Probit Analysis: Confidence Interval for the LD50 using
Fieller's and Heterogeneity (UNCLASSIFIED) (David Winsemius)
106. Re: Probit Analysis: Confidence Interval for the LD50 using
Fieller's and Heterogeneity (UNCLASSIFIED) (Dennis Murphy)
107. empity value in colnames (M.Ribeiro)
108. Re: ?summaryRprof running at 100% cpu for one hour ...
(Kjetil Halvorsen)
109. Re: empity value in colnames (David Winsemius)
110. Re: ?summaryRprof running at 100% cpu for one hour ...
(Mike Marchywka)
111. Sporadic errors when training models using CARET (Kendric Wang)
112. Re: I need a very specific unique like function and I don't
know even how to properly call this (Phil Spector)
113. Re: how do remove those predictor which have p value greater
than 0.05 in GLM? (David Winsemius)
114. Re: plotting a timeline (Peter Ehlers)
115. Gap between graph and axis (Sebastian Rudnick)
116. Re: Gap between graph and axis (Bill.Venables at csiro.au)
117. R on Androids? (Erin Hodgess)
118. Re: how to loop through variables in R? (watashi at post.com)
119. How to start default browser on R (Stephen Liu)
120. question on "uniCox" (Shi, Tao)
121. Re: Find in R and R books (Spencer Graves)
122. Re: calculating martingale residual on new data using
"predict.coxph" (Shi, Tao)
123. Re: calculating martingale residual on new data using (Shi, Tao)
124. Re: calculating martingale residual on new data using
"predict.coxph" (Shi, Tao)
125. Re: Find in R and R books (Mike Marchywka)
126. Re: Fast Two-Dimensional Optimization (Ben Bolker)
127. Re: how to loop through variables in R? (watashi at post.com)
128. Re: How to start default browser on R (David Scott)
129. Re: Find in R and R books (Spencer Graves)
130. using the "apply" method for functions with multiple inputs
(joeponzio)
131. permalgorithm (Kere Klein)
132. Re: using the "apply" method for functions with multiple
inputs (David Winsemius)
133. Re: How to start default browser on R (Stephen Liu)
134. Re: How to start default browser on R (Ista Zahn)
135. Re: how to calculate derivative (Ravi Varadhan)
136. Re: How to start default browser on R (Stephen Liu)
137. Re: How to start default browser on R (David Scott)
138. Re: how to calculate derivative (Spencer Graves)
139. Re: Is it possible to make a matrix to start at row 0?
(David Stoffer)
140. overlay histograms on map at map coordinates (Steve Bellan)
141. Re: Kalman filter (David Stoffer)
142. (no subject) (Mari Pesek)
143. factorial ANOVA for block/split-plot design (Mari Pesek)
144. Re: factorial ANOVA for block/split-plot design
(RICHARD M. HEIBERGER)
145. Re: question about constraint minimization (dhacademic at gmail.com)
146. Explained GLZ model variation (Shai)
147. Lattice and Quartz (Sarah Berry)
148. compare GLM coefficients (Kayce anderson)
149. Re: compare GLM coefficients (Michael Bedward)
150. Calculating correlation (gireesh bogu)
151. Re: Some questione about plot (Jim Lemon)
152. Re: How to start default browser on R (Stephen Liu)
153. Re: Calculating correlation (Tal Galili)
154. About available datasets on PC (Stephen Liu)
155. More detail in chart axis? (Noah Silverman)
156. Error: cannot allocate vector of size x Gb (64-bit ... yet
again) (derek eder)
157. Re: About available datasets on PC (Jeff Newmiller)
158. Re: More detail in chart axis? (Jim Lemon)
159. Re: how to get rid of unused space on all 4 borders in
plot() render (Petr PIKAL)
160. Re: how to loop through variables in R? (Ivan Calandra)
161. Odp: save a regression model that can be used later (Petr PIKAL)
162. Re: Lost in POSIX (Jeff Newmiller)
163. Re: About available datasets on PC (Stephen Liu)
164. Re: Calculating correlation (Tal Galili)
----------------------------------------------------------------------
Message: 1
Date: Mon, 22 Nov 2010 06:29:34 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <jdnewmil at dcn.davis.ca.us>, <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] "unexpected numeric constant" while reading tab
delimited csv file
Message-ID: <BLU113-W14BF3EA0E3821E3C0CA8AEBE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> Date: Mon, 22 Nov 2010 01:57:54 -0800
> From: jdnewmil at dcn.davis.ca.us
> To: madrazel at interia.pl
> CC: r-help at r-project.org
> Subject: Re: [R] "unexpected numeric constant" while reading tab
delimited
csv file>
> madr wrote:
> > my csv file is very simple - just one line for purpose of this test:
> > 0{TAB}0
> >
> > and read function is this:
> > csvdata =
read.csv(file="d:/s/test.csv",head=FALSE,sep="\t")
> >
> > then error comes:
> >
> > Error in source("d:/test.csv") :
> > d:/test.csv:1:9: unexpected numeric constant
> > 1: 0 0
> >
> >
> > but when I change delimiter to ; (colon) then error not shows up
anymore
> >
> You seem to be referencing two different files somehow... one in the
> root directory of your drive D, and the other in a subdirectory D:/s.
> This may have something to do with it... or may be extraneous.
>
> You haven't indicated what your working environment is, though the OS
> mention a distinction between whatever this environment is (RGui?) and
> "console". Are you using Cygwin? could end-of-line termination
(CRLF vs
> LF) be causing you difficulty?
The OP explained that and if you believe OP changing intended file changes
the error message. And, yes, I would strongly suggest getting cygwin
so you have some tools other than posting incomplete information of calling
tech support LOL. In this case, you would use something like "od" to
verify
that your file is as you expect. Just as printing numerical data often
truncated digits, unprintable chars don't always show up on printing.
od -ax or something may be informative. Changing the tab may have caused
editor to change line endings or something else. Smart editors often
mess stuff up.
>
> Perhaps you should follow the posting guide instructions...
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 2
Date: Mon, 22 Nov 2010 03:36:17 -0800 (PST)
From: madr <madrazel at interia.pl>
To: r-help at r-project.org
Subject: [R] how to sample lowess/loess into matrix ?
Message-ID: <1290425777216-3053458.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
code:
x <- rnorm(32)
y <- rnorm(32)
plot(x,y)
lines(lowess(x,y),col='red')
Now I need to sample the lowess function into matrix where one series will
be X and other will be values of lowess at particular X.
--
View this message in context:
http://r.789695.n4.nabble.com/how-to-sample-lowess-loess-into-matrix-tp30534
58p3053458.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 3
Date: Mon, 22 Nov 2010 06:38:52 -0500
From: Duncan Murdoch <murdoch.duncan at gmail.com>
To: madr <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] "unexpected numeric constant" while reading tab
delimited csv file
Message-ID: <4CEA564C.4000908 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
madr wrote:> my csv file is very simple - just one line for purpose of this test:
> 0{TAB}0
>
> and read function is this:
> csvdata =
read.csv(file="d:/s/test.csv",head=FALSE,sep="\t")
>
> then error comes:
>
> Error in source("d:/test.csv") :
> d:/test.csv:1:9: unexpected numeric constant
> 1: 0 0
>
>
> but when I change delimiter to ; (colon) then error not shows up anymore
You used source, not read.csv. They aren't the same thing.
If you typed what you said you typed, then you've hidden the real
read.csv function behind your own, and your own calls source. But I
don't think you typed what you said you typed.
Duncan Murdoch
------------------------------
Message: 4
Date: Mon, 22 Nov 2010 20:11:39 +0800
From: Luis Felipe Parra <felipe.parra at quantil.com.co>
To: r-help <r-help at r-project.org>
Subject: [R] Rexcel
Message-ID:
<AANLkTi=rWSJheF2WLtmhe8Lg0byHZf1nr3Cdj18Q8+mq at mail.gmail.com>
Content-Type: text/plain
Hello I am new to RExcel and I would like to run a source code form the
excel worksheet. I would like to run the following code
source("C:\\Quantil Aplicativos\\Genercauca\\BackwardSelectionNC.r")
from the excel wroksheet. Does anybody know how to do this?
Thank you
Felipe Parra
[[alternative HTML version deleted]]
------------------------------
Message: 5
Date: Mon, 22 Nov 2010 23:22:25 +1100
From: Nevil Amos <nevil.amos at gmail.com>
To: R-help at r-project.org
Subject: [R] how to change number of characters per line for print()
to sink()?
Message-ID: <4CEA6081.70202 at sci.monash.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I am using r to read and reformat data that is then saved to a text file
using sink(), the file has a number of initial lines of comments and
summary data followed by print of a data.frame with no row names.
for example
a<-c(100:120)
b<-c(rnorm(100:120))
c<-c(rnorm(200:220))
mydata<-data.frame(rbind(a,b,c))
sink("datafile.txt")
cat("comments about my data \n")
cat("other calculations returned as separate text comments on a line
\n")
print(mydata,row.names=F)
sink()
I need the content of the text file to keep each row of the data frame
on a single line thus (with intervening columns present of course)
"datafile.txt"
comments about my data
other calculations returned as separate text comments on a line
X1 X2 X3 X4 X5
X6
.....................................................................
X19 X20 X21
100.0000000 101.000000 102.0000000 103.0000000 104.0000000
105.0000000 ......................118.0000000 119.0000000 120.0000000
-0.3380570 -1.400905 1.0396499 -0.5802181 -0.2340614
0.6044928 ...................................-0.4854702 -0.3677461
-1.2033173
-0.9002824 1.544242 -0.8668653 0.3066256 0.2490254 -1.6429223
..................................... 0.0861146 0.4276929 -0.3408604
How doI change setting for print() or use another function to keep each
row of the data frame as a single line ( of greater length up to approx
300 characters) instead of wrapping the data frame into multiple lines
of text?
The problem : I end up with the data frame split into several sections
one under another thus
"datafile.txt"
comments about my data
other calculations returned as separate text comments on a line
X1 X2 X3 X4 X5 X6
100.0000000 101.000000 102.0000000 103.0000000 104.0000000 105.0000000
-0.3380570 -1.400905 1.0396499 -0.5802181 -0.2340614 0.6044928
-0.9002824 1.544242 -0.8668653 0.3066256 0.2490254 -1.6429223
X7 X8 X9 X10 X11 X12
106.0000000 107.00000000 108.0000000 109.0000000 110.0000000 111.0000000
0.3152427 0.15093494 -0.3316172 -0.3603724 -2.0516402 -0.4556241
-0.6502265 -0.08842649 -0.3775335 -0.4942572 -0.0976565 -0.7716651
X13 X14 X15 X16 X17 X18
112.0000000 113.0000000 114.0000000 115.0000000 116.00000000 117.000000
0.8829135 0.8851043 -0.7687383 -0.9573476 -0.03041968 1.425754
0.2666777 0.6405255 0.2342905 -0.7705545 -1.18028004 1.303601
X19 X20 X21
118.0000000 119.0000000 120.0000000
-0.4854702 -0.3677461 -1.2033173
0.0861146 0.4276929 -0.3408604
------------------------------
Message: 6
Date: Mon, 22 Nov 2010 04:31:29 -0800 (PST)
From: Aline Uwimana via LinkedIn <member at linkedin.com>
To: James Holtman <r-help at r-project.org>
Subject: [R] Invitation ? se connecter sur LinkedIn
Message-ID:
<1473926269.6681467.1290429089742.JavaMail.app at ech3-cdn12.prod>
Content-Type: text/plain
LinkedIn
------------Aline Uwimana requested to add you as a connection on LinkedIn:
------------------------------------------
James,
J'aimerais vous inviter C rejoindre mon rC)seau professionnel en ligne, sur
le site LinkedIn.
Aline
Accept invitation from Aline Uwimana
http://www.linkedin.com/e/j2w180-ggtc5u4r-5e/dwA6EuZvdiRUO9LjukuviNUAHj8vHaN
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4Mc3cTd399bSlUk6ZDtQd6bPkOcP4Sd3kPej4LrCBxbOYWrSlI/EML_comm_afe/
View invitation from Aline Uwimana
http://www.linkedin.com/e/j2w180-ggtc5u4r-5e/dwA6EuZvdiRUO9LjukuviNUAHj8vHaN
g/blk/I2473001097_2/39vdPAMcj0McPsQcAALqnpPbOYWrSlI/svi/
------------------------------------------
DID YOU KNOW you can be the first to know when a trusted member of your
network changes jobs? With Network Updates on your LinkedIn home page,
you'll be notified as members of your network change their current position.
Be the first to know and reach out!
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--
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[[alternative HTML version deleted]]
------------------------------
Message: 7
Date: Mon, 22 Nov 2010 07:32:11 -0500
From: Gabor Grothendieck <ggrothendieck at gmail.com>
To: rnick <nikos.rachmanis at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] How to combine Date and time in one column
Message-ID:
<AANLkTimU-LvRyziVgf0n_=W+WTH0TPYqgR4ZvxkWSXSu at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Mon, Nov 22, 2010 at 2:24 AM, rnick <nikos.rachmanis at gmail.com>
wrote:>
> Hello everyone,
>
> I am trying to built an xts object and i have run into some problems on
the> data handling. I would really appreciate if someone could help me with the
> following:
>
> 1) I have a OHLC dataset with Time and date in different columns. How
could> i combine date and time in one column in order to pass on the new column
to> xts? I have use cbind and data.frame before but i did not manage to yield
> any good results as the formating of the file changes.
>
> Date ? ? ? ? ? ?Time ? ? ? ? ? O ? ? ? ? ? ? ? ?H ? ? ? ? ? ? ? L ? ? ? ?
? ? ? C> 1/2/2005 ? ? ? ?17:05 ? ? ? ? ?1.3546 ? 1.3553 ?1.3546 ?1.35495
> 1/2/2005 ? ? ? ?17:10 ? ? ? ? ?1.3553 ? 1.3556 ?1.3549 ?1.35525
> 1/2/2005 ? ? ? ?17:15 ? ? ? ? ?1.3556 ? 1.35565 1.35515 1.3553
> 1/2/2005 ? ? ? ?17:25 ? ? ? ? ?1.355 ? ? ? ? ? ?1.3556 ?1.355 ? ? ? ? ? 1.
3555> 1/2/2005 ? ? ? ?17:30 ? ? ? ? ?1.3556 ? 1.3564 ?1.35535 1.3563
>
> 2) It is not clear to me what is the best way to construct the .xts
object?> Should i use only the Date&time to index or should i also combine it
with
> the rest of the variables?
>
Use read.zoo and then as.xts to convert it to xts. The following
shows it for chron date/times. Replace textConnection(Lines) with
"myfile.dat" to read it from that file. You can replace the FUNpart
with a conversion to any date/time class supported by xts. Here
we show it for chron. In the example below we are assuming that the
date format is month/day/year. See R News 4/1.
Lines <- "Date Time O H L C
1/2/2005 17:05 1.3546 1.3553 1.3546 1.35495
1/2/2005 17:10 1.3553 1.3556 1.3549 1.35525
1/2/2005 17:15 1.3556 1.35565 1.35515 1.3553
1/2/2005 17:25 1.355 1.3556 1.355 1.3555
1/2/2005 17:30 1.3556 1.3564 1.35535 1.3563"
library(xts) # this also pulls in zoo and its read.zoo
library(chron)
z <- read.zoo(textConnection(Lines), header = TRUE, index = list(1, 2),
FUN = function(d, t) as.chron(paste(as.Date(chron(d)), t)))
x <- as.xts(z)
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
------------------------------
Message: 8
Date: Mon, 22 Nov 2010 09:43:18 -0300
From: Jose Claudio Faria <joseclaudio.faria at gmail.com>
To: r-help at r-project.org
Subject: [R] Tinn-R 2.3.7.0 released
Message-ID:
<AANLkTimGQHOWj_EzDhR_J-38QxG99KDGmq0OvGZ29eiZ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dears users,
A new version of Tinn-R was released today. Below details:
2.3.7.0 (Nov/22/2010)
* Bug(s) fixed:
- A bug related with the intermittent loose of connection
(or appear to freeze) with Rgui.exe was fixed.
* The versions 2.3.6.4, 2.3.6.5, 2.3.6.6 and 2.3.6.7 restricted to
pre-release testers.
* The Application options interface was a bit changed:
- The Application options/R/Rterm was split in two tabs:
Error and Options. The tab Error has a new option: Try to find error
in the editor. It enables the user to set Tinn-R in order to find
errors in the editor when sending instructions to Rterm.
* This version is full compatible with Windows 7 and R 2.12.0.
* The component XPmenu was removed from the project. Windows XP
users, perhaps, will find the Tinn-R appearance less attractive, but
the applicative is now more stable. As soon as possible, the project
will get a better option for skins.
* Parts of the source code were optimized.
All the best,
--
///\\\///\\\///\\\///\\\///\\\///\\\///\\\///\\\
Jose Claudio Faria
Estatistica - prof. Titular
UESC/DCET/Brasil
joseclaudio.faria at gmail.com
///\\\///\\\///\\\///\\\///\\\///\\\///\\\///\\\
------------------------------
Message: 9
Date: Mon, 22 Nov 2010 20:53:14 +0800
From: Luis Felipe Parra <felipe.parra at quantil.com.co>
To: r-help <r-help at r-project.org>
Subject: [R] Rexcel
Message-ID:
<AANLkTimtvxE9BvWqZ+=bK7LZOcAou_jrA3OFDJOZ5Gcj at mail.gmail.com>
Content-Type: text/plain
Hello, I am trying to use RExcel and I would like to know if it is possible
to use in excel the following function I made for R
Pron = function(path="C:\\Quantil Aplicativos\\Genercauca\\V5\\"){
library(timeSeries)
library(maSigPro)
### CARGAR FUNCIONES
source(paste(path,"\\fUtilidades\\BackwardSelectionNC.r",sep<file://futilida
des//BackwardSelectionNC.r%22,sep>
=""))
source(paste(path,"\\fUtilidades\\CriteriosDeComparacion.r",sep<file://futil
idades//CriteriosDeComparacion.r%22,sep>
=""))
dataTSORG<-read.csv('entrada.csv', header = TRUE, sep =
",", quote="\"",
dec=".",fill = TRUE, comment.char="")
dataTSORG = ts(dataTSORG, start=c(1950,1), frequency=12)
dataTSORG = as.timeSeries(dataTSORG)
X = prcomp(dataTSORG[,2:40])$x
return(X)
}
Does somebody know if its possible? and if so how can I do it?
Thank you
Felipe Parra
[[alternative HTML version deleted]]
------------------------------
Message: 10
Date: Mon, 22 Nov 2010 07:59:05 -0500
From: jim holtman <jholtman at gmail.com>
To: nevil.amos at sci.monash.edu.au
Cc: R-help at r-project.org
Subject: Re: [R] how to change number of characters per line for
print() to sink()?
Message-ID:
<AANLkTi=_J6jSVAuVX8SiF8g+9w6pVLPx7v+HTqa-4_wm at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
?options
width
options(width = 1000)
On Mon, Nov 22, 2010 at 7:22 AM, Nevil Amos <nevil.amos at gmail.com>
wrote:> I am using r to read and reformat data that is then saved to a text file
> using sink(), the file has a number of initial lines of comments and
summary> data followed by print of a data.frame with no row names.
> for example
>
> a<-c(100:120)
> b<-c(rnorm(100:120))
> c<-c(rnorm(200:220))
> mydata<-data.frame(rbind(a,b,c))
> sink("datafile.txt")
>
> cat("comments about my data \n")
> cat("other calculations returned as separate text comments on a line
\n")
> print(mydata,row.names=F)
> sink()
>
>
> I need the content of the text file to keep each row of the data frame on
a> single line thus (with intervening columns present of course)
>
> "datafile.txt"
>
> comments about my data
> other calculations returned as separate text comments on a line
> ? ? ? ? ?X1 ? ? ? ? X2 ? ? ? ? ?X3 ? ? ? ? ?X4 ? ? ? ? ?X5 ? ? ? ? ?X6
> ? ? .....................................................................
> ? ? ? X19 ? ? ? ? X20 ? ? ? ? X21
>
>
> ?100.0000000 101.000000 102.0000000 103.0000000 104.0000000 105.0000000
> ?......................118.0000000 119.0000000 120.0000000
> ?-0.3380570 ?-1.400905 ? 1.0396499 ?-0.5802181 ?-0.2340614 ? 0.6044928
> ...................................-0.4854702 ?-0.3677461 ?-1.2033173
> ?-0.9002824 ? 1.544242 ?-0.8668653 ? 0.3066256 ? 0.2490254 ?-1.6429223
> ..................................... ? 0.0861146 ? 0.4276929 ?-0.3408604
>
> How doI change setting for print() or use another function to keep each
row> of the data frame as a single line ( of greater length up to approx 300
> characters) instead of wrapping the data frame into multiple lines of
text?>
> The problem : I end up with the data frame split into several sections one
> under another thus
>
> "datafile.txt"
>
> comments about my data
> other calculations returned as separate text comments on a line
> ? ? ? ? ?X1 ? ? ? ? X2 ? ? ? ? ?X3 ? ? ? ? ?X4 ? ? ? ? ?X5 ? ? ? ? ?X6
> ?100.0000000 101.000000 102.0000000 103.0000000 104.0000000 105.0000000
> ?-0.3380570 ?-1.400905 ? 1.0396499 ?-0.5802181 ?-0.2340614 ? 0.6044928
> ?-0.9002824 ? 1.544242 ?-0.8668653 ? 0.3066256 ? 0.2490254 ?-1.6429223
> ? ? ? ? ?X7 ? ? ? ? ? X8 ? ? ? ? ?X9 ? ? ? ? X10 ? ? ? ? X11 ? ? ? ? X12
> ?106.0000000 107.00000000 108.0000000 109.0000000 110.0000000 111.0000000
> ? 0.3152427 ? 0.15093494 ?-0.3316172 ?-0.3603724 ?-2.0516402 ?-0.4556241
> ?-0.6502265 ?-0.08842649 ?-0.3775335 ?-0.4942572 ?-0.0976565 ?-0.7716651
> ? ? ? ? X13 ? ? ? ? X14 ? ? ? ? X15 ? ? ? ? X16 ? ? ? ? ?X17 ? ? ? ?X18
> ?112.0000000 113.0000000 114.0000000 115.0000000 116.00000000 117.000000
> ? 0.8829135 ? 0.8851043 ?-0.7687383 ?-0.9573476 ?-0.03041968 ? 1.425754
> ? 0.2666777 ? 0.6405255 ? 0.2342905 ?-0.7705545 ?-1.18028004 ? 1.303601
> ? ? ? ? X19 ? ? ? ? X20 ? ? ? ? X21
> ?118.0000000 119.0000000 120.0000000
> ?-0.4854702 ?-0.3677461 ?-1.2033173
> ? 0.0861146 ? 0.4276929 ?-0.3408604
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
------------------------------
Message: 11
Date: Mon, 22 Nov 2010 13:02:17 +0000
From: "S Ellison" <S.Ellison at lgc.co.uk>
To: "emorway" <emorway at engr.colostate.edu>, "Uwe
Ligges"
<ligges at statistik.tu-dortmund.de>
Cc: r-help at r-project.org
Subject: Re: [R] boxplot: reverse y-axis order
Message-ID: <scea69e8.069 at tedmail.lgc.co.uk>
Content-Type: text/plain; charset=US-ASCII
A simple alternative is to use "at" to contrl plot locations:
boxplot( ..., at=rev(1:nlevels(depthM)))
which just rearranges where they are plotted.
Example:
set.seed(1023)
x <- gl(5, 5)
y<-rnorm(25)
boxplot(y~x, horizontal=TRUE)
boxplot(y~x, at=rev(1:nlevels(x)), , horizontal=TRUE)
Steve E
>>> Uwe Ligges <ligges at statistik.tu-dortmund.de> 21/11/2010
19:38:54
>>>
On 21.11.2010 20:30, emorway wrote:>
> Hello,
>
> Searching this forum has enabled me to get pretty far in what I'm
trying to> do. However, there is one more manipulation I would like to make and
I> haven't found a solution. Using the data and code below, I generate
the> plot produced by the last command. If possible I would like to
reverse the> order of the y-axis (bearing in mind horizontal=T) so that 0 is
plotted at> the upper most part of the y-axis and 3 at the axis intercepts. I've
tried> the experiment approach to no avail, meaning I've placed rev(...)
around> various arguments but with wrong results.
>
> Thanks,
> Eric
>
>
> df<-read.table(textConnection("Field Date AvgWTD Region variable
value hole> depth depthM
> 204 17-Aug-00 2.897428989 US R1 NA R 1 0
[SNIP]
> 9A 09-Aug-00 1.482089996 US C6 NA C 6 1.8
> 9B 01-Jun-01 1.409700036 US C6 NA C 6 1.8
> 9B 09-Aug-00 3.837660074 US C6 NA C 6 1.8"),header=T)
> closeAllConnections()
> #The folling call doesn't preserve the correct spacing between data
> boxplot(value~depthM,data=df,horizontal=T,outline=F)
> #The following command preserves correct spacing, but need to reverse
the> order
>
boxplot(value~factor(depthM,levels=c(0.0,0.3,0.6,0.9,1.2,1.5,1.8,2.1,2.4,2.7
,3)),data=df,horizontal=T,outline=F)
So if you want to reverse, either specify the levels in reverse order
or
use rev() as in:
boxplot(value ~ factor(depthM,
levels = rev(c(0.0,0.3,0.6,0.9,1.2,1.5,1.8,2.1,2.4,2.7,3))),
data = df, horizontal = TRUE, outline = FALSE)
Uwe Ligges
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
*******************************************************************
This email and any attachments are confidential. Any use...{{dropped:8}}
------------------------------
Message: 12
Date: Mon, 22 Nov 2010 05:19:21 -0800 (PST)
From: Alaios <alaios at yahoo.com>
To: Rhelp <r-help at r-project.org>
Subject: [R] plot inside function does not work
Message-ID: <413924.42773.qm at web120105.mail.ne1.yahoo.com>
Content-Type: text/plain
Hello everyone,
when I commit a plot using console(command line?) plot works fine. I have
created a function that plots based on the input. This function is called
plot_shad. When I call this function alone in the command line I get my
plot.
Then I tried to use another function as depicted_below to do some
calculation before calling the function that does the plotting.
plot_shad_map<-function(f,CRagent,agentid){
for (i in c(1:nrow(shad_map))){
for (j in c(1:ncol(shad_map))){
# Do something
}
}
plot_shad_f(shad_map) # This plots fine when used in command line. But
inside this #function does not
return(shad_map)
}
Unfortunately I get no plot . What might be the problem?
One more question how to get more plots at the same time. It seems that when
I issue a new plot replaces the old plot.
I would like to thank you in advance for you help
Regards
Alex
[[alternative HTML version deleted]]
------------------------------
Message: 13
Date: Mon, 22 Nov 2010 05:32:05 -0800 (PST)
From: madr <madrazel at interia.pl>
To: r-help at r-project.org
Subject: Re: [R] how to sample lowess/loess into matrix ?
Message-ID: <1290432725271-3053601.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
I found it, it was SO simple:
lowessline <- lowess(x,y)
write.csv(lowessline, "loess.csv")
--
View this message in context:
http://r.789695.n4.nabble.com/how-to-sample-lowess-loess-into-matrix-tp30534
58p3053601.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 14
Date: Mon, 22 Nov 2010 14:34:02 +0100
From: Claudia Beleites <cbeleites at units.it>
To: r-help at r-project.org
Subject: Re: [R] plot inside function does not work
Message-ID: <4CEA714A.5070406 at units.it>
Content-Type: text/plain; charset=UTF-8; format=flowed
Alex, this may be FAQ 7.22
Claudia
On 11/22/2010 02:19 PM, Alaios wrote:> Hello everyone,
> when I commit a plot using console(command line?) plot works fine. I have
created a function that plots based on the input. This function is called
plot_shad. When I call this function alone in the command line I get my
plot.>
> Then I tried to use another function as depicted_below to do some
calculation before calling the function that does the
plotting.>
> plot_shad_map<-function(f,CRagent,agentid){
> ? for (i in c(1:nrow(shad_map))){
> ??? for (j in c(1:ncol(shad_map))){
> ???? # Do something
> ??? }
> ? }
> ? plot_shad_f(shad_map) # This plots fine when used in command line. But
inside this #function does not> ? return(shad_map)
> }
>
> Unfortunately I get no plot . What might be the problem?
>
> One more question how to get more plots at the same time. It seems that
when I issue a new plot replaces the old plot.>
> I would like to thank you in advance for you help
> Regards
> Alex
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Universit? degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbeleites at units.it
------------------------------
Message: 15
Date: Mon, 22 Nov 2010 05:36:06 -0800 (PST)
To: Luis Felipe Parra <felipe.parra at quantil.com.co>, r-help
<r-help at r-project.org>
Subject: Re: [R] Rexcel
Message-ID: <666026.40186.qm at web113206.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi,
For RExcel I would suggest subscribing;
http://mailman.csd.univie.ac.at/listinfo/rcom-l
They have a website on;
http://rcom.univie.ac.at/
B.R.
Stephen L
----- Original Message ----
From: Luis Felipe Parra <felipe.parra at quantil.com.co>
To: r-help <r-help at r-project.org>
Sent: Mon, November 22, 2010 8:11:39 PM
Subject: [R] Rexcel
Hello I am new to RExcel and I would like to run a source code form the
excel worksheet. I would like to run the following code
source("C:\\Quantil Aplicativos\\Genercauca\\BackwardSelectionNC.r")
from the excel wroksheet. Does anybody know how to do this?
Thank you
Felipe Parra
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 16
Date: Mon, 22 Nov 2010 05:47:35 -0800 (PST)
To: r-help at r-project.org, Claudia Beleites <cbeleites at units.it>
Subject: Re: [R] plot inside function does not work
Message-ID: <946840.29824.qm at web120104.mail.ne1.yahoo.com>
Content-Type: text/plain
Dear Claudia,
I would like to thank you for your reply, according to 7.22 I have to put
some print() statement inside my function. What I do not understand is where
to put this line (at the beginning or at the end of the code?) I tried both
but I get error message.
Moreover I would like to ask you if any inputs should be passed to the
print(). I tried to pass inside the argument of ggplot but it didnt like it
:(
Best Regards
7.22 Why do lattice/trellis graphics not work?
The most likely reason is that you forgot to tell R to display the
graph. Lattice functions such as xyplot() create a graph object,
but do not display it (the same is true of ggplot2 graphics,
and Trellis graphics in S-Plus). The print() method for the
graph object produces the actual display. When you use these functions
interactively at the command line, the result is automatically printed,
but in source() or inside your own functions you will need an
explicit print() statement.
--- On Mon, 11/22/10, Claudia Beleites <cbeleites at units.it> wrote:
From: Claudia Beleites <cbeleites at units.it>
Subject: Re: [R] plot inside function does not work
To: r-help at r-project.org
Date: Monday, November 22, 2010, 1:34 PM
Alex, this may be FAQ 7.22
Claudia
On 11/22/2010 02:19 PM, Alaios wrote:> Hello everyone,
> when I commit a plot using console(command line?) plot works fine. I have
created a function that plots based on the input. This function is called
plot_shad. When I call this function alone in the command line I get my
plot.>
> Then I tried to use another function as depicted_below to do some
calculation before calling the function that does the
plotting.>
> plot_shad_map<-function(f,CRagent,agentid){
> o?= for (i in c(1:nrow(shad_map))){
> o?=o?=o?= for (j in c(1:ncol(shad_map))){
> o?=o?=o?=o?= # Do something
> o?=o?=o?= }
> o?= }
> o?= plot_shad_f(shad_map) # This plots fine when used in command line. But
inside this #function does not> o?= return(shad_map)
> }
>
> Unfortunately I get no plot . What might be the problem?
>
> One more question how to get more plots at the same time. It seems that
when I issue a new plot replaces the old plot.>
> I would like to thank you in advance for you help
> Regards
> Alex
>
>
>
>
> B B B [[alternative HTML version deleted]]
>
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
UniversitC degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste
phone: +39 0 40 5 58-37 68
email: cbeleites at units.it
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
------------------------------
Message: 17
Date: Mon, 22 Nov 2010 05:53:40 -0800 (PST)
From: Yann Lancien via LinkedIn <member at linkedin.com>
To: James Holtman <r-help at r-project.org>
Subject: [R] Invitation ? se connecter sur LinkedIn
Message-ID:
<210238489.6957030.1290434020449.JavaMail.app at ech3-cdn05.prod>
Content-Type: text/plain
LinkedIn
------------Yann Lancien requested to add you as a connection on LinkedIn:
------------------------------------------
James,
J'aimerais vous inviter C rejoindre mon rC)seau professionnel en ligne, sur
le site LinkedIn.
Yann
Accept invitation from Yann Lancien
http://www.linkedin.com/e/j2w180-ggtf3iot-z/dwA6EuZvdiRUO9LjukuviNUAHj8vHaNg
/blk/I2473133047_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPsQc3c
PcjcTd399bPxgum8Utk5QbPcNdzkQe3kPej4LrCBxbOYWrSlI/EML_comm_afe/
View invitation from Yann Lancien
http://www.linkedin.com/e/j2w180-ggtf3iot-z/dwA6EuZvdiRUO9LjukuviNUAHj8vHaNg
/blk/I2473133047_2/39vdPgMcPcNcPsQcAALqnpPbOYWrSlI/svi/
------------------------------------------
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People Yann Lancien knows can discover your profile:
Connecting to Yann Lancien will attract the attention of LinkedIn users. See
who's been viewing your profile:
http://www.linkedin.com/e/j2w180-ggtf3iot-z/wvp/inv18_wvmp/
--
(c) 2010, LinkedIn Corporation
[[alternative HTML version deleted]]
------------------------------
Message: 18
Date: Mon, 22 Nov 2010 06:06:30 -0800 (PST)
From: Joel <joda2457 at student.uu.se>
To: r-help at r-project.org
Subject: [R] Prob with merge
Message-ID: <1290434790326-3053652.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi
Im trying to merge 2 data frames using merge but I dont get the result i
want
Lets make this a small test as my data set is to big to put in here :).
t1<-data.frame(a=c(1,2,3,4,5,6),b=c(11,11,NA,11,11,11))
t1<-data.frame(a=c(1,2,3,4,5,8),b=c(12,12,12,12,12,32))
this gives me:
> t1
a b
1 1 12
2 2 12
3 3 12
4 4 12
5 5 12
6 8 32> t2
a b
1 1 11
2 2 11
3 3 NA
4 4 11
5 5 11
6 6 11
now when i merge i get:> merge(t1,t2, by="a")
a b.x b.y
1 1 12 11
2 2 12 11
3 3 12 NA
4 4 12 11
5 5 12 11
But what I want is it to look like:
a b.x b.y
1 1 12 11
2 2 12 11
3 3 12 NA
4 4 12 11
5 5 12 11
6 8 32 NA
So I keep all of the rows from t1 and get an NA in dose slots at the t2 part
of the merge.
Anyone know how to accomplice this?
Thx
//Joel
--
View this message in context:
http://r.789695.n4.nabble.com/Prob-with-merge-tp3053652p3053652.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 19
Date: Mon, 22 Nov 2010 06:08:10 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
To: Luis Felipe Parra <felipe.parra at quantil.com.co>
Cc: r-help <r-help at r-project.org>
Subject: Re: [R] Making a line in a legend shorter
Message-ID: <4CEA794A.3000607 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-11-21 18:38, Luis Felipe Parra wrote:> Hello, I am putting a legend with lines in a line plot and I would like to
> make the lines in the legend shorter. Does anybody knows how to do this?
I think the segment length is still hard-coded in legend().
Last July there was a request to lengthen the segment.
Maybe this post will help you:
https://stat.ethz.ch/pipermail/r-help/2010-July/246599.html
Peter Ehlers
>
> Thank you
>
> Felipe Parra
>
> [[alternative HTML version deleted]]
------------------------------
Message: 20
Date: Mon, 22 Nov 2010 15:09:31 +0100
From: "ONKELINX, Thierry" <Thierry.ONKELINX at inbo.be>
To: Joel <joda2457 at student.uu.se>, <r-help at r-project.org>
Subject: Re: [R] Prob with merge
Message-ID: <3DB16098F738284D8DBEB2FC369916384D6283 at inboexch.inbo.be>
Content-Type: text/plain; charset="us-ascii"
merge(t1,t2, by="a", all.x = TRUE)
------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
> -----Oorspronkelijk bericht-----
> Van: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] Namens Joel
> Verzonden: maandag 22 november 2010 15:07
> Aan: r-help at r-project.org
> Onderwerp: [R] Prob with merge
>
>
> Hi
>
> Im trying to merge 2 data frames using merge but I dont get
> the result i want
>
> Lets make this a small test as my data set is to big to put
> in here :).
>
> t1<-data.frame(a=c(1,2,3,4,5,6),b=c(11,11,NA,11,11,11))
> t1<-data.frame(a=c(1,2,3,4,5,8),b=c(12,12,12,12,12,32))
>
> this gives me:
>
> > t1
> a b
> 1 1 12
> 2 2 12
> 3 3 12
> 4 4 12
> 5 5 12
> 6 8 32
> > t2
> a b
> 1 1 11
> 2 2 11
> 3 3 NA
> 4 4 11
> 5 5 11
> 6 6 11
>
> now when i merge i get:
> > merge(t1,t2, by="a")
> a b.x b.y
> 1 1 12 11
> 2 2 12 11
> 3 3 12 NA
> 4 4 12 11
> 5 5 12 11
>
>
> But what I want is it to look like:
>
> a b.x b.y
> 1 1 12 11
> 2 2 12 11
> 3 3 12 NA
> 4 4 12 11
> 5 5 12 11
> 6 8 32 NA
>
> So I keep all of the rows from t1 and get an NA in dose slots
> at the t2 part of the merge.
> Anyone know how to accomplice this?
>
> Thx
> //Joel
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Prob-with-merge-tp3053652p3053652.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 21
Date: Mon, 22 Nov 2010 08:11:15 -0600
From: Terry Therneau <therneau at mayo.edu>
Cc: r-help at r-project.org, dieter.menne at menne-biomed.de,
r_tingley at hotmail.com
Subject: Re: [R] calculating martingale residual on new data using
"predict.coxph"
Message-ID: <1290435075.7350.3.camel at punchbuggy>
Content-Type: text/plain
This feature has been added in survival 2.36-1, which is now on CRAN.
(2.36-2 should appear in another day or so)
Terry T.
---------begin included message --------
I was trying to use "predict.coxph" to calculate martingale residuals
on
a test
data, however, as pointed out before
http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html
predict(mycox1, newdata, type="expected") is not implemented yet.
------------------------------
Message: 22
Date: Mon, 22 Nov 2010 06:20:51 -0800 (PST)
From: Joel <joda2457 at student.uu.se>
To: r-help at r-project.org
Subject: Re: [R] Prob with merge
Message-ID: <1290435651761-3053675.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Thx alot mate.
--
View this message in context:
http://r.789695.n4.nabble.com/Prob-with-merge-tp3053652p3053675.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 23
Date: Mon, 22 Nov 2010 09:27:08 -0500
From: Jimmy Martina <jimmyjuan1 at hotmail.com>
To: R-geo <r-sig-geo at stat.math.ethz.ch>, R <r-help at
r-project.org>
Subject: [R] What if geoRglm results showed that a non-spacial model
fits?
Message-ID: <BAY110-W26A01692A4E820BEE2C8BF943D0 at phx.gbl>
Content-Type: text/plain
Hi R-people:
Working in geoRglm, it shows me, according to AIC criterion, that the
non-spacial model describes the process in a better way. It's the first time
that I'm facing up to.
These are my results:
OP2003Seppos.AICnonsp-OP2003Seppos.AICsp
#[1] -4
(OP2003Seppos.lf0.p<-exp(OP2003Seppos.lf0$beta)/(1+exp(OP2003Seppos.lf0$beta
))) #P non spatial
#[1] 0.9717596
(OP2003Seppos.lf.p<-exp(OP2003Seppos.lf$beta)/(1+exp(OP2003Seppos.lf$beta)))
#P spatial
#[1] 0.9717596
It must what have an important influence at kriging, because it shows as
following:
OP2003Sepposbin.krig<-glsm.krige(OP2003Seppos.tune,loc=OP2003Seppospro.pred.
grid,bor=OP2003Sepposbor)
#glsm.krige: Prediction for a generalised linear spatial model
#There are 50 or mode advices (use warnings() to see them)
#> warnings()
#Warning messages:
#1: In asympvar(kpl.result$predict, messages = FALSE) ... :
# value of argument lag.max is not suffiently long
#2: In asympvar(kpl.result$predict, messages = FALSE) ... :
# value of argument lag.max is not suffiently long
Help me, please.
[[alternative HTML version deleted]]
------------------------------
Message: 24
Date: Mon, 22 Nov 2010 15:32:51 +0100
From: Stella Pachidi <stella.pachidi at gmail.com>
To: r-help at stat.math.ethz.ch
Subject: [R] Help with plotting kohonen maps
Message-ID:
<AANLkTini0qSwDHVo_Pe9f2zh2Ga5mEWfBWhCXiwwQWYr at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear all,
I recently started using the kohonen package for my thesis project. I
have a very simple question which I cannot figure out by myself:
When I execute the following example code, from the paper of Wehrens
and Buydens (http://www.jstatsoft.org/v21/i05/paper):
R> library("kohonen")
Loading required package: class
R> data("wines")
R> wines.sc <- scale(wines)
R> set.seed(7)
R> wine.som <- som(data = wines.sc, grid = somgrid(5, 4,
"hexagonal"))
R> plot(wine.som, main = "Wine data")
I get to have a plot of the codebook vectors of the 5-by-4 mapping of
the wine data, and it also includes which variable names correspond
to each color. (same picture as in the paper)
However, when I run the som() function with my own data and I try to
get the plot afterwards:
library("kohonen")
self_Organising_Map <- som(data = tableToCluster, grid = somgrid(5, 2,
"rectangular"), rlen=1000)
plot(self_Organising_Map, main = "Kohonen Map of Clustered Profiles")
the resulting plot does not contain the color labels i.e. the
variable names of my data table, even though they exist and are
included as column names of tableToCluster.
I also tried the following line:
plot(self_Organising_Map, type="codes", codeRendering =
"segments",
ncolors=length(colnames(self_Organising_Map$codes)),
palette.name=rainbow, main = "Kohonen Map of Clustered Profiles \n
Codes", zlim =colnames(self_Organising_Map$codes))
but it had the same result.
If you could please help with what argument I should use to show the
[[elided Yahoo spam]]
Kind regards,
Stella
--
Stella Pachidi
Master in Business Informatics student
Utrecht University
------------------------------
Message: 25
Date: Mon, 22 Nov 2010 12:03:54 -0300
From: Kjetil Halvorsen <kjetilbrinchmannhalvorsen at gmail.com>
To: Uwe Ligges <ligges at statistik.tu-dortmund.de>
Cc: r-devel <r-help at r-project.org>
Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
Message-ID:
<AANLkTim7qsgaidiEV65pbJfPLOhrHG4yy8jf6Eha==t9 at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
see below.
2010/11/21 Uwe Ligges <ligges at
statistik.tu-dortmund.de>:>
>
> On 21.11.2010 18:13, Kjetil Halvorsen wrote:
>>> ?save.image
>>
>> And at this point it has been running with one cpu at 100% for over an
>> hour!
>
>
> It's OK to take an hour (due to memory <-> disc IO) if it uses
swap space
> heavily. Factor of 60 is not much given memory is faster than harddiscs by
> orders of magnitude.
>
> Uwe
It takes much more than an hour! I started anew a process with the
problem yesterday aroun 18.00, had to kill it this morning around
09.00. That's more than 1|5 hours.
Kjetil>
------------------------------
Message: 26
Date: Mon, 22 Nov 2010 10:13:01 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <kjetilbrinchmannhalvorsen at gmail.com>,
<ligges at statistik.tu-dortmund.de>
Cc: r-help at r-project.org
Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
Message-ID: <BLU113-W11A7426FDE41EECEB92F7BBE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> Date: Mon, 22 Nov 2010 12:03:54 -0300
> From: kjetilbrinchmannhalvorsen at gmail.com
> To: ligges at statistik.tu-dortmund.de
> CC: r-help at r-project.org
> Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
>
> see below.
>
> 2010/11/21 Uwe Ligges :
> >
> >
> > On 21.11.2010 18:13, Kjetil Halvorsen wrote:
>
> >>> ?save.image
> >>
> >> And at this point it has been running with one cpu at 100% for
over an
> >> hour!
> >
> >
> > It's OK to take an hour (due to memory <-> disc IO) if it
uses swap
space> > heavily. Factor of 60 is not much given memory is faster than
harddiscs
by> > orders of magnitude.
> >
> > Uwe
>
> It takes much more than an hour! I started anew a process with the
> problem yesterday aroun 18.00, had to kill it this morning around
> 09.00. That's more than 1|5 hours.
Again, see if you can run it under gdb or at least look at
tools you have to determine page faults. My brain has been corrupted
with 'dohs but in task manager CPU usage drops when page faults start
or lock startvation etc. A blocking thread should yield IIRC. Waiting
for it to die a natural death may not be practical.
I just posted something on this after following another's suggestion but
it should be easy for you to get developer tools, execute gdb,
point it at R and then break a few times. Debuggers don't speed anything
up but presumably it gets into its limit cycle ( infinite futile loop )
within a short time. Also sometimes you get these loops due to memory
corruption
with native code etc etc so confusing results may take a few different
approaches
to figure out.
Turning on profiling will at best destry any memory coherence and worse
ad to VM thrashing. At least try to determine if you are faulting all over.
>
> Kjetil
> >
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 27
Date: Mon, 22 Nov 2010 09:13:19 -0600
From: Mike Lawrence <Mike.Lawrence at dal.ca>
To: "r-help at lists.R-project.org" <r-help at r-project.org>
Subject: [R] hierarchical mixture modelling
Message-ID:
<AANLkTi=fzD+Jz1-DnOY239U3xycCRfriyZ1bF-AJjjAh at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi folks,
I have circular data that I'd like to model as a mixture of a uniform
and a Von Mises centered on zero. The data are from 2 groups of human
participants, where each participant is measured repeatedly within
each of several conditions. So, the data frame would look something
like:
########
design = expand.grid(
person = 1:20
, variable1 = 1:2
, variable2 = 1:3
, repetition = 1:100
)
design$group = design$person %% 2
########
where each row would have a data point.
Now, I know how to fit the mixture of a uniform and Von Mises to each
individual cell of the data independently using the EM algorithm,
yielding estimates of the mixture proportion and Von Mises
concentration per cell. However, I of course want to assess the degree
to which the group and other variables in the design affect these
model parameters, and at least in the case of the proportion estimate,
I'm uncomfortable submitting the raw proportion to a test that is
going to assume Gaussian error (eg. ANOVA, or lmer(...,
family=gaussian)). I'm aware that lmer lets one specify non-gaussian
links, but as I understand it, if I wanted to, say, specify the
binomial link (which seems appropriate for a proportion), lmer wants
the data to be the raw 1's and 0's, not the proportion estimate
obtained from EM.
I've heard that there are hierarchical mixture modelling methods out
there (possibly Bayesian hierarchical mixture modelling) that might
let me achieve model fitting and inference in one step (eg. model the
mixture and influence on each parameter from the between and
within-person variables, and treating people as random effects), but
I'm having trouble tacking down instructions on how to do this.
[[elided Yahoo spam]]
Cheers,
Mike
--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
Looking to arrange a meeting? Check my public calendar:
http://tr.im/mikes_public_calendar
~ Certainty is folly... I think. ~
------------------------------
Message: 28
Date: Mon, 22 Nov 2010 20:44:51 +0530
From: "Santosh Srinivas" <santosh.srinivas at gmail.com>
To: <r-help at r-project.org>
Subject: [R] Check for is.object
Message-ID: <4cea88f0.1f44960a.1cfe.fffff56a at mx.google.com>
Content-Type: text/plain; charset="us-ascii"
Hello,
I am trying to recursively append some data from multiple files into a
common object
For this, I am using in a loop
NewObject <- rbind(NewObject,tempObject)
For the first loop, obviously there is no NewObject ... so I wanted to do
NewObject <- tempObject[0,]
Now when it loops again I want to put the statement do "NewObject <-
tempObject[0,]" inside a if statement ... so that it does I can skip it
once
NewObject has been initialized.
But, is.object doesn't seem to work.
What is the alternative check that I can do? And is there a better way to
achieve what I want?
Thanks,
S
------------------------------
Message: 29
Date: Mon, 22 Nov 2010 07:17:22 -0800 (PST)
From: Wonsang You <you at ifn-magdeburg.de>
To: r-help at r-project.org
Subject: [R] Fast Two-Dimensional Optimization
Message-ID:
<AANLkTikBQPjKypX7Y9X7sn3h41nO=r8WOcRtbr2dEO40 at mail.gmail.com>
Content-Type: text/plain
Dear R Helpers,
I have attempted "optim" function to solve a two-dimensional
optimization
problem. It took around 25 second to complete the procedure.
However, I want to reduce the computation time: less than 7 second. Is there
any optimization function in R which is very rapid?
Best Regards,
Wonsang
-----
Wonsang You
Leibniz Institute for Neurobiology
--
View this message in context:
http://r.789695.n4.nabble.com/R-Fast-Two-Dimensional-Optimization-tp3053782p
3053782.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]
------------------------------
Message: 30
Date: Mon, 22 Nov 2010 16:19:14 +0100
From: ?ukasz R?c?awowicz <lukasz.reclawowicz at gmail.com>
To: Marcin Gomulka <mrgomel at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] plotting a timeline
Message-ID:
<AANLkTimfz8Eo1GZouw5hf_ROvSVDzk8mgJGjLMwCb5d4 at mail.gmail.com>
Content-Type: text/plain
2010/11/20 Marcin Gomulka <mrgomel at gmail.com>
> I'd rather do this with a dedicated
> package function ( like axis() ).
Probably you have to write your own function, or tune up manually plot.
plot(the_data$eventtime, abs(the_data$impact), type="h",
frame.plot=FALSE,
axes FALSE, xlab="",ylab="",
col="grey",lwd=2,ylim=c(-2,2),xlim=c(1913,2005))
text(the_data$eventtime,the_data$impact+.1, the_data$label,cex=.6,adj=1)
lines(x=c(1914,2003),y=c(0,0),lwd=2,col="blue",t="l")
axis(1,the_data$eventtime,pos=0,cex.axis=.5,padj=-2,tck=-.01)
--
Mi3ego dnia
[[alternative HTML version deleted]]
------------------------------
Message: 31
Date: Mon, 22 Nov 2010 07:24:56 -0800
From: Patrick Leyshock <ngkbr8es at gmail.com>
To: Uwe Ligges <ligges at statistik.tu-dortmund.de>, r-help at
r-project.org
Subject: Re: [R] memory profiling
Message-ID:
<AANLkTim62ptR2idZzbLDTZ5Mtm31_09pzSAyjT6EkK_1 at mail.gmail.com>
Content-Type: text/plain
> Using:
>
> summaryRprof(memory="both")
>
> did the trick, thank you. I had not been using that setting when calling
> summaryRprof.
>
> Thanks, Patrick
>
> 2010/11/20 Uwe Ligges <ligges at statistik.tu-dortmund.de>
>
>
>>
>> On 19.11.2010 21:48, Patrick Leyshock wrote:
>>
>>> I'm trying to configure Version 2.12.0 or R to do memory
profiling.
>>>
>>> I've reconfigured the code:
>>>
>>> % ./compile --enable-memory-profiling=YES
>>>
>>> and verified that it's configured correctly by examining the
output. I
>>> then
>>> rebuild R:
>>>
>>> % make
>>>
>>> Then I fire up R and run a script, using Rprof with the
memory-profiling
>>> switch set to TRUE:
>>>
>>> Rprof("output", memory.profiling=TRUE);
>>> # a bunch of R code
>>> Rprof(NULL);
>>>
>>
>>
>> Wen I do
>>
>> summaryRprof(memory="both")
>>
>> I see an additional column ...
>>
>> but since you have not said what you tried exactly, we cannot help very
>> much.
>>
>> Uwe Ligges
>>
>>
>>
>> When I examine the output, however, using either R CMD Rprof from the
>>> shell,
>>> or summaryRprof from within R, the output I see is identical to the
>>> output I
>>> got when I ran R BEFORE I recompiled with memory profiling enabled.
>>>
>>> Anyone see something that I'm missing?
>>>
>>> Thanks, Patrick
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>
[[alternative HTML version deleted]]
------------------------------
Message: 32
Date: Mon, 22 Nov 2010 12:41:06 -0300
From: Kjetil Halvorsen <kjetilbrinchmannhalvorsen at gmail.com>
To: Mike Marchywka <marchywka at hotmail.com>
Cc: r-help at r-project.org, ligges at statistik.tu-dortmund.de
Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
Message-ID:
<AANLkTimevZO2TA=5tZj92eZBwd5pc7GaNzRXfO=Rskx=@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
see below.
On Mon, Nov 22, 2010 at 12:13 PM, Mike Marchywka <marchywka at
hotmail.com>
wrote:>
>
>
>
>
> ----------------------------------------
>> Date: Mon, 22 Nov 2010 12:03:54 -0300
>> From: kjetilbrinchmannhalvorsen at gmail.com
>> To: ligges at statistik.tu-dortmund.de
>> CC: r-help at r-project.org
>> Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
>>
>> see below.
>>
>> 2010/11/21 Uwe Ligges :
>> >
>> >
>> > On 21.11.2010 18:13, Kjetil Halvorsen wrote:
>>
>> >>> ?save.image
>> >>
>> >> And at this point it has been running with one cpu at 100% for
over an
>> >> hour!
>> >
>> >
>> > It's OK to take an hour (due to memory <-> disc IO) if
it uses swap
space>> > heavily. Factor of 60 is not much given memory is faster than
harddiscs
by>> > orders of magnitude.
>> >
>> > Uwe
>>
>> It takes much more than an hour! I started anew a process with the
>> problem yesterday aroun 18.00, had to kill it this morning around
>> 09.00. That's more than 1|5 hours.
>
>
> Again, see if you can run it under gdb or at least look at
> tools you have to determine page faults. My brain has been corrupted
> with 'dohs but in task manager CPU usage drops when page faults start
> or lock startvation etc. A blocking thread should yield IIRC. Waiting
> for it to die a natural death may not be practical.
>
Thanks. Will try. Really, I tried yesterday, to run R under gdb within
emacs, but it did'nt work out. What I did (in emacs 23) was, typing
Ctrl-u M-x R
and then enter the option
--debugger=gdb
[[elided Yahoo spam]]
Kjetil
> I just posted something on this after following another's suggestion
but
> it should be easy for you to get developer tools, execute gdb,
> point it at R and then break a few times. Debuggers don't speed
anything
> up but presumably it gets into its limit cycle ( infinite futile loop )
> within a short time. Also sometimes you get these loops due to memory
corruption> with native code etc etc so confusing results may take a few different
approaches> to figure out.
>
> Turning on profiling will at best destry any memory coherence and worse
> ad to VM thrashing. At least try to determine if you are faulting all
over.>
>
>>
>> Kjetil
>> >
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html>> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 33
Date: Mon, 22 Nov 2010 16:44:27 +0100
From: Martin Maechler <maechler at stat.math.ethz.ch>
Cc: r-help at r-project.org
Subject: Re: [R] An empty grey diagram
Message-ID: <19690.36827.343657.468114 at lynne.math.ethz.ch>
Content-Type: text/plain; charset=us-ascii
>>>>> on Sat, 20 Nov 2010 00:12:07 -0800 (PST) writes:
> Hi Josh and David,
> Problem solved.
> Both following steps work.
> 1)
>> ToothGrowth
>> attach(ToothGrowth)
>> plot(dose,len) # this step is needed. Don't close the
diagram.
Otherwise
>> following command won't work.
>> matrics=lm(len~dose)
>> abline(matrics)
> Graph displayed
> 2)
>> ToothGrowth
>> attach(ToothGrowth)
>> plot(dose, len) # this step is needed. Don't close the
diagram.
Otherwise
>> following command won't work.
>> abline(lm(len ~ dose, data = ToothGrowth))
> Graph displayed
Well, it is *VERY BAD* style and error-prone practice nowadays,
to attach a data set.
[The only thing to attach() are save()d data *files*;
there it's often tidier to attach() instead of to load() ...]
I have not followed all the things you tried .. or did not try.
A much better way of achieving the above (and yes; *never* close
the graphics window within these) should be
plot ( len ~ dose, data=ToothGrowth)
abline(lm(len ~ dose, data=ToothGrowth))
and you can see {if you use a fixed-width font in your e-mail,
it "springs into your eyes"}
how nicely the formula notation of graphics alings with
the same in models.
If the above two simple lines do not work correctly,
then your R environment is "broken" in some way,
and maybe first doing
rm(list = ls())
may help.
Martin Maechler,
ETH Zurich and R Core Team
> B.R.
> Stephen L
> ----- Original Message ----
> From: Joshua Wiley <jwiley.psych at gmail.com>
> Cc: r-help at r-project.org
> Sent: Sat, November 20, 2010 1:39:45 PM
> Subject: Re: [R] An empty grey diagram
wrote:
>> Hi David,
>>
>>
>>> What happens when you follow the directions... i.e. type:
>>> plot.new() #???
>>
>> abline(lm(len ~ dose, data = ToothGrowth))
>> plot.new()
>>
>> The grey background changes to white, still an empty graph
> You cannot just use abline() on an empty graphic (well, you can but
> you get an empty graph). Please actually run my code, it will create
> a scatter plot, then add a line. Do not close the graphic device in
> between.
> with(ToothGrowth, plot(dose, len))
> abline(lm(len ~ dose, data = ToothGrowth))
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 34
Date: Mon, 22 Nov 2010 10:57:06 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <kjetilbrinchmannhalvorsen at gmail.com>
Cc: r-help at r-project.org, ligges at statistik.tu-dortmund.de
Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
Message-ID: <BLU113-W27D876C2B7D93140F1135BE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> Date: Mon, 22 Nov 2010 12:41:06 -0300
> Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
> From: kjetilbrinchmannhalvorsen at gmail.com
> To: marchywka at hotmail.com
> CC: ligges at statistik.tu-dortmund.de; r-help at r-project.org
>
> see below.
>
> On Mon, Nov 22, 2010 at 12:13 PM, Mike Marchywka wrote:
> >
> >
> Thanks. Will try. Really, I tried yesterday, to run R under gdb within
> emacs, but it did'nt work out. What I did (in emacs 23) was, typing
> Ctrl-u M-x R
> and then enter the option
> --debugger=gdb
>
[[elided Hotmail spam]]>
> Kjetil
I rarely use gdb but it did seem to work with R but I executed gdb from
cygwin windoh and IIRC ctrl-C worked fine as it broke into debugger.
I guess you could try that- start gdb and attach or invoke R from gdb.
------------------------------
Message: 35
Date: Mon, 22 Nov 2010 11:02:55 -0500
From: Jonathan P Daily <jdaily at usgs.gov>
To: "Santosh Srinivas" <santosh.srinivas at gmail.com>
Cc: r-help at r-project.org, r-help-bounces at r-project.org
Subject: Re: [R] Check for is.object
Message-ID:
<OF1BD5F51B.26988C10-ON852577E3.00581042-852577E3.005830E8 at usgs.gov>
Content-Type: text/plain; charset="US-ASCII"
I think you want the function ?exists
>if(!exists("NewObject"))
--------------------------------------
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
"Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it."
- Jubal Early, Firefly
r-help-bounces at r-project.org wrote on 11/22/2010 10:14:51 AM:
> [image removed]
>
> [R] Check for is.object
>
> Santosh Srinivas
>
> to:
>
> r-help
>
> 11/22/2010 10:17 AM
>
> Sent by:
>
> r-help-bounces at r-project.org
>
> Hello,
>
> I am trying to recursively append some data from multiple files into a
> common object
>
> For this, I am using in a loop
>
> NewObject <- rbind(NewObject,tempObject)
>
>
> For the first loop, obviously there is no NewObject ... so I wanted to
do> NewObject <- tempObject[0,]
>
> Now when it loops again I want to put the statement do "NewObject
<-
> tempObject[0,]" inside a if statement ... so that it does I can skip
it
once> NewObject has been initialized.
>
> But, is.object doesn't seem to work.
>
> What is the alternative check that I can do? And is there a better way
to> achieve what I want?
>
> Thanks,
> S
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 36
Date: Mon, 22 Nov 2010 08:07:24 -0800 (PST)
From: Berend Hasselman <bhh at xs4all.nl>
To: r-help at r-project.org
Subject: Re: [R] solve nonlinear equation using BBsolve
Message-ID: <1290442044850-3053902.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
After my reply you sent me the following privately:
> Thank you for your respond. Now I adjust the parameters which are close
> to the value that I'm expected and it gives me the following message:
I
> tried a few combination. My question is why it said "Unsuccessful
> convergence" but still give some answers? Can I use the answers?
>
>
>> p0 <- c(2.5,25,25,0.8)
>> mgf_gammasum(p0)
> [1] -17.3600000 -3410.6900000 0.3508769 -1.1028287
>> BBsolve(par = p0, fn = mgf_gammasum)[[1]]
> Unsuccessful convergence.
> [1] 2.066909 44.068739 24.809270 0.972542
>> source(.trPaths[5], echo=TRUE, max.deparse.length=10000)
>> p0 <- c(1.7,36,50,0.9)
>> mgf_gammasum(p0)
> [1] 3.8400000 2601.0300000 0.7232021 0.2866732
>> BBsolve(par = p0, fn = mgf_gammasum)[[1]]
> Unsuccessful convergence.
> [1] 2.0823407 18.3757502 49.9935914 0.9456666
>> p0 <- c(2,40,40,0.8)
>> mgf_gammasum(p0)
> [1] 17.6400000 2798.7100000 0.4883676 -0.5653881
>> BBsolve(par = p0, fn = mgf_gammasum)[[1]]
> Unsuccessful convergence.
> [1] 2.059853 29.215478 39.882727 0.914894
>
It is only giving you the values it stopped at.
You are only printing [[1]] of BBsolve's result.
BBsolve provides more information.
You can easily check if the result is usable.
Do something like this.
p0 <- c(2.5,25,25,0.8)
bb.result <- BBsolve(par = p0, fn = mgf_gammasum)
bb.result
mgf_gammasum(bb.result$par)
You will see that BBsolve has NOT found a solution.
If you use nleqslv as follows you will see that the jacobian matrix in your
starting point is very ill-conditioned.
nleqslv(p0,mgf_gammasum)
All your other starting points have similar problems.
You really need to rethink your system of equations.
In future please also reply to the list and not only to me privately.
best
Berend
--
View this message in context:
http://r.789695.n4.nabble.com/solve-nonlinear-equation-using-BBsolve-tp30521
67p3053902.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 37
Date: Mon, 22 Nov 2010 11:07:43 -0500
From: Ista Zahn <izahn at psych.rochester.edu>
Cc: R Project Help <R-help at r-project.org>
Subject: Re: [R] Alternatives to image(...) and filled.contour(...)
for 2-D filled Plots
Message-ID:
<AANLkTi=9Z+ozud2YRj4C2Jqu5xRJGph4vSusQw4UbRHp at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Jason,
You do not say what you want the alternative to do, so its hard to
know if this will be helpful. But one alternative is
dat <- as.data.frame(ak.fan)
dat <- melt(dat, id.vars=c("x", "y"))
p <- ggplot(dat, aes(x=x, y=variable))
p + geom_tile(aes(fill=value))
-Ista
wrote:>
> By any chance are there any alternatives to image(...) and
filled.contour(...)>
> I used Rseek to search for that very topic, but didn't turn over any
leads...>
http://www.rseek.org/?cx=010923144343702598753%3Aboaz1reyxd4&newwindow=1&q=a
lternative+to+image+and+filled.contour&sa=Search&cof=FORID%3A11&siteurl=www.
rseek.org%252F#1238>
>
> I'm sure there are some out there, but curious about some of the
favorites
and> ones folks have had success using.
>
>
> Thanks for any insights and feedback.
>
> I would like to use the alternative 2-D fill function with the example I
have> been messing with in place of image(...) or filled.contour(...):
>
>
>
> library(akima)
>
> hyp_distance<-seq(1,15)
> angle_deg_val<-seq(0,15)
>
>
> x_distance_val<-NULL
> y_distance_val<-NULL
>
> for(ii in 1:length(hyp_distance))
> {
> ? ? ? ?for(jj in 1:length(angle_deg_val))
> ? ? ? ?{
> ? ? ? ? ? ? ?
?x_distance_tmp<-hyp_distance[ii]*cos(angle_deg_val[jj]*pi/180)> ? ? ? ? ? ? ?
?y_distance_tmp<-hyp_distance[ii]*sin(angle_deg_val[jj]*pi/180)>
> ? ? ? ? ? ? ? ?x_distance_val<-c(x_distance_val, x_distance_tmp)
> ? ? ? ? ? ? ? ?y_distance_val<-c(y_distance_val, y_distance_tmp)
> ? ? ? ?}
>
> }
>
>
> temperature_vals<-rnorm(length(x_distance_val), 75, 2)
>
> temp_samples<-cbind(x_distance_val, y_distance_val, temperature_vals)
>
> temp_samples_DF<-data.frame(x = x_distance_val, y = ?y_distance_val, z
> temperature_vals)
>
>
> ak.fan <- interp(temp_samples[,1], temp_samples[,2], temp_samples[,3] )
>
> length_val<-floor(max(temperature_vals) - min(temperature_vals))*2
>
> color_vals_red_to_yellow_to_green<-colorRampPalette(c("red",
"yellow",
"green"),> space="Lab")(length_val)
> color_vals_green_to_yellow_to_red<-colorRampPalette(c("green",
"yellow",
"red"),> space="Lab")(length_val)
>
> plot(1,1, col = 0, xlim = c(min(x_distance_val), max(x_distance_val)),
ylim > c(min(y_distance_val), max(y_distance_val)), xlab = "Room X
Position
(FT)", ylab> = "Room Y Position (FT)", main = "Room Temp vs
Position")
>
> grid()
>
> # filled.contour(ak.fan, col = color_vals_red_to_yellow_to_green)
> # filled.contour(ak.fan, col = color_vals_green_to_yellow_to_red)
>
> # image(ak.fan, col = color_vals_red_to_yellow_to_green, add = TRUE)
> image(ak.fan, col = color_vals_green_to_yellow_to_red, add = TRUE)
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
------------------------------
Message: 38
Date: Mon, 22 Nov 2010 11:09:10 -0500
From: Matt Shotwell <shotwelm at musc.edu>
To: "martin.tomko at geo.uzh.ch" <martin.tomko at geo.uzh.ch>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] statistical test for comparison of two
classifications (nominal)
Message-ID: <1290442150.1756.74.camel at matt-laptop>
Content-Type: text/plain; charset="UTF-8"
Martin,
Pardon the delayed reply.
Bootstrap methods have been around for some time (late seventies?), but
their popularity seems to have exploded in correspondence with computing
technology. You should be able to find more information in most modern
books on statistical inference, but here is a brief:
The bootstrap is a method often used to establish an empirical null
distribution for a test statistic when traditional (analytical) methods
fail. The bootstrap works by imposing a null hypothesis on the observed
data, followed by re-sampling with replacement. The test statistic is
computed at each re-sample and used to build up an empirical null
distribution. The idea is to impose the null hypothesis while preserving
variability in the observed data, and thus the test statistic.
For example, suppose we observe some continuous scalar data and
hypothesize that the sample was observed from a population with mean
zero. We can impose this hypothesis by subtracting the sample mean from
each observation. Re-samples from these transformed data are treated as
having been observed under the null hypothesis.
In the case of classification and partitioning, the difficulty is
formulating a meaningful null hypothesis about the collection of
classifications, and imposing the null hypothesis in a bootstrap
sampling scheme.
-Matt
On Wed, 2010-11-17 at 10:01 -0500, Martin Tomko wrote: > Thanks Mat,
> I have in the meantime identified the Rand index, but not the others. I
> will also have a look at profdpm, that did not pop-up in my searches.
> Indeed, the interpretation is going to be critical... Could you please
> elaborate on what you mean by the bootstrap process?
>
> Thanks a lot for your helps,
> Martin
>
> On 11/17/2010 3:50 PM, Matt Shotwell wrote:
> > There are several statistics used to compare nominal classifications,
or
> > _partitions_ of a data set. A partition isn't quite the same in
this
> > context because partitioned data are not restricted to a fixed number
of
> > classes. However, the statistics used to compare partitions should
also
> > work for these 'restricted' partitions. See the Rand index,
Fowlkes and
> > Mallows index, Wallace indices, and the Jaccard index. The profdpm
> > package implements a function (?profdpm::pci) that computes these
> > indices for two factors representing partitions of the same data.
> >
> > The difficult part is drawing statistical inference about these
indices.
> > It's difficult to formulate a null hypothesis, and even more
difficult
> > to determine a null distribution for a partition comparison index. A
> > bootstrap test might work, but you will probably have to implement
this
> > yourself.
> >
> > -Matt
> >
> > On Wed, 2010-11-17 at 08:33 -0500, Martin Tomko wrote:
> >
> >> Dear all,
> >> I am having a hard time to figure out a suitable test for the
match
> >> between two nominal classifications of the same set of data.
> >> I have used hierarchical clustering with multiple methods (ward,
> >> k-means,...) to classify my dat into a set number of classesa, and
I
> >> would like to compare the resulting automated classification with
the
> >> actual - objective benchmark one.
> >> So in principle I have a data frame with n columns of nominal
> >> classifications, and I want to do a mutual comparison and test for
> >> significance in difference in classification between pairs of
columns.
> >>
> >> I just need to identify a suitable test, but I fail. I am
currently
> >> exploring the possibility of using Cohen's Kappa, but I am
open to
other> >> suggestions. Especially the fact that kappa seems to be moslty
used on
> >> failible, human annotators seems to bring in limitations taht do
not
> >> apply to my automatic classification.
> >> Any help will be appreciated, especially if also followed by a
pointer
> >> to an R package that implements it.
> >>
> >> Thanks
> >> Martin
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
>
>
--
Matthew S. Shotwell
Graduate Student
Division of Biostatistics and Epidemiology
Medical University of South Carolina
------------------------------
Message: 39
Date: Mon, 22 Nov 2010 08:58:30 -0800 (PST)
From: Phil Spector <spector at stat.berkeley.edu>
To: Santosh Srinivas <santosh.srinivas at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Check for is.object
Message-ID:
<alpine.DEB.2.00.1011220852200.14043 at springer.Berkeley.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Santosh -
The simple answer to your question is to initialize
NewObject to NULL before the loop, i.e.
newObject = NULL
However, I should point out this is one of the most
inefficient ways to program in R. A far better way is
to allocate enough space for NewObject outside your
loop, and "fill it in" in the loop. Here's a simple
example to give you an idea of the difference in time
the two methods require:
> system.time({answer = matrix(NA,1000,5);
+ for(i in 1:1000)answer[i,] <- sample(10,5)})
user system elapsed
0.020 0.000 0.017 > system.time({answer=NULL;
+ for(i in 1:1000)answer=rbind(answer,sample(10,5))})
user system elapsed
0.072 0.000 0.070
However, it gets even worse if the sample size is larger:
> system.time({answer = matrix(NA,10000,5);
+ for(i in 1:10000)answer[i,] <- sample(10,5)})
user system elapsed
0.184 0.000 0.184 > system.time({answer=NULL;for(i in 1:10000)
+ answer=rbind(answer,sample(10,5))})
user system elapsed
5.492 0.032 5.562
Even if you don't know how big your newObject matrix will
become, it's still far more efficient to overallocate the
matrix and then truncate it at the end.
I'd strongly recommend that you avoid building your matrix
[[elided Yahoo spam]]
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spector at stat.berkeley.edu
On Mon, 22 Nov 2010, Santosh Srinivas wrote:
> Hello,
>
> I am trying to recursively append some data from multiple files into a
> common object
>
> For this, I am using in a loop
>
> NewObject <- rbind(NewObject,tempObject)
>
>
> For the first loop, obviously there is no NewObject ... so I wanted to do
> NewObject <- tempObject[0,]
>
> Now when it loops again I want to put the statement do "NewObject
<-
> tempObject[0,]" inside a if statement ... so that it does I can skip
it
once> NewObject has been initialized.
>
> But, is.object doesn't seem to work.
>
> What is the alternative check that I can do? And is there a better way to
> achieve what I want?
>
> Thanks,
> S
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 40
Date: Mon, 22 Nov 2010 12:04:59 -0500
From: Ista Zahn <izahn at psych.rochester.edu>
To: madr <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] "negative alpha" or custom gradient colors of data
dots in scatterplot ?
Message-ID:
<AANLkTikVspi-vK+qeB+QmH_qvqFi2+T2deeKhqyLxjTJ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
I suggest taking a look at the plotting functions in the ggplot2
package. For example:
x <- rnorm(10000)
y <- x+rnorm(10000)
dat <- data.frame(x,y)
library(ggplot2)
p <- ggplot(dat, aes(x=x, y=y))
p + geom_point() # too much overplotting: compare to
dev.new()
p + geom_hex(binwidth=c(.1,.1))
Best,
Ista
On Sun, Nov 21, 2010 at 9:13 AM, madr <madrazel at interia.pl>
wrote:>
> I know that by setting alpha to for example col = rgb(0, 0, 0, 0.1) it is
> possible to see how many overlapping is in the plot. But disadvantage of
it> is that single points are barely visible on the background. So I wonder if
> there is possible to make setting that single points would be almost
black,> but with more and more data on the same spot it would get more and more
> whiteish. Or maybe it is possible to make sole data points black but
> overlapped tending to some particular color of choice ?
> --
> View this message in context:
http://r.789695.n4.nabble.com/negative-alpha-or-custom-gradient-colors-of-da
ta-dots-in-scatterplot-tp3052394p3052394.html> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
------------------------------
Message: 41
Date: Mon, 22 Nov 2010 18:16:42 +0100
From: wphantomfr <wphantomfr at gmail.com>
To: r-help at r-project.org
Subject: [R] Problem setting the number of digits in xtable
Message-ID: <8E449FB3-99DF-4BC3-A1DA-EBDC075F6D0A at gmail.com>
Content-Type: text/plain
DEar list members,
I am currently using Sweave with LaTeX which is great.
I can use xtable for formatting outp of tables but I have a problem setting
the number of decimals in xtables when used with dataframe.
I have found an example on the net ith matrix and it works.
For example this works :> > tmp <- matrix(rnorm(9), 3, 3)
> > xtmp <- xtable(tmp)
> > digits(xtmp) <- c(0,0,3,4)
> > print(xtmp, include.rownames = FALSE) # row names
produced :> % latex table generated in R 2.12.0 by xtable 1.5-6 package
> % Mon Nov 22 17:35:00 2010
> \begin{table}[ht]
> \begin{center}
> \begin{tabular}{rrr}
> \hline
> 1 & 2 & 3 \\
> \hline
> -2 & -2.158 & 2.8886 \\
> 1 & 1.330 & 0.4677 \\
> -0 & 0.486 & -0.3319 \\
> \hline
> \end{tabular}
> \end{center}
> \end{table}
But this won't work :> > mydata
> TEST t ddl p CONDITION
> 2 R1 3.01109061083632 16 0.00828552765650315 C1
> 3 R2 3.30476953908811 16 0.00447412002109504 C1
> 4 DR 2.86343993410509 16 0.0112631908739966 C1
> 5 R1 1.05386387510206 16 0.30760068470456 C2
> 6 R2 3.04997140665209 16 0.00763921045771104 C2
> 7 DR 2.25175987512241 16 0.0387401575011488 C2
but > > xtable(mydata,digits=2)
produced
> % latex table generated in R 2.12.0 by xtable 1.5-6 package
> % Mon Nov 22 18:13:47 2010
> \begin{table}[ht]
> \begin{center}
> \begin{tabular}{rlllll}
> \hline
> & TEST & t & ddl & p & CONDITION \\
> \hline
> 2 & R1 & 3.01109061083632 & 16 & 0.00828552765650315 &
C1 \\
> 3 & R2 & 3.30476953908811 & 16 & 0.00447412002109504
& C1 \\
> 4 & DR & 2.86343993410509 & 16 & 0.0112631908739966 &
C1 \\
> 5 & R1 & 1.05386387510206 & 16 & 0.30760068470456 &
C2 \\
> 6 & R2 & 3.04997140665209 & 16 & 0.00763921045771104
& C2 \\
> 7 & DR & 2.25175987512241 & 16 & 0.0387401575011488 &
C2 \\
> \hline
> \end{tabular}
> \end{center}
> \end{table}
I have also tried setting the digits with c(0,0,4,0,4,0), using also the
'display' argument to specify the type of each column... noway...
What am I missing ?
Thanks in advance
Sylvain Climent
[[alternative HTML version deleted]]
------------------------------
Message: 42
Date: Mon, 22 Nov 2010 18:33:07 +0100 (CET)
From: omerle <omerle at laposte.net>
To: r-help at r-project.org
Subject: [R] RCurl : All connection are used ?
Message-ID: <1277930.342.1290447187435.JavaMail.www at wwinf8202>
Content-Type: text/plain
B B B B B Hi everybody,
I got a problem with the ftpUpload function from the RCurl package. My goal
is to Upload a lot of files from a local directory to a web server.
1st try :
for (i in 1:length(file)){
B B B B B ftpUpload(what=files[i],to=files[i])
}
At i=11 I get : (my server has only 10 available open connections available)
:
Erreur dans curlPerform(url = to, upload = TRUE, readfunction
uploadFunctionHandler(what,B :
B Got a 421 ftp-server response when 220 was expected
2 nd Try :
ftpConnection=getCurlHandle(userpwd=ftp$userpwd,maxconnects=1,fresh.connect0)
for (i in 1:length(file)){
B B B B B ftpUpload(what=files[i],to=files[i],curl=ftpConnection)
}
And I got this error after 30 files (the error is not linked to the web
server but to the R session) :
Error in file(file, "rb") : all conection are used
I read the documentation and the options from curl library but I can't find
how to solve my problem even if I think that the problem is linked to not
closing the position I opened. Do you have any idea how to solve it ?
Thanks,
Olivier Merle
Une messagerie gratuite, garantie C vie et des services en plus, C'a vous
tente ?
Je crC)e ma boC.te mail www.laposte.net
[[alternative HTML version deleted]]
------------------------------
Message: 43
Date: Mon, 22 Nov 2010 18:47:16 +0100
From: Lucia Ca?as <lucia.canas at co.ieo.es>
To: <r-help at R-project.org>
Subject: [R] sm.ancova graphic
Message-ID:
<50EB6473669C6741AC34FF5692DCC4560DA79E at ieocoruna.co.ieo.es>
Content-Type: text/plain
Hi R-Users,
I am working with sm.ancova (in the package sm) and I have two problems with
the graph, which is automatically generated when sm.ancova() is run.
1-Besides of the fitted lines, the observed data appeared automatically in
the graph. I prefer that only fitted lines appear. I check the sm.options,
but I could not find the way that the observed data do not appear in the
graph.
2-I would like to change the size of the numbers in the axis. Again, I
check the sm.options, but I could not find the correct way.
Thank you in advance,
Lucma
[[alternative HTML version deleted]]
------------------------------
Message: 44
Date: Mon, 22 Nov 2010 18:51:04 +0100
From: JiHO <jo.lists at gmail.com>
To: R Help <r-help at stat.math.ethz.ch>
Subject: [R] Plotting a cloud/fog of variable density in rgl
Message-ID:
<AANLkTi=eYZV6xjQdKHnP1ak0yO4VQDrPMp_hRpMX=d6Z at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi everyone,
I want to plot a 3D interpolation of the concentration of aquatic
organisms. My goal would be to have the result represented as clouds
with a density proportional to the abundance of organisms, so that I
could fly (well, swim actually ;) ) through the scene and see the
patches here and there. Basically, I want to do something like this:
http://www.youtube.com/watch?v=27mo_Y-aU-c
but simpler and with only clouds.
I though about doing it this way:
1- interpolate to a fine grid
2- plot points at each grid intersection of transparency inversely
proportional to abundance
3- blur/fog a bit each point to create the general impression of a cloud
So far I am stuck on 3 but maybe there is a better overall solution.
Here is some code that reads the result of the interpolation on a
coarse grid and plots it:
# read a set of gridded data points in 3D
d = read.table("http://dl.dropbox.com/u/1047321/R/test3Ddata.txt",
header=T)
# plot
library("rgl")
spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05)
And here is a version that actually performs the interpolation a
random set of points in 3D through kriging in case you want to try
with increase precision.
# create a set of random data points in 3D
n = 50
data3D = data.frame(x = runif(n), y = runif(n), z = runif(n), v rnorm(n))
# do 3d interpolation via kriging
library("gstat")
coordinates(data3D) = ~x+y+z
range1D = seq(from = 0, to = 1, length = 10)
grid3D = expand.grid(x = range1D, y = range1D, z = range1D)
gridded(grid3D) = ~x+y+z
res3D = krige(formula = v ~ 1, data3D, grid3D, model = vgm(1, "Exp",
.2))
# convert the result to a data.frame
d = as.data.frame(res3D)
# compute transparency (proportional to the interpolated value)
maxD = max(d$var1.pred)
minD = min(d$var1.pred)
alpha = (d$var1.pred - minD)/(maxD - minD)
# reduce maximum alpha (all points are semi-transparent)
alpha = alpha/5
# plot
library("rgl")
spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05)
I saw the fog effect but it seems to add a fog in the scene to
increase depth. What I want is my scene to actually look like a fog.
Thanks in advance for any help. Sincerely,
JiHO
---
http://maururu.net
------------------------------
Message: 45
Date: Mon, 22 Nov 2010 13:13:55 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <omerle at laposte.net>, <r-help at r-project.org>
Subject: Re: [R] RCurl : All connection are used ?
Message-ID: <BLU113-W1133131680D4E669D5227EBE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
I guess I would just comment that for many tasks I try
to keep the work in dedicated tools. In this case, command
line versions of curl or even wget. The reason is things
like this that come up talking to foreign entitites.
Also the learning curve can be amortized over many other
efforts that require same file transfers etc.
I just mention this for rebuttals from R experts.
----------------------------------------
From: omerle at laposte.net
To: r-help at r-project.org
Date: Mon, 22 Nov 2010 18:33:07 +0100
Subject: [R] RCurl : All connection are used ?
Hi everybody,
I got a problem with the ftpUpload function from the RCurl package. My goal
is to Upload a lot of files from a local directory to a web server.
1st try :
for (i in 1:length(file)){
ftpUpload(what=files[i],to=files[i])
}
At i=11 I get : (my server has only 10 available open connections available)
:
Erreur dans curlPerform(url = to, upload = TRUE, readfunction
uploadFunctionHandler(what, :
Got a 421 ftp-server response when 220 was expected
2 nd Try :
ftpConnection=getCurlHandle(userpwd=ftp$userpwd,maxconnects=1,fresh.connect0)
for (i in 1:length(file)){
ftpUpload(what=files[i],to=files[i],curl=ftpConnection)
}
And I got this error after 30 files (the error is not linked to the web
server but to the R session) :
Error in file(file, "rb") : all conection are used
I read the documentation and the options from curl library but I can't find
how to solve my problem even if I think that the problem is linked to not
closing the position I opened. Do you have any idea how to solve it ?
Thanks,
Olivier Merle
Une messagerie gratuite, garantie ? vie et des services en plus, ?a vous
tente ?
Je cr?e ma bo?te mail www.laposte.net
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 46
Date: Mon, 22 Nov 2010 10:35:02 -0800 (PST)
From: Manta <mantino84 at libero.it>
To: r-help at r-project.org
Subject: Re: [R] Ordeing Zoo object
Message-ID: <1290450902168-3054192.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
And how about if I want to order the series from the smallest to the largest
value, keeping the date index in order to see when the values were
predominantly negative etc...
Thanks,
Marco
--
View this message in context:
http://r.789695.n4.nabble.com/Ordeing-Zoo-object-tp955868p3054192.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 47
Date: Mon, 22 Nov 2010 13:55:13 -0500
From: Duncan Murdoch <murdoch.duncan at gmail.com>
To: JiHO <jo.lists at gmail.com>
Cc: R Help <r-help at stat.math.ethz.ch>
Subject: Re: [R] Plotting a cloud/fog of variable density in rgl
Message-ID: <4CEABC91.1080402 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 22/11/2010 12:51 PM, JiHO wrote:> Hi everyone,
>
> I want to plot a 3D interpolation of the concentration of aquatic
> organisms. My goal would be to have the result represented as clouds
> with a density proportional to the abundance of organisms, so that I
> could fly (well, swim actually ;) ) through the scene and see the
> patches here and there. Basically, I want to do something like this:
> http://www.youtube.com/watch?v=27mo_Y-aU-c
> but simpler and with only clouds.
rgl doesn't make everything in OpenGL available. I'm not sure exactly
how those clouds were done, but it wouldn't really be easy to do them in
rgl.
I think you can come closest to what you want within rgl by using
sprites rather than rendering transparent spheres. See
examples(sprites3d).
Duncan Murdoch
> I though about doing it this way:
> 1- interpolate to a fine grid
> 2- plot points at each grid intersection of transparency inversely
> proportional to abundance
> 3- blur/fog a bit each point to create the general impression of a cloud
>
> So far I am stuck on 3 but maybe there is a better overall solution.
> Here is some code that reads the result of the interpolation on a
> coarse grid and plots it:
>
> # read a set of gridded data points in 3D
> d =
read.table("http://dl.dropbox.com/u/1047321/R/test3Ddata.txt",
header=T)>
> # plot
> library("rgl")
> spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05)
>
> And here is a version that actually performs the interpolation a
> random set of points in 3D through kriging in case you want to try
> with increase precision.
>
> # create a set of random data points in 3D
> n = 50
> data3D = data.frame(x = runif(n), y = runif(n), z = runif(n), v rnorm(n))
>
> # do 3d interpolation via kriging
> library("gstat")
> coordinates(data3D) = ~x+y+z
> range1D = seq(from = 0, to = 1, length = 10)
> grid3D = expand.grid(x = range1D, y = range1D, z = range1D)
> gridded(grid3D) = ~x+y+z
> res3D = krige(formula = v ~ 1, data3D, grid3D, model = vgm(1,
"Exp",
.2))>
> # convert the result to a data.frame
> d = as.data.frame(res3D)
>
> # compute transparency (proportional to the interpolated value)
> maxD = max(d$var1.pred)
> minD = min(d$var1.pred)
> alpha = (d$var1.pred - minD)/(maxD - minD)
> # reduce maximum alpha (all points are semi-transparent)
> alpha = alpha/5
>
> # plot
> library("rgl")
> spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05)
>
>
> I saw the fog effect but it seems to add a fog in the scene to
> increase depth. What I want is my scene to actually look like a fog.
>
> Thanks in advance for any help. Sincerely,
>
> JiHO
> ---
> http://maururu.net
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 48
Date: Mon, 22 Nov 2010 12:01:26 -0700
From: Greg Snow <Greg.Snow at imail.org>
To: Sonja Klein <sonja.klein.07 at aberdeen.ac.uk>,
"r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] How to produce a graph of glms in R?
Message-ID:
<B37C0A15B8FB3C468B5BC7EBC7DA14CC633FEC591B at LP-EXMBVS10.CO.IHC.COM>
Content-Type: text/plain; charset="us-ascii"
Look at Predict.Plot (and possibly TkPredict) in the TeachingDemos package.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Sonja Klein
> Sent: Saturday, November 20, 2010 4:52 AM
> To: r-help at r-project.org
> Subject: [R] How to produce a graph of glms in R?
>
>
> I'm very new to R and modeling but need some help with visualization of
> glms.
>
> I'd like to make a graph of my glms to visualize the different effects
> of
> different parameters.
> I've got a binary response variable (bird sightings) and use binomial
> glms.
> The 'main' response variable is a measure of distance to a track
and
> the
> parameters I'm testing for are vegetation parameters that effect the
> response in terms of distance.
> My glm is: glm(Response~NEdist+I(NEdist^2)+Distance+I(Distance^2) which
> is
> the basic model and where I add interactions to, like for exampls
> Visibility
> as an interaction to Distance
> (glm(Response~NEdist+I(NEdist^2)+Distance*Visibility+I(Distance^2)))
>
> I'd now like to make a graph which has the response variable on the y-
> axis
> (obviously). But the x-axis should have distance on it. The NEdist is a
> vector that is just co-influencing the curve and has to stay in the
> model
> but doesn't have any interactions with any other vectors.
> I'd then like to put in curves/lines for the different models to see if
> for
> example visibility effects the distance of the track to the first bird
> sighting.
>
> Is there a way to produce a graph in R that has these features?
> --
> View this message in context: http://r.789695.n4.nabble.com/How-to-
> produce-a-graph-of-glms-in-R-tp3051471p3051471.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 49
Date: Mon, 22 Nov 2010 14:05:52 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <murdoch.duncan at gmail.com>, <jo.lists at gmail.com>
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Plotting a cloud/fog of variable density in rgl
Message-ID: <BLU113-W6EEA06C04558173792A5ABE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> Date: Mon, 22 Nov 2010 13:55:13 -0500
> From: murdoch.duncan at gmail.com
> To: jo.lists at gmail.com
> CC: r-help at stat.math.ethz.ch
> Subject: Re: [R] Plotting a cloud/fog of variable density in rgl
>
> On 22/11/2010 12:51 PM, JiHO wrote:
> > Hi everyone,
> >
> > I want to plot a 3D interpolation of the concentration of aquatic
> > organisms. My goal would be to have the result represented as clouds
> > with a density proportional to the abundance of organisms, so that I
> > could fly (well, swim actually ;) ) through the scene and see the
> > patches here and there. Basically, I want to do something like this:
> > http://www.youtube.com/watch?v=27mo_Y-aU-c
> > but simpler and with only clouds.
>
> rgl doesn't make everything in OpenGL available. I'm not sure
exactly
> how those clouds were done, but it wouldn't really be easy to do them
in
> rgl.
>
> I think you can come closest to what you want within rgl by using
> sprites rather than rendering transparent spheres. See
> examples(sprites3d).
>
If you only have 2 things with simple properties, namely point emitters
as your organisms and a uniform concsntration of transparent scatters ( the
fog) you can probably derive geometrical optics expressions for the ray
trace
results and just integrate those over your source distribution. This should
be reasonably easy in R. I haven't been to siggraph since 1983 so can't
help
much but you can probably find analyitcal solutions for fog on google
and just sum up your source distribution. I guess you could even do some
wave optics etc as presumably the fog could be done as a function
of wavelength just as easily. In any case, if you only have two basic things
with simple disto should be reasonably easy to do in R with your own code.
------------------------------
Message: 50
Date: Mon, 22 Nov 2010 15:28:29 +0100
From: "B.-Markus Schuller" <b.markus.schuller at googlemail.com>
To: r-help at r-project.org
Subject: Re: [R] data acquisition with R?
Message-ID: <4CEA7E0D.2090606 at googlemail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Thanks a lot, Matt!
I will have a look at the options you suggested.
Cheers,
Mango
--
-----------------------------------------
Never run for the bus.
Never skip tea.
------------------------------
Message: 51
Date: Mon, 22 Nov 2010 10:23:07 -0800 (PST)
From: bogdanno <bodinsoul at gmail.com>
To: r-help at r-project.org
Subject: [R] Is it possible to make a matrix to start at row 0?
Message-ID:
<ef7292d4-2217-4646-97ce-0e8d53c732c9 at n30g2000vbb.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1
I want to make the matrix to be indexed from row (column) 0, not 1
Can I do that? How?
Thanks
------------------------------
Message: 52
Date: Mon, 22 Nov 2010 16:15:17 -0200
From: csrabak <crabak at acm.org>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] Rexcel
Message-ID: <icebvm$qdh$1 at dough.gmane.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Em 22/11/2010 10:11, Luis Felipe Parra escreveu:> Hello I am new to RExcel and I would like to run a source code form the
> excel worksheet. I would like to run the following code
>
> source("C:\\Quantil
Aplicativos\\Genercauca\\BackwardSelectionNC.r")
>
> from the excel wroksheet. Does anybody know how to do this?
>
> Thank you
>
Felipe,
Look at the section "Startup" in the RExcel help. In a nutshell, if
you
want the code to run immediately at the loading of the spreadsheet,
create a workbook called "RCode" and put your source there.
Other options are available. See the docs.
--
Cesar Rabak
------------------------------
Message: 53
Date: Mon, 22 Nov 2010 08:10:07 -0800 (PST)
From: "dhacademic at gmail.com" <dhacademic at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] question about constraint minimization
Message-ID:
<AANLkTi=21mXKG4dEskMMN66xt0n_GYxT7dzc_ceb1f3m at mail.gmail.com>
Content-Type: text/plain
Hi,
I have struggled on this "bound optimization with equality constraint"
by
using optim function for two days, but still fail to prepare a good input.
Can anyone help to prepare the input for my specific case? Many thanks.
Best,
Hao
On Sat, Nov 20, 2010 at 3:17 AM, Hans W Borchers [via R] <
ml-node+3051338-309339578-202837 at
n4.nabble.com<ml-node%2B3051338-309339578-2
02837 at n4.nabble.com>> wrote:
> dhacademic <at> gmail.com <dhacademic <at> gmail.com>
writes:
>
> >
> >
> > Hi,
> >
> > I am a beginner of R. There is a question about constraint
minimization.
> A
> > function, y=f(x1,x2,x3....x12), needs to be minimized. There are 3
> > requirements for the minimization:
> >
> > (1) x2+x3+...+x12=1.5 (x1 is excluded);
> > (2) x1=x3=x4;
> > (3) x1, x3 and x5 are in the range of -1~0, respectively. The rest
> variables
> > (x2, x4, x6, x7, ...., x12) are in the range of 0~1, respectively.
> >
> > The "optim" function is used. And part of my input is as
follow, where
> > "xx1r" represents the x12:
> >
> > xx1r=1.5-x[2]-x[1]-x[1]-x[3]-x[4]-x[5]-x[6]-x[7]-x[8]-x[9]
> > start=rnorm(9)
> > up=1:9/1:9*1
> > lo=1:9/1:9*-1
> >
out=optim(start,f,lower=lo,upper=up,method="L-BFGS-B",hessian=TRUE,
> > control=list(trace=6,maxit=1000))
> >
> > There are two problems in this input. the "up" and
"lo" only define a
> range
> > of -1~1 for x1 to x11, which can not meet the requirement (3). In
> addition,
> > there is not any constraint imposed on x12. I have no idea how to
specify> a
> > matrix that can impose different constraints on individual variables
in
a>
> > function. Any suggestion is highly appreciated.
> >
> > Best,
> > Hao
> >
>
> I don't see any direct need for real 'constraint' optimization
here,
> it is a 'bounded' optimization where you are allowed to use
>
> lower <- c(-1,0,-1,0,-1,0,0,0,0,0,0,0)
> upper <- c( 0,1, 0,0, 0,1,1,1,1,1,1,1)
>
> Otherwise, your description is confusing:
> (1) Did you change f to a new function with 9 variables, eliminating
> x3, x4, and x12 ?
> (2) x4 (being equal to x1) has to be in [-1, 0] but also in [0, 1]?
> (3) If you need to restrict x12 to [0, 1] also, you cannot eliminate it.
> Either keep x12 and use an equality constraint, or use inequality
> constraints on xxlr.
>
> Hans Werner
>
> ______________________________________________
> [hidden email]
<http://user/SendEmail.jtp?type=node&node=3051338&i=0>mailing
list> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
> ------------------------------
> View message @
>
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80p3051338.html>
> To unsubscribe from question about constraint minimization, click
here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscrib
e_by_code&node=3050880&code=ZGhhY2FkZW1pY0BnbWFpbC5jb218MzA1MDg4MHwtNjM2Nzc0
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------------------------------
Message: 54
Date: Mon, 22 Nov 2010 01:41:42 -0800 (PST)
From: Dimitri Shvorob <dimitri.shvorob at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] Lost in POSIX
Message-ID: <1290418902451-3053329.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
> Nor would I call this much of an improvement in clarity... what about
"min"? You want to know the minimum?
LOL. (And apologies for the insensitivity). Thank you for help, Jeff. This
works, but I am still curious to see a solution based on "trunc", if
anyone
can find it.
--
View this message in context:
http://r.789695.n4.nabble.com/Lost-in-POSIX-tp3052768p3053329.html
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------------------------------
Message: 55
Date: Mon, 22 Nov 2010 11:19:29 +0000
From: Georg Otto <gwo at well.ox.ac.uk>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] Find in R and R books
Message-ID: <xotr5edbo72.fsf at well.ox.ac.uk>
Content-Type: text/plain; charset=us-ascii
> Also when I try to search in google using for example the word R inside
the search lemma I get very few results as the R confuses the search engine.
When I was looking something in matlab ofcourse it was easier to get results
as the search engine performs better.> What are your tricks when you want to find some function that provides
some functionality?
To search R-specific sites the best place to go is this one:
http://www.rseek.org/
Cheers,
Georg
------------------------------
Message: 56
Date: Mon, 22 Nov 2010 00:20:09 -0800 (PST)
From: meytar <meytar at techunix.technion.ac.il>
To: r-help at r-project.org
Subject: Re: [R] using rpart with a tree misclassification condition
Message-ID: <1290414009182-3053230.post at n4.nabble.com>
Content-Type: text/plain
[[elided Yahoo spam]]
Yes, I meant the apparent error rate.
According to your advice, if I use "rpart" to build a full tree, what
pruning command will be appropriate and will able me to add as an input to
the pruning procedure the total error rate i'm looking for?
Thank you very much
Meytar
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View this message in context:
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ition-tp3053167p3053230.html
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------------------------------
Message: 57
Date: Mon, 22 Nov 2010 07:23:25 -0800
From: Patrick Leyshock <pleyshock at gmail.com>
To: Uwe Ligges <ligges at statistik.tu-dortmund.de>
Cc: r-help at r-project.org
Subject: Re: [R] memory profiling
Message-ID:
<AANLkTinWYjpGPjFre3Q43rNi1x3ZgLYG7Y6wAQcqzd31 at mail.gmail.com>
Content-Type: text/plain
Using:
summaryRprof(memory="both")
did the trick, thank you. I had not been using that setting when calling
summaryRprof.
Thanks, Patrick
2010/11/20 Uwe Ligges <ligges at statistik.tu-dortmund.de>
>
>
> On 19.11.2010 21:48, Patrick Leyshock wrote:
>
>> I'm trying to configure Version 2.12.0 or R to do memory profiling.
>>
>> I've reconfigured the code:
>>
>> % ./compile --enable-memory-profiling=YES
>>
>> and verified that it's configured correctly by examining the
output. I
>> then
>> rebuild R:
>>
>> % make
>>
>> Then I fire up R and run a script, using Rprof with the
memory-profiling
>> switch set to TRUE:
>>
>> Rprof("output", memory.profiling=TRUE);
>> # a bunch of R code
>> Rprof(NULL);
>>
>
>
> Wen I do
>
> summaryRprof(memory="both")
>
> I see an additional column ...
>
> but since you have not said what you tried exactly, we cannot help very
> much.
>
> Uwe Ligges
>
>
>
> When I examine the output, however, using either R CMD Rprof from the
>> shell,
>> or summaryRprof from within R, the output I see is identical to the
output>> I
>> got when I ran R BEFORE I recompiled with memory profiling enabled.
>>
>> Anyone see something that I'm missing?
>>
>> Thanks, Patrick
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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------------------------------
Message: 58
Date: Mon, 22 Nov 2010 03:14:17 -0800 (PST)
From: romzero <romzero at yahoo.it>
To: r-help at r-project.org
Subject: [R] Some questione about plot
Message-ID: <1290424457967-3053430.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Q1: How can i draw LSD (Least significant difference) on a plot?
Like this...
http://r.789695.n4.nabble.com/file/n3053430/LSD.jpg
Q2: How can i draw the axis secondary scale?
Thanks for help.
--
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ml
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------------------------------
Message: 59
Date: Mon, 22 Nov 2010 08:13:32 -0800 (PST)
From: shubha <shuba.pandit at gmail.com>
To: r-help at r-project.org
Subject: [R] how do remove those predictor which have p value greater
than 0.05 in GLM?
Message-ID: <1290442412855-3053921.post at n4.nabble.com>
Content-Type: text/plain; charset=UTF-8
Hi R user,
I am a kind of an intermediate user of R. Now I am using GLM model (library
MASS, VEGUS). I used a backward stepwise logistic regression, but i got a
problem in removing those predictors which are above 0.05. I don't want to
include those variables which were above 0.05 in final backward stepwise
logetsic regression model.
for example: first I run the model,
"name<-glm(dep~env1+env2..., family= binomial, data=new)"
after that, I did stepwise for name
name.step<-step(name, direction="backward")
here, I still got those variables which were not significant, for example:
secchi was not significant (see below example), but still it was in the
model. how can I remove those variables which are not significant in
forward/backward stepwise?.
another question, when I wrote direction="backward", I got the results
same
as in the process of "forward". It is really strange. why is it same
results
for backward and forward. I checked in other two statistical software
(Statistica and SYSTAT), they provided a correct results, I think. But, I
need to use R for further analysis, therefore I need to fix the problem. I
am spending so much time to figure it out, but I could not. could you please
give your suggestions. It would be really a great help. please see the
example of retaining predictors which have p value is greater that 0.05
after stepwise logistic regression.
Thank
Shubha Pandit, PhD
University of Windsor
Windsor, ON, Canada
===
> summary(step.glm.int.ag1)
Call:
glm(formula = ag1less ~ GEARTEMP + DOGEAR + GEARDEPTH + SECCHI +
GEARTEMP:SECCHI + DOGEAR:SECCHI + GEARTEMP:DOGEAR + GEARTEMP:GEARDEPTH +
DOGEAR:GEARDEPTH, family = binomial, data = training)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1983 -0.8272 -0.4677 0.8014 2.6502
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.231623 1.846593 1.750 0.080110 .
GEARTEMP -0.004408 0.085254 -0.052 0.958761
DOGEAR -0.732805 0.182285 -4.020 5.82e-05 ***
GEARDEPTH -0.249237 0.060825 -4.098 4.17e-05 ***
SECCHI 0.311875 0.297594 1.048 0.294645
GEARTEMP:SECCHI -0.080664 0.010079 -8.003 1.21e-15 ***
DOGEAR:SECCHI 0.066555 0.022181 3.000 0.002695 **
GEARTEMP:DOGEAR 0.030988 0.008907 3.479 0.000503 ***
GEARTEMP:GEARDEPTH 0.008856 0.002122 4.173 3.01e-05 ***
DOGEAR:GEARDEPTH 0.006680 0.004483 1.490 0.136151
---
Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3389.5 on 2751 degrees of freedom
Residual devia\
n\
ce: 2720.4 on 2742 degrees of freedom
AIC: 2740.4uh
Number of Fisher Scoring iterations: 6
=========================>
glm.int.ag1<-glm(ag1less~GEARTEMP+DOGEAR+GEARDEPTH+SECCHI+SECCHI*GEARTEMP+SE
CCHI*DOGEAR+SECCHI*GEARDEPTH+GEARTEMP*DOGEAR+GEARTEMP*GEARDEPTH+GEARDEPTH*DO
GEAR,data=training,> family=binomial)
> summary(glm.int.ag1)
Call:
glm(formula = ag1less ~ GEARTEMP + DOGEAR + GEARDEPTH + SECCHI +
SECCHI * GEARTEMP + SECCHI * DOGEAR + SECCHI * GEARDEPTH +
GEARTEMP * DOGEAR + GEARTEMP * GEARDEPTH + GEARDEPTH * DOGEAR,
family = binomial, data = training)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1990 -0.8287 -0.4668 0.8055 2.6673
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.909805 1.928375 1.509 0.131314
GEARTEMP 0.005315 0.087159 0.061 0.951379
DOGEAR -0.721864 0.183708 -3.929 8.52e-05 ***
GEARDEPTH -0.235961 0.064828 -3.640 0.000273 ***
SECCHI 0.391445 0.326542 1.199 0.230622
GEARTEMP:SECCHI -0.082296 0.010437 -7.885 3.14e-15 ***
DOGEAR:SECCHI 0.065572 0.022319 2.938 0.003305 **
GEARDEPTH:SECCHI -0.003176 0.005295 -0.600 0.548675
GEARTEMP:DOGEAR 0.030571 0.008961 3.412 0.000646 ***
GEARTEMP:GEARDEPTH 0.008692 0.002159 4.027 5.66e-05 ***
DOGEAR:GEARDEPTH 0.006544 0.004495 1.456 0.145484
---
Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3389.5 on 2751 degrees of freedom
Residual deviance: 2720.0 on 2741 degrees of freedom
AIC: 2742
Number of Fisher Scoring iterations: 6
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ue-greater-than-0-05-in-GLM-tp3053921p3053921.html
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------------------------------
Message: 60
Date: Mon, 22 Nov 2010 09:56:37 -0800 (PST)
From: wangwallace <talenttree at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] how to apply sample function to each row of a data
frame?
Message-ID: <1290448597442-3054117.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
I tried it. it works out perfectly. you save my life.
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-a-data-frame-tp3050933p3054117.html
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------------------------------
Message: 61
Date: Mon, 22 Nov 2010 10:43:15 -0800 (PST)
From: tomreilly <tomreilly at autobox.com>
To: r-help at r-project.org
Subject: Re: [R] arima
Message-ID: <1290451395576-3054206.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Nuncio,
No, there is no requirement to subtract the mean.
It is required that the residuals are N.I.I.D. (ie constant mean and
constant variance). If you have an upward trending series, for example,
then the series would need to be "deseasonalized" so that it is
constant.
There are many many steps to doing this right. Email me at
sales at autobox.com to hear more.
Tom
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------------------------------
Message: 62
Date: Mon, 22 Nov 2010 11:13:13 -0800
From: Nathan Miller <natemiller77 at gmail.com>
To: r-help at r-project.org
Subject: [R] Wait for user input with readline()
Message-ID:
<AANLkTik-U6f+OXv3M=C11+3D7168PwPe1SN6rHcYN5Vv at mail.gmail.com>
Content-Type: text/plain
Hello,
I am trying write a script that includes a prompt for user input using
readlines(). I am running into the problem that when I run readlines() as a
single line the prompt works perfectly, but when I try to run a block of
code which includes the readline function, the script doesn't wait for the
user input. I have seen this question posted before when I did a search, but
I didn't find an suitable answer. Is there a means of ensuring that the
script does not proceed until a value has been entered to readline(). Can I
put readline in a function that will wait for input?
Are there other options for getting user input that allow require that the
script wait for user input?
Thanks for your help,
Nate
[[alternative HTML version deleted]]
------------------------------
Message: 63
Date: Mon, 22 Nov 2010 16:09:40 +0100
From: "Viechtbauer Wolfgang (STAT)"
<wolfgang.viechtbauer at maastrichtuniversity.nl>
To: Jalla <zazzala at googlemail.com>, "r-help at r-project.org"
<r-help at r-project.org>
Subject: Re: [R] txtProgressBar strange behavior in R 2.12.0
Message-ID:
<077E31A57DA26E46AB0D493C9966AC730BE0812678 at UM-MAIL4112.unimaas.nl>
Content-Type: text/plain; charset="utf-8"
I believe nobody has responded to far, so maybe this is not a wide-spread
issue. However, I have also encountered this since upgrading to R 2.12.0
(Windows 7, 64-bit). In my simulations where I use txtProgressBar(), the
problem usually disappears after the bar has progressed to a certain amount,
but it's quite strange nonetheless. The characters that appear are gibberish
and include some Asian symbols. Here is a screenshot:
http://www.wvbauer.com/screenshot.jpg
sessionInfo():
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
No idea what could be causing this.
Best,
--
Wolfgang Viechtbauer
Department of Psychiatry and Neuropsychology
School for Mental Health and Neuroscience
Maastricht University, P.O. Box 616
6200 MD Maastricht, The Netherlands
Tel: +31 (43) 368-5248
Fax: +31 (43) 368-8689
Web: http://www.wvbauer.com
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org]
> On Behalf Of Jalla
> Sent: Saturday, November 20, 2010 23:49
> To: r-help at r-project.org
> Subject: [R] txtProgressBar strange behavior in R 2.12.0
>
>
> Hi,
> I am running R 2.12.0 (windows).
>
> example(txtProgressBar)
>
> gives me some funny screen output with all kinds of special characters
> appearing and disappearing. It's happening on two different mashines
since
> vs. 2.12.0. Is this a known issue?
>
> Best,
> Jalla
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/txtProgressBar-strange-behavior-in-R-2-12-0-
> tp3051976p3051976.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 64
Date: Mon, 22 Nov 2010 17:51:10 +0800
From: ?? <xiagao1982 at gmail.com>
To: r-help at r-project.org
Subject: [R] How to call web service in R
Message-ID:
<AANLkTintJO3AVsFhBn0eTrPnOK832E1E7GLa2Wsi9Q+a at mail.gmail.com>
Content-Type: text/plain
Hello everyone,
[[elided Yahoo spam]]
Gao Xia
[[alternative HTML version deleted]]
------------------------------
Message: 65
Date: Mon, 22 Nov 2010 15:02:20 +0000
From: "Ni, Melody Zhifang" <z.ni at imperial.ac.uk>
To: "'r-help at r-project.org'" <r-help at
r-project.org>
Subject: [R] save a regression model that can be used later
Message-ID:
<BD9258C2D51F8040927E2E5D2DD39C7C2930926AA6 at ICEXM3.ic.ac.uk>
Content-Type: text/plain
Hi everyone
I have a question about how to save a regression model in R and how to
retrieve it for making predictions in a new session.
To be more specific, I fitted a multilevel logistic regression model using
the lmer from the "lme4" package. I then successfully make
predictions
using fitted(mymodel).
Since data are complex (three levels, nested, numerous categorical and
continuous data describing types of laparoscopic surgery), the computer
takes quite a while to fit the MLM model. I wonder whether it's possible to
save the fitted model so that I don't have to fit it again for making
predictions every time I start a new R session.
I searched the mailing-list archive. Suggestions include using save () to
save the model as "mymodel.rda" and then use load(mymodel.rda) into
the
workspace. I tried without success (in Windows), returning the error
message: "Error in object$fitted : $ operator is invalid for atomic
vectors"
Did I do anything wrong? Any help on this topic is much appreciated
BW, Melody
--
Dr Melody Ni
Imperial College
Department of Surgery and Cancer
10th floor, QEQM Building
St. Mary's Hospital
London W2 1NY
Tel/Fax: +44 (0) 20 331 27657/26309
z.ni at imperial.ac.uk<mailto:z.ni at imperial.ac.uk>
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------------------------------
Message: 66
Date: Mon, 22 Nov 2010 14:24:47 -0500
From: "Ravi Varadhan" <rvaradhan at jhmi.edu>
To: <dhacademic at gmail.com>, <r-help at r-project.org>
Subject: Re: [R] question about constraint minimization
Message-ID: <004f01cb8a7a$ed137670$c73a6350$@edu>
Content-Type: text/plain; charset="us-ascii"
I do not understand the constraint x1 = x3 = x4. If this is correct, you
only have 10 unknown parameters.
If you can correctly formulate your problem, you can have a look at the
packages "alabama" or "BB". The function `auglag' in
"alabama" or the
function `spg' in "BB" may be useful.
Ravi.
-------------------------------------------------------
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology School of Medicine Johns
Hopkins University
Ph. (410) 502-2619
email: rvaradhan at jhmi.edu
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of dhacademic at gmail.com
Sent: Monday, November 22, 2010 11:10 AM
To: r-help at r-project.org
Subject: Re: [R] question about constraint minimization
Hi,
I have struggled on this "bound optimization with equality constraint"
by
using optim function for two days, but still fail to prepare a good input.
Can anyone help to prepare the input for my specific case? Many thanks.
Best,
Hao
On Sat, Nov 20, 2010 at 3:17 AM, Hans W Borchers [via R] <
ml-node+3051338-309339578-202837 at
n4.nabble.com<ml-node%2B3051338-309339578-2
02837 at n4.nabble.com>> wrote:
> dhacademic <at> gmail.com <dhacademic <at> gmail.com>
writes:
>
> >
> >
> > Hi,
> >
> > I am a beginner of R. There is a question about constraint
minimization.
> A
> > function, y=f(x1,x2,x3....x12), needs to be minimized. There are 3
> > requirements for the minimization:
> >
> > (1) x2+x3+...+x12=1.5 (x1 is excluded);
> > (2) x1=x3=x4;
> > (3) x1, x3 and x5 are in the range of -1~0, respectively. The rest
> variables
> > (x2, x4, x6, x7, ...., x12) are in the range of 0~1, respectively.
> >
> > The "optim" function is used. And part of my input is as
follow, where
> > "xx1r" represents the x12:
> >
> > xx1r=1.5-x[2]-x[1]-x[1]-x[3]-x[4]-x[5]-x[6]-x[7]-x[8]-x[9]
> > start=rnorm(9)
> > up=1:9/1:9*1
> > lo=1:9/1:9*-1
> >
out=optim(start,f,lower=lo,upper=up,method="L-BFGS-B",hessian=TRUE,
> > control=list(trace=6,maxit=1000))
> >
> > There are two problems in this input. the "up" and
"lo" only define a
> range
> > of -1~1 for x1 to x11, which can not meet the requirement (3). In
> addition,
> > there is not any constraint imposed on x12. I have no idea how to
specify> a
> > matrix that can impose different constraints on individual variables
in
a>
> > function. Any suggestion is highly appreciated.
> >
> > Best,
> > Hao
> >
>
> I don't see any direct need for real 'constraint' optimization
here,
> it is a 'bounded' optimization where you are allowed to use
>
> lower <- c(-1,0,-1,0,-1,0,0,0,0,0,0,0)
> upper <- c( 0,1, 0,0, 0,1,1,1,1,1,1,1)
>
> Otherwise, your description is confusing:
> (1) Did you change f to a new function with 9 variables, eliminating
> x3, x4, and x12 ?
> (2) x4 (being equal to x1) has to be in [-1, 0] but also in [0, 1]?
> (3) If you need to restrict x12 to [0, 1] also, you cannot eliminate it.
> Either keep x12 and use an equality constraint, or use inequality
> constraints on xxlr.
>
> Hans Werner
>
> ______________________________________________
> [hidden email]
<http://user/SendEmail.jtp?type=node&node=3051338&i=0>mailing
list> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
> ------------------------------
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>
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______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 67
Date: Mon, 22 Nov 2010 11:27:09 -0800
From: Joshua Wiley <jwiley.psych at gmail.com>
To: bogdanno <bodinsoul at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Is it possible to make a matrix to start at row 0?
Message-ID:
<AANLkTikfD_yAkHNwdV26dQmqADiMUmHS_AZ4qfrMy70=@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
You can do it, but it would be very difficult (think reworking all
indexing yourself) and you probably should not even try (nothing else
that was expecting indexing to work as the R gods intended it to would
work once you had done your rework).
What has lead you to want to index from 0? If it is some problem you
are having, I can almost certainly promise you it will be easier for
us to show you how to approach it differently and index from 1 than to
change the underlying framework so you can index from 0.
Cheers,
Josh
On Mon, Nov 22, 2010 at 10:23 AM, bogdanno <bodinsoul at gmail.com>
wrote:>
> I want to make the matrix to be indexed from row (column) 0, not 1
> Can I do that? How?
> Thanks
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
------------------------------
Message: 68
Date: Mon, 22 Nov 2010 11:37:29 -0800
From: Bert Gunter <gunter.berton at gene.com>
To: bogdanno <bodinsoul at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Is it possible to make a matrix to start at row 0?
Message-ID:
<AANLkTinwygygCqK3LNRKm4JrpVOmMek5ecNwjMceL-tA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Eh??? Why would you want to do that?? (R isn't C).
So the simple answer is: you can't.
The other answer is, well of course you sort of can via, e.g.
for(i in 0:9) {
z <- myMatrix[i+1,]
...
}
But as Josh said, I think this falls into the class of "You are just
asking for trouble, so don't do it."
Cheers,
Bert
On Mon, Nov 22, 2010 at 10:23 AM, bogdanno <bodinsoul at gmail.com>
wrote:> I want to make the matrix to be indexed from row (column) 0, not 1
> Can I do that? How?
> Thanks
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Bert Gunter
Genentech Nonclinical Biostatistics
------------------------------
Message: 69
Date: Mon, 22 Nov 2010 14:38:18 -0500
From: Harlan Harris <harlan at harris.name>
To: Tal Galili <tal.galili at gmail.com>, Farrel Buchinsky
<fjbuch at gmail.com>
Cc: r-help at r-project.org, Duncan Temple Lang <duncan at
wald.ucdavis.edu>
Subject: Re: [R] RGoogleDocs stopped working
Message-ID:
<AANLkTin=c2Ashu8SQtgV=9A6__MCmyFxwQewMpzoUAML at mail.gmail.com>
Content-Type: text/plain
No joy for me. :(
I'd had version 0.4-1 installed previously, and re-pulling that URL and
reinstalling, plus setting RCurlOptions as specified, do not help for me.
Exactly the same behavior. It doesn't matter whether I call getGoogleAuth
directly or let getGoogleDocsConnection do it for me.
-Harlan
On Fri, Nov 19, 2010 at 10:27 PM, Farrel Buchinsky <fjbuch at gmail.com>
wrote:
> Harlan and Tal have had problems. I had lots too. I spent hours getting it
> to work. Terrible process to go through but RGoogleDocs is so useful that
[[elided Yahoo spam]]>
> My problems were overcome when
>
> 1. I used the latest zip file by Duncan Temple Lang see below
> 2. I inserted an options line that loosened the ssl security - do not
> know if that was a good thing or not but it got it to work
>
> Duncan said:
> "I have put an updated version of the source of the package with
> these changes. It is available from
> http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.tar.gz
> There is a binary for Windows in
> http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.zip
>
> Here is my script that works. Does yours look like this?
>
> library(RGoogleDocs)
> packageDescription("
RGoogleDocs")> ps <-readline(prompt="get the password in ")
> options(RCurlOptions = list(capath = system.file("CurlSSL",
"cacert.pem",
> package = "RCurl"), ssl.verifypeer = FALSE))
> sheets.con = getGoogleDocsConnection(getGoogleAuth("fjbuch at
gmail.com", ps,
> service ="wise"))
> ts2=getWorksheets("OnCall",sheets.con) #OnCall is just the name
of a
> spreadsheet
> names(ts2)
> y2005<-sheetAsMatrix(ts2$y2005,header=TRUE, as.data.frame=TRUE,
trim=TRUE)
>
> Finally, I am willing to offer you a TeamViewer session where we can take
> control of one another's computers and see if the problem is code or
the
> installation. I warn you that I am neither a programmer nor a developer,
> just a very enthusiastic RGoogleDocs user who probably perseveres more
than> is good for him.
>
> Farrel Buchinsky
>
>
On Fri, Nov 19, 2010 at 1:35 PM, Tal Galili <tal.galili at gmail.com>
wrote:
> I second Harlan's call.
>
>
> ----------------Contact
> Details:-------------------------------------------------------
> Contact me: Tal.Galili at gmail.com | 972-52-7275845
> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
> www.r-statistics.com (English)
>
>
----------------------------------------------------------------------------
------------------>
>
>
>
> On Fri, Nov 19, 2010 at 5:00 PM, Harlan Harris <harlan at
harris.name> wrote:
>
>> Any new thoughts on this? I really want to get this working again! Is
>> there
>> someone else that can help or somewhere else I should be asking?
>>
>> Thanks!
>>
>> -Harlan
>>
>>
>> On Wed, Nov 17, 2010 at 10:16 AM, Harlan Harris <harlan at
harris.name>
>> wrote:
>>
>> > Following up again. I found on the forums for the Google Apps API
this
>> > thread that seems to be about a similar issue:
>> >
>>
http://www.google.com/support/forum/p/apps-apis/thread?tid=1c22cb44eb5cbba6&
hl=en&search_impression_id=ab161b010ecf8803%3A12c5a65ce83&search_source=rela
ted_question>> >
>> > It's using Java and is rather over my head, but it seems to
suggest
that>> > something related to the content type might be wrong? Does this
offer
>> any
>> > suggestions on how to fix my use of RGoogleDocs?
>> >
>> > Thanks,
>> >
>> > -Harlan
>> >
>> >
>> > On Mon, Nov 15, 2010 at 12:16 PM, Harlan Harris <harlan at
harris.name
>> >wrote:
>> >
>> >> Thanks, Duncan. Finally getting a chance to follow up on
this...
>> >>
>> >> I tried again, changing and resetting my password, and trying
to
>> specify
>> >> my login and password manually in the getGoogleDocsConnection
argument
>> list.
>> >> I also tried removing either or both of the service and error
options.
>> No
>> >> luck in any case. I also tried a different Google account,
also with
no>> >> luck.
>> >>
>> >> I've also tried tweaking the URL being generated by the
code, and in
>> all
>> >> cases, I get a 403: Forbidden error with content
>> "Error=BadAuthentication".
>> >>
>> >> I don't really know enough about how authentication is
supposed to
work>> to
>> >> get much farther. Can you help? Should I try the Google API
forum
>> instead?
>> >>
>> >> -Harlan
>> >>
>> >>
>> >>
>> >>> From: Duncan Temple Lang <duncan at
wald.ucdavis.edu>
>> >>> To: r-help at r-project.org
>> >>> Date: Wed, 10 Nov 2010 10:33:47 -0800
>> >>> Subject: Re: [R] RGoogleDocs stopped working
>> >>>
>> >>> Hi Harlan
>> >>>
>> >>> I just tried to connect to Google Docs and I had
ostensibly the same
>> >>> problem.
>> >>> However, the password was actually different from what I
had
>> specified.
>> >>> After resetting it with GoogleDocs, the
getGoogleDocsConnection()
>> worked
>> >>> fine. So I don't doubt that the login and password are
correct, but
>> >>> you might just try it again to ensure there are no typos.
>> >>> The other thing to look at is the values for Email and
Passwd
>> >>> sent in the URL, i.e. the string in url in your debugging
>> >>> below. (Thanks for that by the way). If either has special
characters,>> >>> e.g. &, it is imperative that they are escaped
correctly, i.e.
>> converted
>> >>> to %24. This should happen and nothing should have
changed, but it
is>> >>> worth verifying.
>> >>>
>> >>> So things still seem to work for me. It is a data point,
but not one
>> >>> that gives you much of a clue as to what is wrong on your
machine.
>> >>>
>> >>> D.
>> >>>
>> >>
>> >> On Wed, Nov 10, 2010 at 10:36 AM, Harlan Harris <harlan at
harris.name
>> >wrote:
>> >>
>> >>> Hello,
>> >>>
>> >>> Some code using RGoogleDocs, which had been working
smoothly since
the>> >>> summer, just stopped working. I know that it worked on
November 3rd,
>> but it
>> >>> doesn't work today. I've confirmed that the login
and password still
>> work
>> >>> when I log in manually. I've confirmed that the URL
gives the same
>> error
>> >>> when I paste it into Firefox. I don't know enough
about this web
>> service to
>> >>> figure out the problem myself, alas...
>> >>>
>> >>> Here's the error and other info (login/password
omitted):
>> >>>
>> >>> > ss.con <- getGoogleDocsConnection(login=gd.login,
>> password=gd.password,
>> >>> service='wise', error=FALSE)
>> >>> Error: Forbidden
>> >>>
>> >>> Enter a frame number, or 0 to exit
>> >>>
>> >>> 1: getGoogleDocsConnection(login = gd.login, password =
gd.password,
>> >>> service = "wise", error = FALSE)
>> >>> 2: getGoogleAuth(..., error = error)
>> >>> 3:
getForm("https://www.google.com/accounts/ClientLogin", accountType
>> >> >>> "HOSTED_OR_GOOGLE", Email = login,
Passw
>> >>> 4: getURLContent(uri, .opts = .opts, .encoding =
.encoding, binary >> >>> binary, curl = curl)
>> >>> 5: stop.if.HTTP.error(http.header)
>> >>>
>> >>> Selection: 4
>> >>> Called from: eval(expr, envir, enclos)
>> >>> Browse[1]> http.header
>> >>> Content-Type
>> >>> Cache-control Pragma
>> >>> "text/plain"
"no-cache,
>> >>> no-store" "no-cache"
>> >>> Expires
Date
>> >>> X-Content-Type-Options
>> >>> "Mon, 01-Jan-1990 00:00:00 GMT" "Wed, 10
Nov 2010 15:24:39
>> >>> GMT" "nosniff"
>> >>> X-XSS-Protection
>> >>> Content-Length Server
>> >>> "1; mode=block"
>> >>> "24" "GSE"
>> >>> status
statusMessage
>> >>> "403"
"Forbidden\r\n"
>> >>> Browse[1]> url
>> >>> [1] "
>> >>>
>>
https://www.google.com/accounts/ClientLogin?accountType=HOSTED%5FOR%5FGOOGLE
&Email=***&Passwd=***&service=wise&source=R%2DGoogleDocs%2D0%2E1>> >>> "
>> >>> Browse[1]> .opts
>> >>> $ssl.verifypeer
>> >>> [1] FALSE
>> >>>
>> >>>
>> >>> > R.Version()
>> >>> $platform
>> >>> [1] "i386-apple-darwin9.8.0"
>> >>>
>> >>> $arch
>> >>> [1] "i386"
>> >>>
>> >>> $os
>> >>> [1] "darwin9.8.0"
>> >>>
>> >>> $system
>> >>> [1] "i386, darwin9.8.0"
>> >>>
>> >>> $status
>> >>> [1] ""
>> >>>
>> >>> $major
>> >>> [1] "2"
>> >>>
>> >>> $minor
>> >>> [1] "10.1"
>> >>>
>> >>> $year
>> >>> [1] "2009"
>> >>>
>> >>> $month
>> >>> [1] "12"
>> >>>
>> >>> $day
>> >>> [1] "14"
>> >>>
>> >>> $`svn rev`
>> >>> [1] "50720"
>> >>>
>> >>> $language
>> >>> [1] "R"
>> >>>
>> >>> $version.string
>> >>> [1] "R version 2.10.1 (2009-12-14)"
>> >>>
>> >>>
>> >>> > installed.packages()[c('RCurl',
'RGoogleDocs'), ]
>> >>> Package
>> >>> LibPath
Version Priority
>> Bundle
>> >>> Contains
>> >>> RCurl "RCurl"
>> >>> "/Users/hharris/Library/R/2.10/library"
"1.4-3" NA
>> NA
>> >>> NA
>> >>> RGoogleDocs "RGoogleDocs"
>> >>>
"/Library/Frameworks/R.framework/Resources/library" "0.4-1"
NA
>> NA
>> >>> NA
>> >>> Depends Imports
LinkingTo
>> >>> Suggests Enhances OS_type License Built
>> >>> RCurl "R (>= 2.7.0), methods, bitops"
NA NA
>> >>> "Rcompression" NA NA "BSD"
"2.10.1"
>> >>> RGoogleDocs "RCurl, XML, methods" NA
NA
>> >>> NA NA NA "BSD"
"2.10.1"
>> >>>
>> >>>
[[elided Yahoo spam]]>> >>>
>> >>> -Harlan
>> >>>
>> >>>
>> >>
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
[[alternative HTML version deleted]]
------------------------------
Message: 70
Date: Mon, 22 Nov 2010 11:49:43 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
To: Lucia Ca?as <lucia.canas at co.ieo.es>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] sm.ancova graphic
Message-ID: <4CEAC957.8040505 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-11-22 09:47, Lucia Ca?as wrote:>
> Hi R-Users,
>
> I am working with sm.ancova (in the package sm) and I have two problems
with the graph, which is automatically generated when sm.ancova() is
run.>
> 1-Besides of the fitted lines, the observed data appeared automatically in
the graph. I prefer that only fitted lines appear. I check the sm.options,
but I could not find the way that the observed data do not appear in the
graph.>
> 2-I would like to change the size of the numbers in the axis. Again, I
check the sm.options, but I could not find the correct
way.>
Your second request is easy: just issue a par(cex.axis = ....) call
before the sm.ancova call.
For your first problem, I can't see a simple way; this seems to be
hard-coded in the function. But the function is easy to modify. Just
look for a couple of short loops containing this:
text(rawdata$
(It's best to work with the source code in the *.tar.gz file.)
Remove or comment out those loops and save the function as, say,
my.sm.ancova. You'll also have to set the environment of
my.sm.ancova to that of sm.ancova.
Seems to me that it might be worth suggesting this and the ability
to fiddle with graphics parameters to the maintainer of sm.
Peter Ehlers
>
>
> Thank you in advance,
>
> Luc?a
>
> [[alternative HTML version deleted]]
>
------------------------------
Message: 71
Date: Mon, 22 Nov 2010 11:55:10 -0800
From: Joshua Wiley <jwiley.psych at gmail.com>
To: Nathan Miller <natemiller77 at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Wait for user input with readline()
Message-ID:
<AANLkTi=w+oQ19cinTY8fJ6NtGn=zwi8pNzxT11tOjO=- at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Nate,
There may be better ways, but on the couple instances I've wanted to
wait for keyboard input I used this type of paradigm:
foo <- function() {
x <- 1:10
y <- rnorm(10)
input <- NA
while(!isTRUE(input == "1") && !isTRUE(input ==
"2")) {
cat("Please type '1' if you want the first variable on the x
axis and '2' if you want the second.", fill = TRUE)
input <- scan("", what = "character")
if(input == "1") {
plot(x, y)
} else if (input == "2") {
plot(y, x)
} else {cat("Sorry, I didn't catch that", fill = TRUE)}
}
}
Perhaps it will be of some use to you.
Best regards,
Josh
On Mon, Nov 22, 2010 at 11:13 AM, Nathan Miller <natemiller77 at
gmail.com>
wrote:> Hello,
>
> I am trying write a script that includes a prompt for user input using
> readlines(). I am running into the problem that when I run readlines() as
a> single line the prompt works perfectly, but when I try to run a block of
> code which includes the readline function, the script doesn't wait for
the
> user input. I have seen this question posted before when I did a search,
but> I didn't find an suitable answer. Is there a means of ensuring that the
> script does not proceed until a value has been entered to readline(). Can
I> put readline in a function that will wait for input?
>
> Are there other options for getting user input that allow require that the
> script wait for user input?
>
> Thanks for your help,
>
> Nate
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
------------------------------
Message: 72
Date: Mon, 22 Nov 2010 14:56:39 -0500
From: Gabor Grothendieck <ggrothendieck at gmail.com>
To: Manta <mantino84 at libero.it>
Cc: r-help at r-project.org
Subject: Re: [R] Ordeing Zoo object
Message-ID:
<AANLkTikKFhcP7r+EWekDXqx=C06xr+TDp9e+7zbpSQ=S at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Mon, Nov 22, 2010 at 1:35 PM, Manta <mantino84 at libero.it>
wrote:>
> And how about if I want to order the series from the smallest to the
largest> value, keeping the date index in order to see when the values were
> predominantly negative etc...
>
If you just want to look at it in this order then:
as.data.frame(dat)[length(dat):1,,drop = FALSE]
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
------------------------------
Message: 73
Date: Mon, 22 Nov 2010 19:59:23 +0000 (UTC)
From: Ben Bolker <bbolker at gmail.com>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] Is it possible to make a matrix to start at row 0?
Message-ID: <loom.20101122T204655-678 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii
Bert Gunter <gunter.berton <at> gene.com> writes:
>
> Eh??? Why would you want to do that?? (R isn't C).
>
> So the simple answer is: you can't.
>
> The other answer is, well of course you sort of can via, e.g.
>
> for(i in 0:9) {
> z <- myMatrix[i+1,]
> ...
> }
>
> But as Josh said, I think this falls into the class of "You are just
> asking for trouble, so don't do it."
>
> Cheers,
> Bert
But if you still want to after all those warnings, you can ...
see the "Oarray" package, where the first letter of the package
name is a capital letter "oh" (O), not a zero (0).
library("fortunes"); fortune("Yoda")
There ought also to be a clever fortune() expressing the sentiment
that you may eventually find (weeks, months, or years later) that
changing the way you solve your problem to go with R's flow would
have been easier than implementing a solution that works around
the flow (examples abound: <<-, zero-based arrays, eval(parse()),
storing names of variables as character vectors and using get()
[FAQ 7.21], etc, etc, etc ...)
------------------------------
Message: 74
Date: Mon, 22 Nov 2010 15:04:01 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: "Ni, Melody Zhifang" <z.ni at imperial.ac.uk>
Cc: "'r-help at r-project.org'" <r-help at
r-project.org>
Subject: Re: [R] save a regression model that can be used later
Message-ID: <EA74D6E5-DAF0-407E-8451-7F23BD7F84BC at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 10:02 AM, Ni, Melody Zhifang wrote:
> Hi everyone
>
> I have a question about how to save a regression model in R and how
> to retrieve it for making predictions in a new session.
>
> To be more specific, I fitted a multilevel logistic regression model
> using the lmer from the "lme4" package. I then successfully make
> predictions using fitted(mymodel).
>
> Since data are complex (three levels, nested, numerous categorical
> and continuous data describing types of laparoscopic surgery), the
> computer takes quite a while to fit the MLM model. I wonder whether
> it's possible to save the fitted model so that I don't have to fit
> it again for making predictions every time I start a new R session.
>
> I searched the mailing-list archive. Suggestions include using save
> () to save the model as "mymodel.rda" and then use
load(mymodel.rda)
> into the workspace. I tried without success (in Windows), returning
> the error message: "Error in object$fitted : $ operator is invalid
> for atomic vectors"
How? ... did you "try" that is. Need code, not vague reports of
failure.
>
> Did I do anything wrong? Any help on this topic is much appreciated
>
> BW, Melody
>
> --
> Dr Melody Ni
> Imperial College
> Department of Surgery and Cancer
> 10th floor, QEQM Building
--
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 75
Date: Mon, 22 Nov 2010 12:10:17 -0800 (PST)
From: madr <madrazel at interia.pl>
To: r-help at r-project.org
Subject: [R] how to round only one column of a matrix ?
Message-ID: <1290456617008-3054363.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
round() function affects all values of a matrix, I want only to round column
that is called 'y'.
--
View this message in context:
http://r.789695.n4.nabble.com/how-to-round-only-one-column-of-a-matrix-tp305
4363p3054363.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 76
Date: Mon, 22 Nov 2010 21:10:20 +0100
From: baptiste auguie <baptiste.auguie at googlemail.com>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] Is it possible to make a matrix to start at row 0?
Message-ID:
<AANLkTi=UTX7mWNAA_wy5Yb=v6oorXTBG21KFwa+-3OnM at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Apparently He who starts from 0 needn't be called unfortunate,
fortune('indexed')
baptiste
On 22 November 2010 20:59, Ben Bolker <bbolker at gmail.com>
wrote:> Bert Gunter <gunter.berton <at> gene.com> writes:
>
>>
>> Eh??? Why would you want to do that?? (R isn't C).
>>
>> So the simple answer is: you can't.
>>
>> The other answer is, well of course you sort of can via, e.g.
>>
>> for(i in 0:9) ?{
>> ? ?z <- myMatrix[i+1,]
>> ? ...
>> }
>>
>> But as Josh said, I think this falls into the class of "You are
just
>> asking for trouble, so don't do it."
>>
>> Cheers,
>> Bert
>
> ?But if you still want to after all those warnings, you can ...
> see the "Oarray" package, where the first letter of the package
> name is a capital letter "oh" (O), not a zero (0).
>
> ?library("fortunes"); fortune("Yoda")
>
> ?There ought also to be a clever fortune() expressing the sentiment
> that you may eventually find (weeks, months, or years later) that
> changing the way you solve your problem to go with R's flow would
> have been easier than implementing a solution that works around
> the flow (examples abound: <<-, zero-based arrays, eval(parse()),
> storing names ?of variables as character vectors and using get()
> [FAQ 7.21], etc, etc, etc ...)
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 77
Date: Mon, 22 Nov 2010 12:17:15 -0800 (PST)
From: Phil Spector <spector at stat.berkeley.edu>
To: madr <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] how to round only one column of a matrix ?
Message-ID:
<alpine.DEB.2.00.1011221216480.14043 at springer.Berkeley.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Is this what you're looking for?
> mymatrix =
matrix(rnorm(15),5,3,dimnames=list(NULL,c('x','y','z')))
> mymatrix
x y z
[1,] -0.4459162 -2.3936837 -0.7401963
[2,] 0.9886466 -1.3955161 -1.3390314
[3,] -0.2086743 1.7984620 -0.8532579
[4,] 1.0985411 0.9315553 -1.3981632
[5,] 0.5787438 0.1719177 0.2246174> mymatrix[,'y'] = round(mymatrix[,'y'])
> mymatrix
x y z
[1,] -0.4459162 -2 -0.7401963
[2,] 0.9886466 -1 -1.3390314
[3,] -0.2086743 2 -0.8532579
[4,] 1.0985411 1 -1.3981632
[5,] 0.5787438 0 0.2246174
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spector at stat.berkeley.edu
On Mon, 22 Nov 2010, madr wrote:
>
> round() function affects all values of a matrix, I want only to round
column> that is called 'y'.
> --
> View this message in context:
http://r.789695.n4.nabble.com/how-to-round-only-one-column-of-a-matrix-tp305
4363p3054363.html> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 78
Date: Mon, 22 Nov 2010 15:19:27 -0500
From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
To: ?? <xiagao1982 at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] How to call web service in R
Message-ID:
<AANLkTimoV-AyGAzu6NVhJX2N6mwRjxFsbmkKXep4pnx4 at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Mon, Nov 22, 2010 at 4:51 AM, ?? <xiagao1982 at gmail.com>
wrote:> Hello everyone,
>
[[elided Yahoo spam]]
Is RCurl what you're looking for?
http://cran.r-project.org/web/packages/RCurl/index.html
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
?| Memorial Sloan-Kettering Cancer Center
?| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
------------------------------
Message: 79
Date: Mon, 22 Nov 2010 15:39:58 -0500
From: "Tan, Richard" <RTan at panagora.com>
To: <r-help at r-project.org>
Subject: [R] aggregate a Date column does not work?
Message-ID:
<3303FA84CE4F7244B27BE264EC4AE2A71510A385 at panemail.panagora.com>
Content-Type: text/plain
Hi, I am trying to aggregate max a Date type column but have weird
result, how do I fix this?
> a <- rbind(
+ data.frame(name='Tom', payday=as.Date('1999-01-01')),
+ data.frame(name='Tom', payday=as.Date('2000-01-01')),
+ data.frame(name='Pete', payday=as.Date('1998-01-01')),
+ data.frame(name='Pete', payday=as.Date('1999-01-01'))
+ )
> a
name payday
1 Tom 1999-01-01
2 Tom 2000-01-01
3 Pete 1998-01-01
4 Pete 1999-01-01
> aggregate(a$payday, list(a$name), max)
Group.1 x
1 Tom 10957
2 Pete 10592
Thanks,
Richard
[[alternative HTML version deleted]]
------------------------------
Message: 80
Date: Mon, 22 Nov 2010 12:41:19 -0800 (PST)
From: bmiddle <bmiddle at sandia.gov>
To: r-help at r-project.org
Subject: [R] R2WinBUGS help
Message-ID: <1290458479607-3054411.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
When I use the 'bugs' function from R, WinBUGS runs correctly, but R
freezes.
The only way to use R after this is to stop calculations (without my file
that documents the calculation). However, I want to save the output in R so
I can use it in further models. Does anyone know how to fix this problem?
--
View this message in context:
http://r.789695.n4.nabble.com/R2WinBUGS-help-tp3054411p3054411.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 81
Date: Mon, 22 Nov 2010 12:44:36 -0800 (PST)
From: tomreilly <tomreilly at autobox.com>
To: r-help at r-project.org
Subject: Re: [R] FW: help with time Series regression please
Message-ID: <1290458676157-3054417.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Cathy,
How does this model look?
[(1-B**4)]Y(T) = 20.767
+[X1(T)][(1-B**4)][(+ 56.1962)] :PULSE 7/
4 I~P00028test
+[X2(T)][(1-B**4)][(+ 74.4301)] :PULSE 9/
4 I~P00036test
+[X3(T)][(1-B**4)][(- 59.9872)] :PULSE 6/
3 I~P00023test
+[X4(T)][(1-B**4)][(- 27.2187)] :PULSE 7/
1 I~P00025test
+ [(1- .435B** 1)]**-1 [A(T)]
--
View this message in context:
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mula-tp1016593p3054417.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 82
Date: Mon, 22 Nov 2010 15:48:15 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <bbolker at gmail.com>, <r-help at stat.math.ethz.ch>
Subject: Re: [R] Is it possible to make a matrix to start at row 0?
Message-ID: <BLU113-W5447FA07F7418936CF2F5BE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> To: r-help at stat.math.ethz.ch
> From: bbolker at gmail.com
> Date: Mon, 22 Nov 2010 19:59:23 +0000
> Subject: Re: [R] Is it possible to make a matrix to start at row 0?
>
> Bert Gunter gene.com> writes:
>
> >
> > Eh??? Why would you want to do that?? (R isn't C).
> >
> > So the simple answer is: you can't.
Eh, it is open source for a reason. I wouldrecommend however
if you let your zero-base version out in the wild you rename
it to R0 or something. Seriosuly 1-based arrays annoy me
but I'm not sure what happens if you modify R LOL.
> >
> > The other answer is, well of course you sort of can via, e.g.
> >
> > for(i in 0:9) {
> > z <- myMatrix[i+1,]
> > ...
> > }
> >
> > But as Josh said, I think this falls into the class of "You are
just
> > asking for trouble, so don't do it."
> >
> > Cheers,
> > Bert
>
> But if you still want to after all those warnings, you can ...
> see the "Oarray" package, where the first letter of the package
> name is a capital letter "oh" (O), not a zero (0).
>
> library("fortunes"); fortune("Yoda")
>
> There ought also to be a clever fortune() expressing the sentiment
> that you may eventually find (weeks, months, or years later) that
> changing the way you solve your problem to go with R's flow would
> have been easier than implementing a solution that works around
> the flow (examples abound: <<-, zero-based arrays, eval(parse()),
> storing names of variables as character vectors and using get()
> [FAQ 7.21], etc, etc, etc ...)
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 83
Date: Mon, 22 Nov 2010 15:50:33 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: "Tan, Richard" <RTan at panagora.com>
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
Message-ID: <41B45939-081A-4A75-A55C-F5348722918C at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 3:39 PM, Tan, Richard wrote:
> Hi, I am trying to aggregate max a Date type column but have weird
> result, how do I fix this?
In the process of getting max() you coerced the Dates to numeric and
now you need to re-coerce them back to Dates
?as.Date
as.Date(<your result>) (possibly with an origin it the default
"1970-01-01" doesn't get used.
--
David.>
>
>
>> a <- rbind(
>
> + data.frame(name='Tom', payday=as.Date('1999-01-01')),
>
> + data.frame(name='Tom', payday=as.Date('2000-01-01')),
>
> + data.frame(name='Pete', payday=as.Date('1998-01-01')),
>
> + data.frame(name='Pete', payday=as.Date('1999-01-01'))
>
> + )
>
>> a
>
> name payday
>
> 1 Tom 1999-01-01
>
> 2 Tom 2000-01-01
>
> 3 Pete 1998-01-01
>
> 4 Pete 1999-01-01
>
>> aggregate(a$payday, list(a$name), max)
>
> Group.1 x
>
> 1 Tom 10957
>
> 2 Pete 10592
>
>
>
> Thanks,
>
> Richard
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 84
Date: Mon, 22 Nov 2010 12:53:41 -0800 (PST)
From: madr <madrazel at interia.pl>
To: r-help at r-project.org
Subject: [R] I need a very specific unique like function and I don't
know even how to properly call this
Message-ID: <1290459221115-3054427.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
consider this matrix:
[,1] [,2]
[1,] 3 7
[2,] 6 5
[3,] 7 5
[4,] 3 5
[5,] 7 5
[6,] 5 5
[7,] 8 4
[8,] 2 4
[9,] 7 4
[10,] 0 6
I need to delete all rows where column 2 above and below has the same value,
so the effect would be:
[,1] [,2]
[1,] 3 7
[2,] 6 5
[6,] 5 5
[7,] 8 4
[9,] 7 4
[10,] 0 6
is there a built in function for that kind of operation or I must write one
from scratch ?
Is there a name for that kind of operation ?
--
View this message in context:
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d-I-don-t-know-even-how-to-properly-call-this-tp3054427p3054427.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 85
Date: Mon, 22 Nov 2010 15:54:37 -0500
From: "Tan, Richard" <RTan at panagora.com>
To: "David Winsemius" <dwinsemius at comcast.net>
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
Message-ID:
<3303FA84CE4F7244B27BE264EC4AE2A71510A392 at panemail.panagora.com>
Content-Type: text/plain; charset="us-ascii"
Thanks, add as.Date('1970-01-01') to the result column works.
Richard
-----Original Message-----
From: David Winsemius [mailto:dwinsemius at comcast.net]
Sent: Monday, November 22, 2010 3:51 PM
To: Tan, Richard
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
On Nov 22, 2010, at 3:39 PM, Tan, Richard wrote:
> Hi, I am trying to aggregate max a Date type column but have weird
> result, how do I fix this?
In the process of getting max() you coerced the Dates to numeric and
now you need to re-coerce them back to Dates
?as.Date
as.Date(<your result>) (possibly with an origin it the default
"1970-01-01" doesn't get used.
--
David.>
>
>
>> a <- rbind(
>
> + data.frame(name='Tom', payday=as.Date('1999-01-01')),
>
> + data.frame(name='Tom', payday=as.Date('2000-01-01')),
>
> + data.frame(name='Pete', payday=as.Date('1998-01-01')),
>
> + data.frame(name='Pete', payday=as.Date('1999-01-01'))
>
> + )
>
>> a
>
> name payday
>
> 1 Tom 1999-01-01
>
> 2 Tom 2000-01-01
>
> 3 Pete 1998-01-01
>
> 4 Pete 1999-01-01
>
>> aggregate(a$payday, list(a$name), max)
>
> Group.1 x
>
> 1 Tom 10957
>
> 2 Pete 10592
>
>
>
> Thanks,
>
> Richard
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 86
Date: Mon, 22 Nov 2010 15:55:50 -0500 (EST)
From: Xiaoqi Cui <xcui at mtu.edu>
To: r-help <r-help at r-project.org>
Subject: [R] R package "kernlab" can not be properly loaded
Message-ID:
<1590317927.1718871290459350354.JavaMail.root at marlbed.merit.edu>
Content-Type: text/plain; charset=utf-8
Hi,
I tried to load the package "kernlab" under R-v11 and R-v10, however
it gave
error message:
Error in library.dynam(lib, package, package.lib) :
shared library 'kernlab' not found
In addition: Warning message:
package 'kernlab' was built under R version 2.12.0
Error: package/namespace load failed for 'kernlab'
Has anybody loaded this successfully before? Thanks,
Xiaoqi
------------------------------
Message: 87
Date: Mon, 22 Nov 2010 21:56:24 +0100
From: Erich Neuwirth <erich.neuwirth at univie.ac.at>
To: csrabak <crabak at acm.org>, r-help <r-help at r-project.org>
Subject: Re: [R] Rexcel
Message-ID: <4CEAD8F8.4030305 at univie.ac.at>
Content-Type: text/plain; charset=ISO-8859-1
a) RExcel has its own mailing list (as the documentation tell you).
Please post RExcel related questions to the mailing list
accessible at rcom.univie.ac.at
b) For running code at startup, you have to create a worksheet (not a
workbook) named RCode in your workbook.
On 11/22/2010 7:15 PM, csrabak wrote:> Em 22/11/2010 10:11, Luis Felipe Parra escreveu:
>> Hello I am new to RExcel and I would like to run a source code form the
>> excel worksheet. I would like to run the following code
>>
>> source("C:\\Quantil
Aplicativos\\Genercauca\\BackwardSelectionNC.r")
>>
>> from the excel wroksheet. Does anybody know how to do this?
>>
>> Thank you
>>
> Felipe,
>
> Look at the section "Startup" in the RExcel help. In a nutshell,
if you
> want the code to run immediately at the loading of the spreadsheet,
> create a workbook called "RCode" and put your source there.
>
> Other options are available. See the docs.
>
> --
> Cesar Rabak
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 88
Date: Mon, 22 Nov 2010 15:57:45 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: "Tan, Richard" <RTan at panagora.com>
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
Message-ID: <60654551-AE43-4C06-9AE7-16B9F968324E at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 3:54 PM, Tan, Richard wrote:
> Thanks, add as.Date('1970-01-01') to the result column works.
But that should make them all the same date in 1970. Since aggregate
renames the date column to "x", this should work:
as.Date( aggregate(a$payday, list(a$name), max)$x )
[1] "2000-01-01" "1999-01-01"
>
> Richard
>
> -----Original Message-----
> From: David Winsemius [mailto:dwinsemius at comcast.net]
> Sent: Monday, November 22, 2010 3:51 PM
> To: Tan, Richard
> Cc: r-help at r-project.org
> Subject: Re: [R] aggregate a Date column does not work?
>
>
> On Nov 22, 2010, at 3:39 PM, Tan, Richard wrote:
>
>> Hi, I am trying to aggregate max a Date type column but have weird
>> result, how do I fix this?
>
> In the process of getting max() you coerced the Dates to numeric and
> now you need to re-coerce them back to Dates
>
> ?as.Date
> as.Date(<your result>) (possibly with an origin it the default
> "1970-01-01" doesn't get used.
>
> --
> David.
>>
>>
>>
>>> a <- rbind(
>>
>> + data.frame(name='Tom', payday=as.Date('1999-01-01')),
>>
>> + data.frame(name='Tom', payday=as.Date('2000-01-01')),
>>
>> + data.frame(name='Pete',
payday=as.Date('1998-01-01')),
>>
>> + data.frame(name='Pete', payday=as.Date('1999-01-01'))
>>
>> + )
>>
>>> a
>>
>> name payday
>>
>> 1 Tom 1999-01-01
>>
>> 2 Tom 2000-01-01
>>
>> 3 Pete 1998-01-01
>>
>> 4 Pete 1999-01-01
>>
>>> aggregate(a$payday, list(a$name), max)
>>
>> Group.1 x
>>
>> 1 Tom 10957
>>
>> 2 Pete 10592
>>
>>
>>
>> Thanks,
>>
>> Richard
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> West Hartford, CT
>
>
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 89
Date: Mon, 22 Nov 2010 16:08:35 -0500
From: "Tan, Richard" <RTan at panagora.com>
To: "David Winsemius" <dwinsemius at comcast.net>
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
Message-ID:
<3303FA84CE4F7244B27BE264EC4AE2A71510A39F at panemail.panagora.com>
Content-Type: text/plain; charset="us-ascii"
Yes, I meant something like one of these:
b <- aggregate(a$payday, list(a$name), max)
b$x <- as.Date('1970-01-01') + b$x
or
b$x <- as.Date(b$x, origin='1970-01-01')
Thanks.
-----Original Message-----
From: David Winsemius [mailto:dwinsemius at comcast.net]
Sent: Monday, November 22, 2010 3:58 PM
To: Tan, Richard
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
On Nov 22, 2010, at 3:54 PM, Tan, Richard wrote:
> Thanks, add as.Date('1970-01-01') to the result column works.
But that should make them all the same date in 1970. Since aggregate
renames the date column to "x", this should work:
as.Date( aggregate(a$payday, list(a$name), max)$x )
[1] "2000-01-01" "1999-01-01"
>
> Richard
>
> -----Original Message-----
> From: David Winsemius [mailto:dwinsemius at comcast.net]
> Sent: Monday, November 22, 2010 3:51 PM
> To: Tan, Richard
> Cc: r-help at r-project.org
> Subject: Re: [R] aggregate a Date column does not work?
>
>
> On Nov 22, 2010, at 3:39 PM, Tan, Richard wrote:
>
>> Hi, I am trying to aggregate max a Date type column but have weird
>> result, how do I fix this?
>
> In the process of getting max() you coerced the Dates to numeric and
> now you need to re-coerce them back to Dates
>
> ?as.Date
> as.Date(<your result>) (possibly with an origin it the default
> "1970-01-01" doesn't get used.
>
> --
> David.
>>
>>
>>
>>> a <- rbind(
>>
>> + data.frame(name='Tom', payday=as.Date('1999-01-01')),
>>
>> + data.frame(name='Tom', payday=as.Date('2000-01-01')),
>>
>> + data.frame(name='Pete',
payday=as.Date('1998-01-01')),
>>
>> + data.frame(name='Pete', payday=as.Date('1999-01-01'))
>>
>> + )
>>
>>> a
>>
>> name payday
>>
>> 1 Tom 1999-01-01
>>
>> 2 Tom 2000-01-01
>>
>> 3 Pete 1998-01-01
>>
>> 4 Pete 1999-01-01
>>
>>> aggregate(a$payday, list(a$name), max)
>>
>> Group.1 x
>>
>> 1 Tom 10957
>>
>> 2 Pete 10592
>>
>>
>>
>> Thanks,
>>
>> Richard
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> West Hartford, CT
>
>
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 90
Date: Mon, 22 Nov 2010 16:13:11 -0500
From: Gabor Grothendieck <ggrothendieck at gmail.com>
To: "Tan, Richard" <RTan at panagora.com>
Cc: r-help at r-project.org
Subject: Re: [R] aggregate a Date column does not work?
Message-ID:
<AANLkTik0iSDu3id5WH3BDzEYPv928D7-YWYCW2yzf=rH at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Mon, Nov 22, 2010 at 3:39 PM, Tan, Richard <RTan at panagora.com>
wrote:> Hi, I am trying to aggregate max a Date type column but have weird
> result, how do I fix this?
>
>> a <- rbind(
>
> + data.frame(name='Tom', payday=as.Date('1999-01-01')),
> + data.frame(name='Tom', payday=as.Date('2000-01-01')),
> + data.frame(name='Pete', payday=as.Date('1998-01-01')),
> + data.frame(name='Pete', payday=as.Date('1999-01-01'))
> + )
>
Since its already sorted try this:
a[!duplicated(a$name, fromLast = TRUE), ]
Using sqldf also works:
library(sqldf)
sqldf("select name, max(payday) payday from a group by name order by
name")
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
------------------------------
Message: 91
Date: Mon, 22 Nov 2010 13:13:41 -0800 (PST)
From: madr <madrazel at interia.pl>
To: r-help at r-project.org
Subject: Re: [R] "negative alpha" or custom gradient colors of data
dots in...
Message-ID: <1290460421895-3054465.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Well I "hacked" it i maybe not so elegant way:
x <- rnorm(100000)
y <- rnorm(100000)
png('out.png',width=600,height=500,units="px")
op <-
par(bg='black',fg='gray',col='gray',col.axis='gray',col.lab='gray',col.main'gray',col.sub='gray',mai=c(0,0,0,0),
tck = 0.01, mgp = c(0, -1.4, 0), xaxs = "i", yaxs = "i")
plot(x,y,ylim=c(-20,20),xlim=c(min(x),max(x)),pch='.',col
rgb(1,1,1,1),yaxt="n", ann=FALSE)
# here is the solution - plot the same data with low alpha and different
color blue is best because is perceived as darkest
points(x,y,col = rgb(0,0,1,0.1),pch='.')
abline(h=0, lty=3, col="green")
abline(v=0, lty=3, col="green")
par <- op
http://i51.tinypic.com/maxmcl.png
[[repost, because subject was deleted and this message won't get into the
list]]
--
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ta-dots-in-scatterplot-tp3052394p3054465.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 92
Date: Mon, 22 Nov 2010 13:20:16 -0800 (PST)
From: Frank Harrell <f.harrell at vanderbilt.edu>
To: r-help at r-project.org
Subject: Re: [R] how do remove those predictor which have p value
greater than 0.05 in GLM?
Message-ID: <1290460816357-3054478.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
What would make you want to delete a variable because P > 0.05? That will
invalidate every aspect of statistical inference for the model.
Frank
-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context:
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ue-greater-than-0-05-in-GLM-tp3053921p3054478.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 93
Date: Mon, 22 Nov 2010 15:29:11 -0600
From: lucia <lucia at thedietdiary.com>
To: r-help at r-project.org
Subject: [R] Help: Standard errors arima
Message-ID: <1E4A2E3E-19B8-4531-AEFB-A57CA477CB75 at thedietdiary.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hello,
I'm an R newbie. I've tried to search, but my search skills don't
seem
up to finding what I need. (Maybe I don't know the correct terms?)
I need the standard errors and not the confidence intervals from an
ARIMA fit.
I can get fits:
> coef(test)
ar1 ma1
intercept time(TempVector) - 1900
0.801459585 0.704126549
12.854527065 0.000520366
And confidence intervals:
> confint(test)
2.5 % 97.5 %
ar1 7.684230e-01 0.834496136
ma1 6.742786e-01 0.733974460
intercept 1.217042e+01 13.538635652
time(TempVector) - 1900 -9.610183e-06 0.001050342
>
http://stat.ethz.ch/R-manual/R-devel/library/stats/html/arima.html
Are any of these standard errors?
> vcov(test)
ar1 ma1 intercept
time(TempVector) - 1900
ar1 2.841144e-04 -5.343792e-05
1.028710e-05 2.725763e-08
ma1 -5.343792e-05 2.319165e-04
9.990842e-07 -3.103661e-09
intercept 1.028710e-05 9.990842e-07
1.218299e-01 8.969206e-05
time(TempVector) - 1900 2.725763e-08 -3.103661e-09
8.969206e-05 7.311670e-08
Or is there a function that can give me standard errors for the
coefficients on AR1, ma, and time? (I don't care about the intercept.)
Thanks,
Lucia
------------------------------
Message: 94
Date: Mon, 22 Nov 2010 16:37:39 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: lucia <lucia at thedietdiary.com>
Cc: r-help at r-project.org
Subject: Re: [R] Help: Standard errors arima
Message-ID: <F1D85621-8D27-46B9-B72F-22E82007414B at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 4:29 PM, lucia wrote:
> Hello,
> I'm an R newbie. I've tried to search, but my search skills
don't
> seem up to finding what I need. (Maybe I don't know the correct
> terms?)
>
> I need the standard errors and not the confidence intervals from an
> ARIMA fit.
>
> I can get fits:
>
> > coef(test)
> ar1 ma1
> intercept time(TempVector) - 1900
> 0.801459585 0.704126549
> 12.854527065 0.000520366
>
> And confidence intervals:
>
> > confint(test)
> 2.5 % 97.5 %
> ar1 7.684230e-01 0.834496136
> ma1 6.742786e-01 0.733974460
> intercept 1.217042e+01 13.538635652
> time(TempVector) - 1900 -9.610183e-06 0.001050342
> >
>
> http://stat.ethz.ch/R-manual/R-devel/library/stats/html/arima.html
That page says that there is a vcov function that can extract the
variance-covariance matrix, so that should let you make s.e.'s pretty
easily.
--
David.
> Are any of these standard errors?
>
> > vcov(test)
> ar1 ma1 intercept
> time(TempVector) - 1900
> ar1 2.841144e-04 -5.343792e-05
> 1.028710e-05 2.725763e-08
> ma1 -5.343792e-05 2.319165e-04
> 9.990842e-07 -3.103661e-09
> intercept 1.028710e-05 9.990842e-07
> 1.218299e-01 8.969206e-05
> time(TempVector) - 1900 2.725763e-08 -3.103661e-09
> 8.969206e-05 7.311670e-08
>
> Or is there a function that can give me standard errors for the
> coefficients on AR1, ma, and time? (I don't care about the
> intercept.)
> Thanks,
> Lucia
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 95
Date: Mon, 22 Nov 2010 22:41:28 +0100
From: Uwe Ligges <ligges at statistik.tu-dortmund.de>
To: bmiddle <bmiddle at sandia.gov>
Cc: r-help at r-project.org
Subject: Re: [R] R2WinBUGS help
Message-ID: <4CEAE388.3070801 at statistik.tu-dortmund.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 22.11.2010 21:41, bmiddle wrote:>
> When I use the 'bugs' function from R, WinBUGS runs correctly, but
R
freezes.> The only way to use R after this is to stop calculations (without my file
> that documents the calculation).
R "freezes" as long as the WinBUGS process is opened. AFter closing
it,
R should "respond" again.
If you like a more inetractive way of dealing with some BUGS
incarnation, try the BRugs package that makes use of OpenBUGS by typing
install.packages("BRugs")
library("BRugs")
?BRugs
?BRugsFit
Uwe Ligges
However, I want to save the output in R so> I can use it in further models. Does anyone know how to fix this problem?
------------------------------
Message: 96
Date: Mon, 22 Nov 2010 16:41:44 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: Xiaoqi Cui <xcui at mtu.edu>
Cc: r-help <r-help at r-project.org>
Subject: Re: [R] R package "kernlab" can not be properly loaded
Message-ID: <A0F114AF-60B6-4672-8C2A-85A7848F42C7 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 3:55 PM, Xiaoqi Cui wrote:
> Hi,
>
> I tried to load the package "kernlab" under R-v11 and R-v10,
however
> it gave error message:
>
> Error in library.dynam(lib, package, package.lib) :
> shared library 'kernlab' not found
> In addition: Warning message:
> package 'kernlab' was built under R version 2.12.0
> Error: package/namespace load failed for 'kernlab'
The current version of R and all of the packages in CRAN _is_ 2.12.0.
load()-ing packages that differ in their major versions is not
advisable and not guaranteed to succeed. The Contributed Packages page
of CRAN has at the very bottom a link to the package Archive.
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 97
Date: Mon, 22 Nov 2010 22:45:21 +0100
From: Uwe Ligges <ligges at statistik.tu-dortmund.de>
To: Xiaoqi Cui <xcui at mtu.edu>
Cc: r-help <r-help at r-project.org>
Subject: Re: [R] R package "kernlab" can not be properly loaded
Message-ID: <4CEAE471.50802 at statistik.tu-dortmund.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 22.11.2010 21:55, Xiaoqi Cui wrote:> Hi,
>
> I tried to load the package "kernlab" under R-v11 and R-v10,
however it
gave error message:>
> Error in library.dynam(lib, package, package.lib) :
> shared library 'kernlab' not found
> In addition: Warning message:
> package 'kernlab' was built under R version 2.12.0
> Error: package/namespace load failed for 'kernlab'
>
> Has anybody loaded this successfully before? Thanks,
Yes, if it was built for R-2.11.x we were using R-2.11.x.
I guess you are under Windows (unstated) where some infrastructure was
changed form R-2.11.x to R-2.12.x and packages compiled for the latter
won't work foer the former.
hcen please run
install.packages("kernlab") in order to get a version that fits to
your
R or even better upgrade your version of R.
Uwe Ligges
> Xiaoqi
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 98
Date: Mon, 22 Nov 2010 21:51:40 +0000
From: Ista Zahn <izahn at psych.rochester.edu>
To: madr <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] I need a very specific unique like function and I
don't know even how to properly call this
Message-ID:
<AANLkTin6Yn1FPKiDZO3-WMKFO48_aqA_QFjHKh_4WC7U at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Here is a method for piecing it together using diff and indexing:
dat <- structure(c(3L, 6L, 7L, 3L, 7L, 5L, 8L, 2L, 7L, 0L, 7L, 5L, 5L,
5L, 5L, 5L, 4L, 4L, 4L, 6L), .Dim = c(10L, 2L), .Dimnames = list(
NULL, c("V1", "V2")))
diffs <- abs(diff(dat[,2], 1)) # get the difference between each
value and the previous value
new.dat <- cbind(dat, c(NA, diffs), c(diffs, NA)) # combine the diffs
with the original matrix, shifted down (is the next valued the same as
the value) and down (is the previous value the same)
new.dat <- cbind(new.dat, rowSums(new.dat[,3:4], na.rm=TRUE)) # sum
the shifted diffs so that the value is 0 if above and below are the
same, and greater than zero if the above and below values are not the
same
final.dat <- new.dat[new.dat[,5] !=0 ,1:2] # get rid of rows for
which the sum of the shifted diffs is not equal to zero.
HTH,
Ista
On Mon, Nov 22, 2010 at 8:53 PM, madr <madrazel at interia.pl>
wrote:>
> consider this matrix:
>
> ? ? ?[,1] [,2]
> ?[1,] ? ?3 ? 7
> ?[2,] ? ?6 ? 5
> ?[3,] ? ?7 ? 5
> ?[4,] ? ?3 ? 5
> ?[5,] ? ?7 ? 5
> ?[6,] ? ?5 ? 5
> ?[7,] ? ?8 ? 4
> ?[8,] ? ?2 ? 4
> ?[9,] ? ?7 ? 4
> [10,] ? ?0 ? 6
>
> I need to delete all rows where column 2 above and below has the same
value,> so the effect would be:
>
> ? ? ?[,1] [,2]
> ?[1,] ? ?3 ? 7
> ?[2,] ? ?6 ? 5
> ?[6,] ? ?5 ? 5
> ?[7,] ? ?8 ? 4
> ?[9,] ? ?7 ? 4
> [10,] ? ?0 ? 6
>
> is there a built in function for that kind of operation or I must write
one> from scratch ?
> Is there a name for that kind of operation ?
> --
> View this message in context:
http://r.789695.n4.nabble.com/I-need-a-very-specific-unique-like-function-an
d-I-don-t-know-even-how-to-properly-call-this-tp3054427p3054427.html> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
------------------------------
Message: 99
Date: Mon, 22 Nov 2010 14:03:43 -0800 (PST)
From: bmiddle <bmiddle at sandia.gov>
To: r-help at r-project.org
Subject: Re: [R] R2WinBUGS help
Message-ID: <1290463423081-3054531.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
When I use the 'bugs' function from R, WinBUGS runs correctly, but R
freezes. > The only way to use R after this is to stop calculations (without my file
> that documents the calculation).
R "freezes" as long as the WinBUGS process is opened. AFter closing
it,
R should "respond" again.
If you like a more inetractive way of dealing with some BUGS
incarnation, try the BRugs package that makes use of OpenBUGS by typing
install.packages("BRugs")
library("BRugs")
?BRugs
?BRugsFit
Thanks, Uwe. I think it was a problem with Windows. WinBUGS should close
automatically and it wasn't. Anyway, it seems that the problem is now fixed.
I may try the BRugs package soon (after I submit this project report!).
--
View this message in context:
http://r.789695.n4.nabble.com/R2WinBUGS-help-tp3054411p3054531.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 100
Date: Mon, 22 Nov 2010 14:10:04 -0800 (PST)
From: shubha <shuba.pandit at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] how do remove those predictor which have p value
greater than 0.05 in GLM?
Message-ID: <1290463804045-3054540.post at n4.nabble.com>
Content-Type: text/plain
Thanks for the response, Frank.
I am not saying that I want to delete a variables because of p>0.5. But my
concern was: I am using backward stepwise logistic regression, it keeps the
variables in the final model if the variable significantly contributing in
the model. Otherwise, it should not be in the final model.
Using other software, they give correct results. But R, did not. I want
those variables if p<0.05, otherwise exclude from the model. If you include
that variables, it will affect the Log likelihood ratio and AIC. I want to
change a P-value criterion <=0.05 in the model. Any suggestions.
thanks
--
View this message in context:
http://r.789695.n4.nabble.com/how-do-remove-those-predictor-which-have-p-val
ue-greater-than-0-05-in-GLM-tp3053921p3054540.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]
------------------------------
Message: 101
Date: Mon, 22 Nov 2010 14:11:13 -0800
From: Dennis Murphy <djmuser at gmail.com>
To: lucia <lucia at thedietdiary.com>
Cc: r-help at r-project.org
Subject: Re: [R] Help: Standard errors arima
Message-ID:
<AANLkTimNjEECU5Ee_+89vsy8D3JzHc9rZbBPhA7458JL at mail.gmail.com>
Content-Type: text/plain
Hi:
Here's an example (never mind the model fit...or lack of it thereof...)
str(AirPassengers) # a built-in R data set
# Series is seasonal with increasing trend and increasing variance
plot(AirPassengers, type = 'l')
# STL decomposition
plot(stl(AirPassengers, 'periodic'))
# ACF and PACF of differenced series
par(mfrow = c(2, 1))
acf(diff(AirPassengers))
pacf(diff(AirPassengers))
par(mfrow = c(1, 1))
# Fit a basic seasonal model: SARIMA(0, 1, 1) x (0, 0, 1):
m1 <- arima(AirPassengers, order = c(0, 1, 1),
seasonal = list(order = c(0, 0, 1), period = 12))
# Most models in R return lists; arima() is no different:
names(m1)
[1] "coef" "sigma2" "var.coef"
"mask" "loglik" "aic"
[7] "arma" "residuals" "call"
"series" "code" "n.cond"
[13] "model"
# var.coef looks promising, so let's extract it:
m1$var.coef
# As David mentioned, vcov() also works (not just for time series, either):
vcov(m1)
Both should return the same covariance matrix of the estimated coefficients.
The standard errors are the square roots of the diagonal elements:
sqrt(diag(m1$var.coef))
sqrt(diag(vcov(m1)))
Compare this to the output from arima():> m1
Call:
arima(x = AirPassengers, order = c(0, 1, 1), seasonal = list(order = c(0, 0,
1), period = 12))
Coefficients:
ma1 sma1
0.2263 0.8015
s.e. 0.0805 0.0674
HTH,
Dennis
On Mon, Nov 22, 2010 at 1:29 PM, lucia <lucia at thedietdiary.com> wrote:
> Hello,
> I'm an R newbie. I've tried to search, but my search skills
don't seem up
> to finding what I need. (Maybe I don't know the correct terms?)
>
> I need the standard errors and not the confidence intervals from an ARIMA
> fit.
>
> I can get fits:
>
> > coef(test)
> ar1 ma1 intercept
> time(TempVector) - 1900
> 0.801459585 0.704126549 12.854527065
> 0.000520366
>
> And confidence intervals:
>
> > confint(test)
> 2.5 % 97.5 %
> ar1 7.684230e-01 0.834496136
> ma1 6.742786e-01 0.733974460
> intercept 1.217042e+01 13.538635652
> time(TempVector) - 1900 -9.610183e-06 0.001050342
> >
>
> http://stat.ethz.ch/R-manual/R-devel/library/stats/html/arima.html
> Are any of these standard errors?
>
> > vcov(test)
> ar1 ma1 intercept
> time(TempVector) - 1900
> ar1 2.841144e-04 -5.343792e-05 1.028710e-05
> 2.725763e-08
> ma1 -5.343792e-05 2.319165e-04 9.990842e-07
> -3.103661e-09
> intercept 1.028710e-05 9.990842e-07 1.218299e-01
> 8.969206e-05
> time(TempVector) - 1900 2.725763e-08 -3.103661e-09 8.969206e-05
> 7.311670e-08
>
> Or is there a function that can give me standard errors for the
> coefficients on AR1, ma, and time? (I don't care about the intercept.)
> Thanks,
> Lucia
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
------------------------------
Message: 102
Date: Mon, 22 Nov 2010 14:24:50 -0500
From: "Kenney, Colleen T CTR USA AMC" <colleen.t.kenney at
us.army.mil>
To: <r-help at r-project.org>
Subject: [R] Probit Analysis: Confidence Interval for the LD50 using
Fieller's and Heterogeneity (UNCLASSIFIED)
Message-ID:
<0DE122C88FD3464296144E13610ADF700CC59A5C at
APGR010BEC80008.nae.ds.army.mil>
Content-Type: text/plain; charset="us-ascii"
Classification: UNCLASSIFIED
Caveats: NONE
A similar question has been posted in the past but never answered. My
question is this: for probit analysis, how do you program a 95%
confidence interval for the LD50 (or LC50, ec50, etc.), including a
heterogeneity factor as written about in "Probit Analysis" by
Finney(1971)? The heterogeneity factor comes into play through the
chi-squared test for homogeneity and is equal to h=chi^2/(k-2), where k
is the number of doses and k-2 are the degrees of freedom.
I have done a lot of research on this and really appreciate any help
[[elided Yahoo spam]]
Classification: UNCLASSIFIED
Caveats: NONE
------------------------------
Message: 103
Date: Mon, 22 Nov 2010 12:35:55 -0700
From: Yogesh Tiwari <yogesh.mpi at googlemail.com>
To: r-help <r-help at stat.math.ethz.ch>
Subject: [R] how to calculate derivative
Message-ID:
<AANLkTind3+hs91==Te155AvYTBB4o4XULE=mEfWTAFwx at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear R Users,
I have trend of two time series of CO2 each 10 years of data. One is
varying
weekly and another is bi-weekly. I want to calculate Growth rate ppmv / year
of these CO2 trends. Therefore I want to calculate time derivative ppmv /
year.
How to do it in R?
Here I attached example data file, I would appreciate if any one kindly can
help on it.
Thanks,
Regards,
Yogesh
-------------- next part --------------
1993.1218 356.8655
1993.1246 356.8723
1993.1273 356.8792
1993.13 356.886
1993.1328 356.8929
1993.1355 356.8998
1993.1383 356.9067
1993.141 356.9136
1993.1437 356.9206
1993.1465 356.9275
1993.1492 356.9345
1993.152 356.9415
1993.1547 356.9485
1993.1574 356.9555
1993.1602 356.9625
1993.1629 356.9695
1993.1656 356.9766
1993.1684 356.9836
1993.1711 356.9907
1993.1739 356.9978
1993.1766 357.0049
1993.1793 357.012
1993.1821 357.0191
1993.1848 357.0263
1993.1875 357.0334
1993.1903 357.0406
1993.193 357.0478
1993.1958 357.0549
1993.1985 357.0621
1993.2012 357.0694
1993.204 357.0766
1993.2067 357.0838
1993.2094 357.0911
1993.2122 357.0983
1993.2149 357.1056
1993.2177 357.1129
1993.2204 357.1202
1993.2231 357.1275
1993.2259 357.1349
1993.2286 357.1422
1993.2313 357.1495
1993.2341 357.1569
1993.2368 357.1643
1993.2396 357.1717
1993.2423 357.1791
1993.245 357.1865
1993.2478 357.1939
1993.2505 357.2013
1993.2533 357.2087
1993.256 357.2162
1993.2587 357.2237
1993.2615 357.2311
1993.2642 357.2386
1993.2669 357.2461
1993.2697 357.2536
1993.2724 357.2611
1993.2752 357.2686
1993.2779 357.2762
1993.2806 357.2837
1993.2834 357.2913
1993.2861 357.2988
1993.2888 357.3064
1993.2916 357.314
1993.2943 357.3216
1993.2971 357.3292
1993.2998 357.3368
1993.3025 357.3444
1993.3053 357.352
1993.308 357.3597
1993.3107 357.3673
1993.3135 357.3747
1993.3162 357.3824
1993.319 357.39
1993.3217 357.3977
1993.3244 357.4054
1993.3272 357.4131
1993.3299 357.4208
1993.3326 357.4285
1993.3354 357.4362
1993.3381 357.4439
1993.3409 357.4516
1993.3436 357.4593
1993.3463 357.4671
1993.3491 357.4748
1993.3518 357.4826
1993.3546 357.4903
1993.3573 357.4981
1993.36 357.5059
1993.3628 357.5136
1993.3655 357.5214
1993.3682 357.5292
1993.371 357.537
1993.3737 357.5448
1993.3765 357.5526
1993.3792 357.5604
1993.3819 357.5683
1993.3847 357.5761
1993.3874 357.5839
1993.3901 357.5918
1993.3929 357.5996
1993.3956 357.6075
1993.3984 357.6153
1993.4011 357.6232
1993.4038 357.631
1993.4066 357.6389
1993.4093 357.6468
1993.412 357.6546
1993.4148 357.6625
1993.4175 357.6702
1993.4203 357.6781
1993.423 357.686
1993.4257 357.6938
1993.4285 357.7017
1993.4312 357.7096
1993.4339 357.7175
1993.4367 357.7254
1993.4394 357.7333
1993.4422 357.7412
1993.4449 357.7491
1993.4476 357.757
1993.4504 357.7649
1993.4531 357.7728
1993.4559 357.7807
1993.4586 357.7886
1993.4613 357.7966
1993.4641 357.8045
1993.4668 357.8124
1993.4695 357.8203
1993.4723 357.8282
1993.475 357.8361
1993.4778 357.8441
1993.4805 357.852
1993.4832 357.8599
1993.486 357.8678
1993.4887 357.8758
1993.4914 357.8837
1993.4942 357.8916
1993.4969 357.8995
1993.4997 357.9074
1993.5024 357.9154
1993.5051 357.9232
1993.5079 357.9311
1993.5106 357.939
1993.5133 357.947
1993.5161 357.9549
1993.5188 357.9628
1993.5216 357.9707
1993.5243 357.9786
1993.527 357.9865
1993.5298 357.9944
1993.5325 358.0023
1993.5352 358.0102
1993.538 358.0181
1993.5407 358.026
1993.5435 358.0339
1993.5462 358.0418
1993.5489 358.0496
1993.5517 358.0575
1993.5544 358.0654
1993.5572 358.0733
1993.5599 358.0811
1993.5626 358.089
1993.5654 358.0969
1993.5681 358.1047
1993.5708 358.1126
1993.5736 358.1204
1993.5763 358.1283
1993.5791 358.1361
1993.5818 358.144
1993.5845 358.1518
1993.5873 358.1596
1993.59 358.1675
1993.5927 358.1753
1993.5955 358.1831
1993.5982 358.1909
1993.601 358.1987
1993.6037 358.2065
1993.6064 358.2142
1993.6092 358.222
1993.6119 358.2298
1993.6146 358.2376
1993.6174 358.2453
1993.6201 358.2531
1993.6229 358.2608
1993.6256 358.2685
1993.6283 358.2763
1993.6311 358.284
1993.6338 358.2917
1993.6366 358.2994
1993.6393 358.3071
1993.642 358.3148
1993.6448 358.3224
1993.6475 358.3301
1993.6502 358.3377
1993.653 358.3454
1993.6557 358.353
1993.6585 358.3607
1993.6612 358.3683
1993.6639 358.3759
1993.6667 358.3835
1993.6694 358.3911
1993.6721 358.3987
1993.6749 358.4062
1993.6776 358.4141
1993.6804 358.4216
1993.6831 358.4292
1993.6858 358.4367
1993.6886 358.4443
1993.6913 358.4518
1993.694 358.4593
1993.6968 358.4668
1993.6995 358.4743
1993.7023 358.4817
1993.705 358.4892
1993.7077 358.4967
1993.7105 358.5041
1993.7132 358.5115
1993.7159 358.5189
1993.7187 358.5263
1993.7214 358.5337
1993.7242 358.5411
1993.7269 358.5484
1993.7296 358.5558
1993.7324 358.5631
1993.7351 358.5704
1993.7379 358.5778
1993.7406 358.585
1993.7433 358.5923
1993.7461 358.5996
1993.7488 358.6068
1993.7515 358.6141
1993.7543 358.6216
1993.757 358.6289
1993.7598 358.6361
1993.7625 358.6433
1993.7652 358.6505
1993.768 358.6576
1993.7707 358.6648
1993.7734 358.6719
1993.7762 358.6791
1993.7789 358.6862
1993.7817 358.6933
1993.7844 358.7003
1993.7871 358.7074
1993.7899 358.7144
1993.7926 358.7215
1993.7953 358.7285
1993.7981 358.7355
1993.8008 358.7424
1993.8036 358.7494
1993.8063 358.7563
1993.809 358.7633
1993.8118 358.7702
1993.8145 358.7771
1993.8172 358.7839
1993.82 358.7908
1993.8227 358.7976
1993.8255 358.8044
1993.8282 358.8117
1993.8309 358.8185
1993.8337 358.8253
1993.8364 358.8321
1993.8392 358.8388
1993.8419 358.8456
1993.8446 358.8523
1993.8474 358.859
1993.8501 358.8657
1993.8528 358.8723
1993.8556 358.879
1993.8583 358.8856
1993.8611 358.8922
1993.8638 358.8988
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1993.872 358.9184
1993.8747 358.9249
1993.8775 358.9314
1993.8802 358.9379
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1993.8884 358.9571
1993.8912 358.9635
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1994.0992 359.3852
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1994.1102 359.4034
1994.1129 359.4079
1994.1157 359.4124
1994.1184 359.4169
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1994.1239 359.4257
1994.1266 359.4301
1994.1294 359.4344
1994.1321 359.4387
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1994.1376 359.4473
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1994.1485 359.4641
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1994.1923 359.5269
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1995.282 360.6112
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1995.2984 360.6522
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1995.3422 360.7681
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1995.3504 360.7908
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1995.3943 360.9177
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1998.4387 367.4185
1998.4415 367.4325
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1998.4716 367.5869
1998.4743 367.6009
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1998.6441 368.4569
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1998.6687 368.5768
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1998.6988 368.7203
1998.7016 368.7332
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1998.707 368.7591
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1998.7125 368.7844
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2000.117 370.4382
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2000.1225 370.4333
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2000.128 370.4284
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2000.1389 370.4188
2000.1417 370.4165
2000.1444 370.4141
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2000.1526 370.4071
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2000.1581 370.4021
2000.1608 370.3998
2000.1636 370.3975
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2000.1691 370.393
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2000.1828 370.3818
2000.1855 370.3796
2000.1882 370.3775
2000.191 370.3753
2000.1937 370.3729
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2000.2567 370.327
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2000.2621 370.3235
2000.2649 370.3217
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2000.2731 370.3164
2000.2758 370.3147
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2000.2813 370.3113
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2000.3415 370.2795
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2000.3717 370.267
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2000.3936 370.2597
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2000.4045 370.2565
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2000.4155 370.2537
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2000.6208 370.2703
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2000.6263 370.2726
2000.629 370.2738
2000.6318 370.275
2000.6345 370.2762
2000.6372 370.2774
2000.64 370.2787
2000.6427 370.28
2000.6454 370.2813
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2000.6537 370.2853
2000.6564 370.2867
2000.6591 370.2882
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2000.6701 370.2941
2000.6728 370.2962
2000.6756 370.2978
2000.6783 370.2994
2000.681 370.301
2000.6838 370.3027
2000.6865 370.3044
2000.6893 370.3061
2000.692 370.3078
2000.6947 370.3096
2000.6975 370.3113
2000.7002 370.3131
2000.7029 370.3149
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------------------------------
Message: 104
Date: Tue, 23 Nov 2010 11:14:05 +1300
From: David Scott <d.scott at auckland.ac.nz>
To: Henri Mone <henriMone at gmail.com>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] cpgram: access data, confidence bands
Message-ID: <4CEAEB2D.3000306 at auckland.ac.nz>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 22/11/10 22:54, Henri Mone wrote:> Dear R experts, beginners and everyone else,
>
> I'm calculating "cumulative periodogram" using the command
"cpgram"
> [1] from the MASS library. Here is a short example with the "lh"
> (hormone level) dataset:
>
> library(MASS)
> plot(lh,type="l",ylab="value",xlab="time",
main="Hormone Levels (lh)")
> spectrum(lh, main="Hormone Levels (lh)") # periodigram
> cpgram(lh, main="Hormone Levels (lh)") # cumul. periodigram
>
> I got following two questions:
>
> 1. The command "cpgram" plots the cumulative periodogram without
any
> problem. But I could not figure out any way to access the data of the
> plot (save it in a variable).
> the following command fails (contains no data):
> >myObject<-cpgram(lh, main="Hormone Levels (lh)")
> >summary(myObject)
> Length Class Mode
> 0 NULL NULL
>
> Is there an easy way to access the data of the cumulative
> periodogram, or do I need to rewrite the "cpgram" function?
>
You need to rewrite cpgram. Have a look at the last line of the
function, it is
invisible()
meaning it doesn't return anything. It is easy to change it, replace the
last line by for example
return(list(pgram = y, cum = cumsum(y)/sum(y)))
or whatever you actually want to return.
> 2. The "cpgram" function plots with the default options the 95%
> confidence bands in the plot. The confidence band are defined such
> that in 95% of the cases the true value will lie inside the bands. For
> most cases which I tested the cumulative periodogram is outside the
> confidence band. Does "cpgram" plot the confidence band of the
the
> cumulative periodogram or for the periodogram (I think it is the
> cumulative periodigram, is this correct?). How should the confidence
> band in "cpgram" be interpreted? Some more description on this
would
> be great.
>
>
It is the cumulative periodogram (as the name suggests). What did you
test? Only a white noise process should stay inside the confidence
bands. There is some information about the use of the cumulative
periodogram in Venables and Ripley's book for which cpgram was written
(but admittedly not a lot).
David Scott
_________________________________________________________________
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
------------------------------
Message: 105
Date: Mon, 22 Nov 2010 17:21:09 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: "Kenney, Colleen T CTR USA AMC" <colleen.t.kenney at
us.army.mil>
Cc: r-help at r-project.org
Subject: Re: [R] Probit Analysis: Confidence Interval for the LD50
using Fieller's and Heterogeneity (UNCLASSIFIED)
Message-ID: <99B2DFBB-F6B5-4555-BBF7-4D5261612C4E at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 2:24 PM, Kenney, Colleen T CTR USA AMC wrote:
> Classification: UNCLASSIFIED
> Caveats: NONE
>
> A similar question has been posted in the past but never answered. My
> question is this: for probit analysis, how do you program a 95%
> confidence interval for the LD50 (or LC50, ec50, etc.), including a
> heterogeneity factor as written about in "Probit Analysis" by
> Finney(1971)? The heterogeneity factor comes into play through the
> chi-squared test for homogeneity and is equal to h=chi^2/(k-2),
> where k
> is the number of doses and k-2 are the degrees of freedom.
>
> I have done a lot of research on this and really appreciate any help
[[elided Yahoo spam]]
The reason it may not have had a rely ... assuming the questions was
homomorphic to this one... is that there is no R content in this
question. You may want to post on:
http://stats.stackexchange.com/
But I suggest you be somewhat more descriptive than just citing a 40
year-old text.
--
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 106
Date: Mon, 22 Nov 2010 14:28:56 -0800
From: Dennis Murphy <djmuser at gmail.com>
To: "Kenney, Colleen T CTR USA AMC" <colleen.t.kenney at
us.army.mil>
Cc: r-help at r-project.org
Subject: Re: [R] Probit Analysis: Confidence Interval for the LD50
using Fieller's and Heterogeneity (UNCLASSIFIED)
Message-ID:
<AANLkTinRodwVPCrXm8SnfAfcn3QQ6-qJg4GnaNZMG0B3 at mail.gmail.com>
Content-Type: text/plain
Hi:
The MASS package has a function dose.p() to produce a CI for ED50, ED90 or
EDp in general (0 < p < 100). It takes a model object (presumably from a
suitable logistic regression) as input. You could always take the code
already available and adapt it to your situation or you could investigate
one or more of the packages devoted to dose-response models.
A useful thing to know in R is the sos package, starting with its primary
function, findFn():
library(sos)
findFn('ED50')
scares up the three major packages related to dose-response models with 40
matches to ED50.
HTH,
Dennis
On Mon, Nov 22, 2010 at 11:24 AM, Kenney, Colleen T CTR USA AMC <
colleen.t.kenney at us.army.mil> wrote:
> Classification: UNCLASSIFIED
> Caveats: NONE
>
> A similar question has been posted in the past but never answered. My
> question is this: for probit analysis, how do you program a 95%
> confidence interval for the LD50 (or LC50, ec50, etc.), including a
> heterogeneity factor as written about in "Probit Analysis" by
> Finney(1971)? The heterogeneity factor comes into play through the
> chi-squared test for homogeneity and is equal to h=chi^2/(k-2), where k
> is the number of doses and k-2 are the degrees of freedom.
>
> I have done a lot of research on this and really appreciate any help
[[elided Yahoo spam]]>
>
> Classification: UNCLASSIFIED
> Caveats: NONE
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
------------------------------
Message: 107
Date: Mon, 22 Nov 2010 14:36:08 -0800 (PST)
To: r-help at r-project.org
Subject: [R] empity value in colnames
Message-ID: <1290465368687-3054564.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi Guys.
I have a matrix which has names in every other column and the other one is
empity ("")
example
X10000 X10001 X10002
[1,] "A" "G" "A" "G" "G"
[2,] "G" "G" "A" "G" "A"
[3,] "G" "G" "A" "A" "A"
[4,] "G" "G" "A" "A" "A"
[5,] "A" "G" "A" "A" "A"
I am creating another matrix (I called here subset) which cbinds information
from another matrix (not shown) and a subset of this example matrix above
(let's say column 1 and 2) and save as .prn file
subset
Sequence family clone female male X10000 V2 X10001 V4
1 40003 400 540003 10005 22055 A G A G
2 40011 400 540011 10005 22055 G G A G
3 40014 400 540014 10005 22055 G G A A
4 40042 400 540042 10005 22055 G G A A
5 40057 400 540057 10005 22055 A G A A
Everytime I do it, it creates a column name ("V2" and "V4"
in bold) where it
should be empty ("").
Do you guys have any clue on how to to this?
Thanks
--
View this message in context:
http://r.789695.n4.nabble.com/empity-value-in-colnames-tp3054564p3054564.htm
l
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 108
Date: Mon, 22 Nov 2010 19:59:04 -0300
From: Kjetil Halvorsen <kjetilbrinchmannhalvorsen at gmail.com>
To: Mike Marchywka <marchywka at hotmail.com>
Cc: r-help at r-project.org, ligges at statistik.tu-dortmund.de
Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
Message-ID:
<AANLkTi=nDYVu_cuYuH3_0HOe1T99B_cy3ZA_VrgG_FnE at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
see below.
On Mon, Nov 22, 2010 at 12:57 PM, Mike Marchywka <marchywka at
hotmail.com>
wrote:>
>
>
>
>
>
>
>
> ----------------------------------------
>> Date: Mon, 22 Nov 2010 12:41:06 -0300
>> Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
>> From: kjetilbrinchmannhalvorsen at gmail.com
>> To: marchywka at hotmail.com
>> CC: ligges at statistik.tu-dortmund.de; r-help at r-project.org
>>
>> see below.
>>
>> On Mon, Nov 22, 2010 at 12:13 PM, Mike Marchywka wrote:
>> >
>> >
>> Thanks. Will try. Really, I tried yesterday, to run R under gdb within
>> emacs, but it did'nt work out. What I did (in emacs 23) was, typing
>> Ctrl-u M-x R
>> and then enter the option
>> --debugger=gdb
>>
[[elided Yahoo spam]]>>
>> Kjetil
>
> I rarely use gdb but it did seem to work with R but I executed gdb from
> cygwin windoh and IIRC ctrl-C worked fine as it broke into debugger.
> I guess you could try that- start gdb and attach or invoke R from gdb.
>
>
OK, thanks. I started R with
R --debugger=gdb
in a shell, outside emacs. then it works.
I did some unsystematic sampling with Ctrl-C. Most of the time it was stuck
in memory.c, apparently doing garbage collection.
Other files which occured was unique.c, duplicate.c
kjetil
>
------------------------------
Message: 109
Date: Mon, 22 Nov 2010 18:13:17 -0500
From: David Winsemius <dwinsemius at comcast.net>
Cc: r-help at r-project.org
Subject: Re: [R] empity value in colnames
Message-ID: <AB076202-FC9B-40FA-891B-9420CCF73EB8 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 5:36 PM, M.Ribeiro wrote:
>
> Hi Guys.
> I have a matrix which has names in every other column and the other
> one is
> empity ("")
>
> example
> X10000 X10001 X10002
> [1,] "A" "G" "A" "G"
"G"
> [2,] "G" "G" "A" "G"
"A"
> [3,] "G" "G" "A" "A"
"A"
> [4,] "G" "G" "A" "A"
"A"
> [5,] "A" "G" "A" "A"
"A"
>
> I am creating another matrix
How?
> (I called here subset) which cbinds information
> from another matrix (not shown) and a subset of this example matrix
> above
Off hand, I would guess that this "other matrix", of undescribed
structure, is really a dataframe and you are actually calling
cbind.data.frame
> (let's say column 1 and 2) and save as .prn file
>
> subset
> Sequence family clone female male X10000 V2 X10001 V4
> 1 40003 400 540003 10005 22055 A G A G
> 2 40011 400 540011 10005 22055 G G A G
> 3 40014 400 540014 10005 22055 G G A A
> 4 40042 400 540042 10005 22055 G G A A
> 5 40057 400 540057 10005 22055 A G A A
>
>
> Everytime I do it, it creates a column name ("V2" and
"V4" in bold)
> where it
> should be empty ("").
That's why I asked "How?"
> Do you guys have any clue on how
Exactly. ............. How? You show us your "how" and we will show
you ours.
> to to this?
>
> Thanks
>
>
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 110
Date: Mon, 22 Nov 2010 18:17:30 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <kjetilbrinchmannhalvorsen at gmail.com>
Cc: r-help at r-project.org, ligges at statistik.tu-dortmund.de
Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
Message-ID: <BLU113-W16E5F5F3BA4752BD2EDCAEBE3D0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> Date: Mon, 22 Nov 2010 19:59:04 -0300
> Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour ...
> From: kjetilbrinchmannhalvorsen at gmail.com
> To: marchywka at hotmail.com
> CC: ligges at statistik.tu-dortmund.de; r-help at r-project.org
>
> see below.
>
> On Mon, Nov 22, 2010 at 12:57 PM, Mike Marchywka wrote:
> >
> >
> >
> >
> >
> >
> >
> >
> > ----------------------------------------
> >> Date: Mon, 22 Nov 2010 12:41:06 -0300
> >> Subject: Re: [R] ?summaryRprof running at 100% cpu for one hour
...
> >> From: kjetilbrinchmannhalvorsen at gmail.com
> >> To: marchywka at hotmail.com
> >> CC: ligges at statistik.tu-dortmund.de; r-help at r-project.org
> >>
> >> see below.
> >>
> >> On Mon, Nov 22, 2010 at 12:13 PM, Mike Marchywka wrote:
> >> >
> >> >
> >> Thanks. Will try. Really, I tried yesterday, to run R under gdb
within
> >> emacs, but it did'nt work out. What I did (in emacs 23) was,
typing
> >> Ctrl-u M-x R
> >> and then enter the option
> >> --debugger=gdb
> >>
[[elided Hotmail spam]]> >>
> >> Kjetil
> >
> > I rarely use gdb but it did seem to work with R but I executed gdb
from
> > cygwin windoh and IIRC ctrl-C worked fine as it broke into debugger.
> > I guess you could try that- start gdb and attach or invoke R from gdb.
> >
> >
>
> OK, thanks. I started R with
> R --debugger=gdb
> in a shell, outside emacs. then it works.
>
> I did some unsystematic sampling with Ctrl-C. Most of the time it was
stuck> in memory.c, apparently doing garbage collection.
> Other files which occured was unique.c, duplicate.c
>
you may want to try the R-develop list for better help now but
presumably you can get symobls somewhere and a readable
stack trace. I guess floundering with memory management
would be consistent with high CPU usage since as far as the OS
is concerned the process is runnable. In java you see stuff like
this with lots of temp objects being created. I guess if it
is gc and you make lots of garbage and then need a big contiguous
area could slow things down a lot.
Once you are pretty sure you stopped it in a hotspot, you can
try stepping in and out of things and see if anything looks odd.
I guess one other exploratory thing to try, this may or may not
work in R with your problem, is get a snapshot of the memory and then use a
utility
like "strings" to see if there is any indication of what is going on.
If objects are annotated at all something may jump out but hard to know.
> kjetil
>
>
> >
------------------------------
Message: 111
Date: Mon, 22 Nov 2010 15:18:40 -0800
From: Kendric Wang <kendricw at interchange.ubc.ca>
To: r-help at r-project.org
Subject: [R] Sporadic errors when training models using CARET
Message-ID:
<AANLkTimKokkPu6L4r1dmaunSvd3PJ-dAjed_CKZ84RWD at mail.gmail.com>
Content-Type: text/plain
Hi. I am trying to construct a svmLinear model using the "caret"
package
(see code below). Using the same data, without changing any setting,
sometimes it constructs the model successfully, and sometimes I get an index
out of bounds error. Is this unexpected behaviour? I would appreciate any
insights this issue.
Thanks.
~Kendric
> train.y
[1] S S S S R R R R R R R R R R R R R R R R R R R R
Levels: R S
> train.x
m1 m2
1 0.1756 0.6502
2 0.1110 -0.2217
3 0.0837 -0.1809
4 -0.3703 -0.2476
5 8.3825 2.8814
6 5.6400 12.9922
7 7.5537 7.4809
8 3.5005 5.7844
9 16.8541 16.6326
10 9.1851 8.7814
11 1.4405 11.0132
12 9.8795 2.6182
13 8.7151 4.5476
14 -0.2092 -0.7601
15 3.6876 2.5772
16 8.3776 5.0882
17 8.6567 7.2640
18 20.9386 20.1107
19 12.2903 4.7864
20 10.5920 7.5204
21 10.2679 9.5493
22 6.2023 11.2333
23 -5.0720 -4.8701
24 6.6417 11.5139
> svmLinearGrid <- expand.grid(.C=0.1)
> svmLinearFit <- train(train.x, train.y, method="svmLinear",
tuneGrid=svmLinearGrid)
Fitting: C=0.1
Error in indexes[[j]] : subscript out of bounds
> svmLinearFit <- train(train.x, train.y, method="svmLinear",
tuneGrid=svmLinearGrid)
Fitting: C=0.1
maximum number of iterations reached 0.0005031579 0.0005026807maximum number
of iterations reached 0.0002505857 0.0002506714Error in indexes[[j]] :
subscript out of bounds
> svmLinearFit <- train(train.x, train.y, method="svmLinear",
tuneGrid=svmLinearGrid)
Fitting: C=0.1
maximum number of iterations reached 0.0003270061 0.0003269764maximum number
of iterations reached 7.887867e-05 7.866367e-05maximum number of iterations
reached 0.0004087571 0.0004087466Aggregating results
Selecting tuning parameters
Fitting model on full training set
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] kernlab_0.9-12 pamr_1.47 survival_2.35-8 cluster_1.12.3
[5] e1071_1.5-24 class_7.3-2 caret_4.70 reshape_0.8.3
[9] plyr_1.2.1 lattice_0.18-8
loaded via a namespace (and not attached):
[1] grid_2.11.1
--
MSc. Candidate
CIHR/MSFHR Training Program in Bioinformatics
University of British Columbia
[[alternative HTML version deleted]]
------------------------------
Message: 112
Date: Mon, 22 Nov 2010 15:20:56 -0800 (PST)
From: Phil Spector <spector at stat.berkeley.edu>
To: madr <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] I need a very specific unique like function and I
don't know even how to properly call this
Message-ID:
<alpine.DEB.2.00.1011221517010.14043 at springer.Berkeley.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Given a vector, x, we can test if the value above
it is equal to itself with
abv = c(FALSE,x[-l] == x[-1])
and if the value below is equal to itself with
blw = c(x[-l] == x[-1],FALSE)
So, for your problem:
> abv = c(FALSE,dat[,2][-l] == dat[,2][-1])
> blw = c(dat[,2][-l] == dat[,2][-1],FALSE)
> dat[!(abv & blw),]
[,1] [,2]
[1,] 3 7
[2,] 6 5
[3,] 5 5
[4,] 8 4
[5,] 7 4
[6,] 0 6
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spector at stat.berkeley.edu
On Mon, 22 Nov 2010, madr wrote:
>
> consider this matrix:
>
> [,1] [,2]
> [1,] 3 7
> [2,] 6 5
> [3,] 7 5
> [4,] 3 5
> [5,] 7 5
> [6,] 5 5
> [7,] 8 4
> [8,] 2 4
> [9,] 7 4
> [10,] 0 6
>
> I need to delete all rows where column 2 above and below has the same
value,> so the effect would be:
>
> [,1] [,2]
> [1,] 3 7
> [2,] 6 5
> [6,] 5 5
> [7,] 8 4
> [9,] 7 4
> [10,] 0 6
>
> is there a built in function for that kind of operation or I must write
one> from scratch ?
> Is there a name for that kind of operation ?
> --
> View this message in context:
http://r.789695.n4.nabble.com/I-need-a-very-specific-unique-like-function-an
d-I-don-t-know-even-how-to-properly-call-this-tp3054427p3054427.html> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 113
Date: Mon, 22 Nov 2010 18:43:41 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: shubha <shuba.pandit at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] how do remove those predictor which have p value
greater than 0.05 in GLM?
Message-ID: <0911E03A-8277-4731-8AF4-E80777201E28 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 5:10 PM, shubha wrote:
>
> Thanks for the response, Frank.
> I am not saying that I want to delete a variables because of p>0.5.
Presumably that was meant to be p > 0.05
> But my
> concern was: I am using backward stepwise logistic regression, it
> keeps the
> variables in the final model if the variable significantly
> contributing in
> the model.
Isn't that what backwards selection does?
> Otherwise, it should not be in the final model.
You're sure? How did you arrive at that conclusion?
> Using other software, they give correct results.
Correct? Please describe your standards for correctness.
> But R, did not. I want
> those variables if p<0.05, otherwise exclude from the model.
But you said above that was _not_ what you wanted. I'm confused about
your posture here.
> If you include
> that variables, it will affect the Log likelihood ratio and AIC.
Yes, perhaps it will, ... so is the standard a p-value or is a
penalized penalized estimate? When you toss out a variable, you are
deluding yourself to then later ignore that act of deletion when
specifying your degrees of freedom for the multiple hypothesis testing
effort you have conducting.
> I want to
> change a P-value criterion <=0.05 in the model. Any suggestions.
More reading. Less reliance on canned software.
> thanks
>
> --
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 114
Date: Mon, 22 Nov 2010 16:22:11 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
To: Marcin Gomulka <mrgomel at gmail.com>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] plotting a timeline
Message-ID: <4CEB0933.30406 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-11-20 14:26, Marcin Gomulka wrote:> I was trying to recreate this kind of timeline plot:
> http://www.vertex42.com/ExcelArticles/create-a-timeline.html
>
> As you can see in their excel example, the events are nicely placed out on
> both sides of the timeline axis.
>
> AFAIK there is no function to do this nicely in R-project. Furthermore,
> graphics and lattice packages are unable to draw the x-axis in the middle
of> the plot. (datapoints cannot be plotted below the axis, as in the Excel
> example).
>
> My question: Is there a function to draw the x-axis inside the plot? (at a
> certain vertical position?) Is there a function for the whole timeline
plot> that I do not know about?
>
> I tried to visually replicate the plot using additional elements to create
> my own x-axis (code below). I have placed the x-axis ticks on a fixed
> y-height (-0.1 and -0.05), but this might look badly with a different
> dataset or at other image proportions. I'd rather do this with a
dedicated
> package function ( like axis() ).
>
It wouldn't be difficult to write such a function.
Here's some code to get you started:
with(the_data, {
plot(eventtime, impact, type="h", axes=FALSE,
ann=FALSE, col="grey", ylim=c(-.7,1.2))
points(eventtime, impact, pch=95, font=5, cex=2, col=4)
text(eventtime, impact, label, pos = 1 + 2*(impact > 0))
})
abline(h=0, lwd=2)
axis(1, pos=0, lwd=2, lwd.ticks=1)
Peter Ehlers
> --
> mrgomel
> -----------------------
> Below is my example code in R:
>
>
> the_data<-
> structure(list(eventtime = c(1914L, 1917L, 1918L, 1939L, 1945L,
> 1963L, 1989L, 2001L, 2003L), impact = c(1, -.5, 0.8, 1, 0.8, 0.5,
> -.5, 0.5, 1), label = structure(c(8L, 7L, 4L, 9L, 5L, 2L, 3L,
> 1L, 6L), .Label = c("9/11", "Cuban crisis", "end
of communism",
> "end WW1", "end WW2", "Iraq war", "start
of communism", "WW1",
> "WW2"), class = "factor")), .Names =
c("eventtime", "impact",
> "label"), class = "data.frame", row.names = c(NA, -9L))
>
>
> plot(the_data$eventtime, the_data$impact, type="h",
frame.plot=FALSE, axes
> FALSE, xlab="",ylab="", col="grey")
> text(the_data$eventtime,the_data$impact, the_data$label)
> #axis(1)
> abline(h=0,lwd=2)
> text(axTicks(1),-0.1, axTicks(1))
> points(axTicks(1),rep(-0.05,length(axTicks(1))), type="h")
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 115
Date: Tue, 23 Nov 2010 01:36:47 +0100
From: "Sebastian Rudnick" <rudnick at igb-berlin.de>
To: r-help at r-project.org
Subject: [R] Gap between graph and axis
Message-ID: <20101123002430.M57525 at igb-berlin.de>
Content-Type: text/plain; charset=utf-8
Hi everyone!
I want to plot some precipitation data via plot(type="h").
Unfortunately
there
is always a gap between the bars and the x-axis, so that the bars reach in
the
"negative area" below 0 at the y-axis, which is very misleading. The
ylim-parameter is set to 0 and max of precipitation, the min value of
precipitation is 0 as well.
I tried to fix this via the fig parameter, but I have no idea how to do it
at
all.
I hope anyone can help.
Thanks a lot,
Sebastian
------------------------------
Message: 116
Date: Tue, 23 Nov 2010 11:52:29 +1100
From: <Bill.Venables at csiro.au>
To: <rudnick at igb-berlin.de>, <r-help at r-project.org>
Subject: Re: [R] Gap between graph and axis
Message-ID:
<1BDAE2969943D540934EE8B4EF68F95FB27A44FC0D at EXNSW-MBX03.nexus.csiro.
au>
Content-Type: text/plain; charset="us-ascii"
perhaps you need something like this.
par(yaxs = "i")
plot(runif(10), type = "h", ylim = c(0, 1.1))
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of Sebastian Rudnick
Sent: Tuesday, 23 November 2010 10:37 AM
To: r-help at r-project.org
Subject: [R] Gap between graph and axis
Hi everyone!
I want to plot some precipitation data via plot(type="h").
Unfortunately
there
is always a gap between the bars and the x-axis, so that the bars reach in
the
"negative area" below 0 at the y-axis, which is very misleading. The
ylim-parameter is set to 0 and max of precipitation, the min value of
precipitation is 0 as well.
I tried to fix this via the fig parameter, but I have no idea how to do it
at
all.
I hope anyone can help.
Thanks a lot,
Sebastian
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 117
Date: Mon, 22 Nov 2010 19:01:16 -0600
From: Erin Hodgess <erinm.hodgess at gmail.com>
To: R help <r-help at stat.math.ethz.ch>
Subject: [R] R on Androids?
Message-ID:
<AANLkTik5jP2cm5Gy0cDRvbkQURoQVc0vgYmE-hDYWG_B at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear R People:
Does R run on the Android, yet, please? I'm about 99% sure that it
does not, but thought that I would double check.
Thanks,
Erin
--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com
------------------------------
Message: 118
Date: Mon, 22 Nov 2010 20:07:08 -0500
From: watashi at post.com
To: yuliya.rmail at gmail.com, r-help at r-project.org
Subject: Re: [R] how to loop through variables in R?
Message-ID: <8CD58C1E2D65661-1718-A0F at web-mmc-m05.sysops.aol.com>
Content-Type: text/plain
-----Original Message-----
From: Yuliya Matveyeva <yuliya.rmail at gmail.com>
To: watashi at post.com
Sent: Mon, Nov 22, 2010 4:32 pm
Subject: Re: [R] how to loop through variables in R?
If you want to have a name-specific loop.
Assign names to your variables after inserting them into the data.frame like
that:
colnames(df) <-
c("var1","var23","var456","var44",...)
for (nam in colnames(df)) {
myfunction(df[[nam]])
}
Data.frames support access by names.
Unfortunately, in this sense I have to type in 1000 times... isn't there any
function that allows retrieving and assigning all columns automatically?
read.table in "the R intro manual" just brief says it can read a table
but
then there's no follow up about how to access the data....
[[alternative HTML version deleted]]
------------------------------
Message: 119
Date: Mon, 22 Nov 2010 17:20:22 -0800 (PST)
To: r-help at r-project.org
Subject: [R] How to start default browser on R
Message-ID: <116352.18459.qm at web113205.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi folks,
Win7 64 bit
IE 64 bit
How to start IE on R? TIA
B.R.
Stephen L
------------------------------
Message: 120
Date: Mon, 22 Nov 2010 17:23:29 -0800 (PST)
To: R help <r-help at stat.math.ethz.ch>
Subject: [R] question on "uniCox"
Message-ID: <741278.83327.qm at web30803.mail.mud.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi list,
I?m testing out uniCox R package (version 1.0, on R2.12.0, WinXP).
When I ran uniCox on my data, there are always some NA?s in the beta matrix,
which in turn causes problems in uniCoxCV call. I don?t see anything wrong
with the corresponding data (e.g. no NAs) and if I fit a univariate Cox
model,
the features that give NA beta estimates are actually pretty significant.
Could you please let me know what happened and how to avoid this?
I?ve attached the outputs of the function calls below.
Thank you very much!
...Tao
> a <- uniCox(x=t(dat.ave.train.base),
y=sampleinfo.ave.train.base$tm2dthr,
>status=sampleinfo.ave.train.base$censrdth)
lambda value 1 out of 20
lambda value 2 out of 20
lambda value 3 out of 20
lambda value 4 out of 20
lambda value 5 out of 20
lambda value 6 out of 20
lambda value 7 out of 20
lambda value 8 out of 20
lambda value 9 out of 20
lambda value 10 out of 20
lambda value 11 out of 20
lambda value 12 out of 20
lambda value 13 out of 20
lambda value 14 out of 20
lambda value 15 out of 20
lambda value 16 out of 20
lambda value 17 out of 20
lambda value 18 out of 20
lambda value 19 out of 20
lambda value 20 out of 20
5 betas missing
> aa <- uniCoxCV(a, x=t(dat.ave.train.base),
>y=sampleinfo.ave.train.base$tm2dthr,
status=sampleinfo.ave.train.base$censrdth)
FOLD= 1
lambda value 1 out of 20
lambda value 2 out of 20
lambda value 3 out of 20
lambda value 4 out of 20
lambda value 5 out of 20
lambda value 6 out of 20
lambda value 7 out of 20
lambda value 8 out of 20
lambda value 9 out of 20
lambda value 10 out of 20
lambda value 11 out of 20
lambda value 12 out of 20
lambda value 13 out of 20
lambda value 14 out of 20
lambda value 15 out of 20
lambda value 16 out of 20
lambda value 17 out of 20
lambda value 18 out of 20
lambda value 19 out of 20
lambda value 20 out of 20
3 betas missing
1
Error in coxph(Surv(y[ii], status[ii]) ~ eta.new) :
No (non-missing) observations
> a[[2]][(rowSums(is.na(a[[2]])))>0,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
[,13]
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 92.6641 NaN NaN NaN 0 0 0 0 0 0 0 0
0
0 0 0 0 0 0 0
[2,] NaN 0 0 0 0 0 0 0 0 0 0 0
0
0 0 0 0 0 0 0
[3,] 567.3650 NaN 0 0 0 0 0 0 0 0 0 0
0
0 0 0 0 0 0 0
------------------------------
Message: 121
Date: Mon, 22 Nov 2010 17:28:57 -0800
From: Spencer Graves <spencer.graves at structuremonitoring.com>
To: Georg Otto <gwo at well.ox.ac.uk>
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Find in R and R books
Message-ID: <4CEB18D9.6030305 at structuremonitoring.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Other people like R Site Search
(http://search.r-project.org/nmz.html), which is available via the
standard R function "RSiteSearch".
For me, the fastest literature search on virtually anything
statistical is the "findFn" function in the "sos" package.
(Disclaimer: I'm the lead author of that package, so I may be biased.)
"findFn" sorts search results to put the package with the most matches
first. The print method opens a table of the results in a web browser
with hot links to the individual matches. "sos" comes with a
vignette,
which includes an example of the "writeFindFn2xls" function. This
writes a "findFn" object to an Excel file with two sheets: The second
is all the matches found. The first is a summary of the packages found
with extra information not available via RSiteSearch.
Hope this helps.
Spencer
On 11/22/2010 3:19 AM, Georg Otto wrote:
>
>
>> Also when I try to search in google using for example the word R inside
the search lemma I get very few results as the R confuses the search engine.
When I was looking something in matlab ofcourse it was easier to get results
as the search engine performs better.>> What are your tricks when you want to find some function that provides
some functionality?> To search R-specific sites the best place to go is this one:
>
> http://www.rseek.org/
>
> Cheers,
>
> Georg
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 122
Date: Mon, 22 Nov 2010 17:33:22 -0800 (PST)
To: Terry Therneau <therneau at mayo.edu>
Cc: r-help at r-project.org, dieter.menne at menne-biomed.de,
r_tingley at hotmail.com
Subject: Re: [R] calculating martingale residual on new data using
"predict.coxph"
Message-ID: <616997.31494.qm at web30804.mail.mud.yahoo.com>
Content-Type: text/plain; charset=us-ascii
Thank you, Terry!
----- Original Message ----> From: Terry Therneau <therneau at mayo.edu>
> Cc: r-help at r-project.org; dieter.menne at menne-biomed.de; r_tingley at
hotmail.
com> Sent: Mon, November 22, 2010 6:11:15 AM
> Subject: Re: calculating martingale residual on new data using
"predict.coxph">
> This feature has been added in survival 2.36-1, which is now on CRAN.
> (2.36-2 should appear in another day or so)
> Terry T.
>
> ---------begin included message --------
> I was trying to use "predict.coxph" to calculate martingale
residuals on
> a test
> data, however, as pointed out before
>
> http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html
>
> predict(mycox1, newdata, type="expected") is not implemented
yet.
>
>
------------------------------
Message: 123
Date: Mon, 22 Nov 2010 17:36:18 -0800 (PST)
To: Frank Harrell <f.harrell at vanderbilt.edu>, r-help at r-project.org
Subject: Re: [R] calculating martingale residual on new data using
Message-ID: <562346.4353.qm at web30805.mail.mud.yahoo.com>
Content-Type: text/plain; charset=us-ascii
[[elided Yahoo spam]]
...Tao
----- Original Message ----> From: Frank Harrell <f.harrell at vanderbilt.edu>
> To: r-help at r-project.org
> Sent: Sun, November 21, 2010 5:49:36 AM
> Subject: Re: [R] calculating martingale residual on new data using
>
>
> The tendency is to use residual-like diagnostics on the entire dataset
that> was available for model development. For test data we typically run
> predictive accuracy analyses. For example, one of the strongest
validations> is to show, in a high-resolution calibration plot, that absolute
predictions> (e.g., probability of survival at 2 years) are accurate.
>
> Frank
>
>
> -----
> Frank Harrell
> Department of Biostatistics, Vanderbilt University
> --
> View this message in context:
>http://r.789695.n4.nabble.com/calculating-martingale-residual-on-new-data-u
sing-predict-coxph-tp3050712p3052377.html>
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 124
Date: Mon, 22 Nov 2010 17:36:54 -0800 (PST)
To: David Winsemius <dwinsemius at comcast.net>
Cc: r-help at r-project.org, dieter.menne at menne-biomed.de,
r_tingley at hotmail.com
Subject: Re: [R] calculating martingale residual on new data using
"predict.coxph"
Message-ID: <212275.29986.qm at web30802.mail.mud.yahoo.com>
Content-Type: text/plain; charset=us-ascii
[[elided Yahoo spam]]
...Tao
----- Original Message ----> From: David Winsemius <dwinsemius at comcast.net>
> Cc: r-help at r-project.org; dieter.menne at menne-biomed.de; r_tingley at
hotmail.
com> Sent: Sun, November 21, 2010 5:50:31 AM
> Subject: Re: [R] calculating martingale residual on new data using
>"predict.coxph"
>
>
> On Nov 21, 2010, at 3:42 AM, Shi, Tao wrote:
>
> > Hi David,
> >
> > Thanks, but I don't quite follow your examples below.
>
> I wasn't really sure they did anything useful anyway.
>
> > The residuals you
> > calculated are still based on the training data from which your cox
model >was
> > generated. I'm interested in the testing data.
>
> The survest function in rms and the survfit function in survival will
>calculate survival probabilities given a model and newdata, and depending
on >your definition of "residual" you could take the difference
between the
>calculation and validation data. That must be what happens (at least at a
gross >level of description) when Harrell runs his validate function on his cph
models >in the rms/Design package, although I don't know if something that you
would >recognize as a martingale residual is an identifiable intermediate.
>
> If you are using survfit, it would appear from my reading that you
would >need to set the "individual" parameter to TRUE. I'm assuming
you planned
to >calculate these (1- expected) at the event times of the validation cohort
>(which it appears the default method fixes via the censor argument)?
>
> --David
>
> >
> >
> > Best,
> >
> > ...Tao
> >
> >
> >
> >
> >
> > ----- Original Message ----
> >> From: David Winsemius <dwinsemius at comcast.net>
> >> To: David Winsemius <dwinsemius at comcast.net>
> >> dieter.menne at menne-biomed.de; r_tingley at hotmail.com
> >> Sent: Fri, November 19, 2010 10:53:26 AM
> >> Subject: Re: [R] calculating martingale residual on new data
using
> >> "predict.coxph"
> >>
> >>
> >> On Nov 19, 2010, at 12:50 PM, David Winsemius wrote:
> >>
> >>>
> >>> On Nov 19, 2010, at 12:32 PM, Shi, Tao wrote:
> >>>
> >>>> Hi list,
> >>>>
> >>>> I was trying to use "predict.coxph" to
calculate martingale
residuals on >a
> >> test
> >>>> data, however, as pointed out before
> >>>
> >>> What about resid(fit) ? It's my reading of Therneau
& Gramsch [and
of> >> help(coxph.object) ] that they consider those martingale
residuals.
> >>
> >> The manner in which I _thought_ this would work was to insert
some
dummy >cases
> >> into the original data and then to get residuals by weighting
the
cases> >> appropriately. That doesn't seem to be as successful as I
imagined:
> >>
> >>> test1 <- list(time=c(4,3,1,1,2,2,3,3),
weights=c(rep(1,7), 0),
> >> + status=c(1,1,1,0,1,1,0,1),
> >> + x=c(0,2,1,1,1,0,0,1),
> >> + sex=c(0,0,0,0,1,1,1,1))
> >>> coxph(Surv(time, status) ~ x , test1,
weights=weights)$weights
> >> Error in fitter(X, Y, strats, offset, init, control, weights
weights,
>:
> >> Invalid weights, must be >0
> >> # OK then make it a small number
> >>> test1 <- list(time=c(4,3,1,1,2,2,3,3),
weights=c(rep(1,7), 0.01),
> >> + status=c(1,1,1,0,1,1,0,1),
> >> + x=c(0,2,1,1,1,0,0,1),
> >> + sex=c(0,0,0,0,1,1,1,1))
> >>> print(resid( coxph(Surv(time, status) ~ x ,
test1,weights=weights)
)> >> ,digits=3)
> >> 1 2 3 4 5 6 7
8
> >> -0.6410 -0.5889 0.8456 -0.1544 0.4862 0.6931 -0.6410 0.0509
> >> Now take out constructed case and weights
> >>
> >>> test1 <- list(time=c(4,3,1,1,2,2,3),
> >> + status=c(1,1,1,0,1,1,0),
> >> + x=c(0,2,1,1,1,0,0),
> >> + sex=c(0,0,0,0,1,1,1))
> >>> print(resid( coxph(Surv(time, status) ~ x , test1) )
,digits=3)
> >> 1 2 3 4 5 6 7
> >> -0.632 -0.589 0.846 -0.154 0.486 0.676 -0.632
> >>
> >> Expecting approximately the same residuals for first 7 cases but
not
>really
> >> getting it. There must be something about weights in coxph that I
don't> >> understand, unless a one-hundreth of a case gets "up
indexed" inside
the> >> machinery of coxph?
> >>
> >> Still think that inserting a single constructed case into a real
dataset >of
> >> sufficient size ought to be able to yield some sort of estimate,
and
only >be a
> >> minor perturbation, although I must admit I'm having
trouble
figuring out >...
> >> why are we attempting such a maneuver? The notion of
"residuals"
around> >> constructed cases makes me statistically suspicious, although I
suppose >that is
> >> just some sort of cumulative excess/deficit death fraction.
> >>
> >>>>
http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html
> >>>>
> >>>> predict(mycox1, newdata, type="expected") is not
implemented yet.
>Dieter
> >>>> suggested to use 'cph' and
'predict.Design', but from my reading so
far,> >> I'm not
> >>>> sure they can do that.
> >>>>
> >>>> Do you other ways to calculate martingale residuals on a
new data?
> >>>>
[[elided Yahoo spam]]> >>>>
> >>>> ...Tao
> >>
> >> --David Winsemius, MD
> >> West Hartford, CT
> >>
> >>
> >
> >
> >
>
> David Winsemius, MD
> West Hartford, CT
>
>
------------------------------
Message: 125
Date: Mon, 22 Nov 2010 20:43:56 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <spencer.graves at structuremonitoring.com>, <gwo at
well.ox.ac.uk>
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Find in R and R books
Message-ID: <BLU113-W111F8D13F02BDD7AC3C938BE3E0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> Date: Mon, 22 Nov 2010 17:28:57 -0800
> From: spencer.graves at structuremonitoring.com
> To: gwo at well.ox.ac.uk
> CC: r-help at stat.math.ethz.ch
> Subject: Re: [R] Find in R and R books
>
> Other people like R Site Search
> (http://search.r-project.org/nmz.html), which is available via the
> standard R function "RSiteSearch".
>
>
> For me, the fastest literature search on virtually anything
> statistical is the "findFn" function in the "sos"
package.
> (Disclaimer: I'm the lead author of that package, so I may be biased.)
> "findFn" sorts search results to put the package with the most
matches
> first. The print method opens a table of the results in a web browser
Again, I have in past taken docs for various things like R, rendered
html to text and used things like grep and built my own indicies.
However, your facility does seem in that line of thought.
Personally I haven't had a problem with google scholar or
probably even citeseer would return good hits, R is not
a common english word so I think google can make use of it.
> with hot links to the individual matches. "sos" comes with a
vignette,
> which includes an example of the "writeFindFn2xls" function. This
> writes a "findFn" object to an Excel file with two sheets: The
second
> is all the matches found. The first is a summary of the packages found
> with extra information not available via RSiteSearch.
>
>
> Hope this helps.
> Spencer
>
>
> On 11/22/2010 3:19 AM, Georg Otto wrote:
> > Alaios writes:
> >
> >
> >> Also when I try to search in google using for example the word R
inside
the search lemma I get very few results as the R confuses the search engine.
When I was looking something in matlab ofcourse it was easier to get results
as the search engine performs better.> >> What are your tricks when you want to find some function that
provides
some functionality?> > To search R-specific sites the best place to go is this one:
> >
> > http://www.rseek.org/
> >
> > Cheers,
> >
> > Georg
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.
html> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 126
Date: Tue, 23 Nov 2010 01:50:28 +0000 (UTC)
From: Ben Bolker <bbolker at gmail.com>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] Fast Two-Dimensional Optimization
Message-ID: <loom.20101123T024136-231 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii
Wonsang You <you <at> ifn-magdeburg.de> writes:
> I have attempted "optim" function to solve a two-dimensional
optimization
> problem. It took around 25 second to complete the procedure.
> However, I want to reduce the computation time: less than 7 second. Is
there> any optimization function in R which is very rapid?
This is not nearly enough information for us to help. The answer
depends on the characteristics of your objective function. You may be
able to quadruple the speed of your optimization by coding your objective
function more efficiently in R or by re-coding it in C or C++. You may
be able to choose better starting conditions. You may be able to pick
an optimization method that is more suitable for your objective function
(see ?optim and the "optimx" package on r-forge).
Ben Bolker
------------------------------
Message: 127
Date: Mon, 22 Nov 2010 21:11:14 -0500
From: watashi at post.com
To: r-help at r-project.org
Subject: Re: [R] how to loop through variables in R?
Message-ID: <8CD58CAD70284B2-1718-DC0 at web-mmc-m05.sysops.aol.com>
Content-Type: text/plain
d<-read.table("D:\\Working\\Statics.txt")
df <- cbind("Q1", "Q2", "Q3", "Q4",
"Q5", "Q5A", "Q5B", "Q5C",
"Q5D", "Q5E",
"Q5F", "Q5G", "Q6", "Q6A",
"Q6B", "Q6C", "Q6D", "Q6E",
"Q6F", "Q7", "Q8",
"Q9")
#Than you can loop through them simply by doing:
result <- numeric(length(df))
for (i in 1:(length(df)-1)) {
result <- chisq.test(table(df[[i]], df[[i+1]]))
}
and then this error comes out:
Error: unexpected '}' in "}"
and how can I redirect the output of the chi-square test to a file instead
of console output?
[[alternative HTML version deleted]]
------------------------------
Message: 128
Date: Tue, 23 Nov 2010 15:16:04 +1300
From: David Scott <d.scott at auckland.ac.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] How to start default browser on R
Message-ID: <4CEB23E4.8090209 at auckland.ac.nz>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 23/11/10 14:20, Stephen Liu wrote:> Hi folks,
>
> Win7 64 bit
> IE 64 bit
>
> How to start IE on R? TIA
>
> B.R.
> Stephen L
>
>
?browseURL
--
_________________________________________________________________
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
------------------------------
Message: 129
Date: Mon, 22 Nov 2010 18:20:35 -0800
From: Spencer Graves <spencer.graves at structuremonitoring.com>
To: Mike Marchywka <marchywka at hotmail.com>
Cc: r-help at stat.math.ethz.ch, gwo at well.ox.ac.uk
Subject: Re: [R] Find in R and R books
Message-ID: <4CEB24F3.3040108 at structuremonitoring.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi, Mike, et al.:
<in line>
On 11/22/2010 5:43 PM, Mike Marchywka wrote:>
>
>
>
>
> ----------------------------------------
>> Date: Mon, 22 Nov 2010 17:28:57 -0800
>> From: spencer.graves at structuremonitoring.com
>> To: gwo at well.ox.ac.uk
>> CC: r-help at stat.math.ethz.ch
>> Subject: Re: [R] Find in R and R books
>>
>> Other people like R Site Search
>> (http://search.r-project.org/nmz.html), which is available via the
>> standard R function "RSiteSearch".
>>
>>
>> For me, the fastest literature search on virtually anything
>> statistical is the "findFn" function in the "sos"
package.
>> (Disclaimer: I'm the lead author of that package, so I may be
biased.)
>> "findFn" sorts search results to put the package with the
most matches
>> first. The print method opens a table of the results in a web browser
> Again, I have in past taken docs for various things like R, rendered
> html to text and used things like grep and built my own indicies.
> However, your facility does seem in that line of thought.
>
> Personally I haven't had a problem with google scholar or
> probably even citeseer would return good hits, R is not
> a common english word so I think google can make use of it.
Thanks for this.
For me, anything that mixes math with worked examples is vastly superior
to either alone, because I no longer have to puzzle sometimes for hours
over a single line or page of mathematics: I can try a variety of
examples and walk through the code line by line until I understand. In
that way, I find R packages much more intelligible than theoretical
treatises. This is especially true when the R package comes with a
vignette or companion documentation with script files working the
examples (e.g., like the "scripts" subdirectories for "nmle"
and "fda").
Spencer
>> with hot links to the individual matches. "sos" comes with a
vignette,
>> which includes an example of the "writeFindFn2xls" function.
This
>> writes a "findFn" object to an Excel file with two sheets:
The second
>> is all the matches found. The first is a summary of the packages found
>> with extra information not available via RSiteSearch.
>>
>>
>> Hope this helps.
>> Spencer
>>
>>
>> On 11/22/2010 3:19 AM, Georg Otto wrote:
>>> Alaios writes:
>>>
>>>
>>>> Also when I try to search in google using for example the word
R inside
the search lemma I get very few results as the R confuses the search engine.
When I was looking something in matlab ofcourse it was easier to get results
as the search engine performs better.>>>> What are your tricks when you want to find some function that
provides
some functionality?>>> To search R-specific sites the best place to go is this one:
>>>
>>> http://www.rseek.org/
>>>
>>> Cheers,
>>>
>>> Georg
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.
html>>> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 130
Date: Mon, 22 Nov 2010 17:38:06 -0800 (PST)
From: joeponzio <joe.ponzio at gmail.com>
To: r-help at r-project.org
Subject: [R] using the "apply" method for functions with multiple
inputs
Message-ID: <1290476286318-3054719.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
hello r users,
i'm trying to use the apply method on a function with several inputs, but
cannot figure out how to send multiple arguments to the function (not
multiple runs of the same function, but one run of the function including
two variables - each used within the function).
a <- c(1:10,999,999,999)
b <- c(11:20,999,999,999)
tfun <- function(x,y){
if( (x = 1 & y !=999) || (x > 1 & x < 999 & y == 999) )
x1 <- 1
else
x1 <-0
}
#this doesn't work - gives an error " 'y' is missing
tfilt <- sapply(data.frame(a,b), tfun)
thanks,
joe
--
View this message in context:
http://r.789695.n4.nabble.com/using-the-apply-method-for-functions-with-mult
iple-inputs-tp3054719p3054719.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 131
Date: Tue, 23 Nov 2010 11:05:23 +1000
From: Kere Klein <k.klein at uq.edu.au>
To: "r-help at R-project.org" <r-help at R-project.org>
Subject: [R] permalgorithm
Message-ID:
<DFD404226A5BC247866AEAE43341B65428367A2CCB at UQEXMB01.soe.uq.edu.au>
Content-Type: text/plain; charset="us-ascii"
To whom may it concern,
What is a proper way to analyse a dataset generated from permalgorithm with
time varying covariates? It seems like to me that interval censoring would
be the choice but Surv suggests that the event would be regarded as occurred
at the end of the time interval...
Best wishes,
Kere
Kerenaftali Klein PhD| Biostatistician | Queensland Clinical Trials &
Biostatistics Centre
The University of Queensland | School of Population Health | Building 33,
Level 1| Princess Alexandra Hospital |Ipswich Road | Woolloongabba QLD 4102
| Australia Ph: +61 7 3176 3062| Fax: +61 7 3176 6826 | Email:
k.klein at uq.edu.au | Web: http://www.sph.uq.edu.au/qctbc
------------------------------
Message: 132
Date: Mon, 22 Nov 2010 21:43:25 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: joeponzio <joe.ponzio at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] using the "apply" method for functions with multiple
inputs
Message-ID: <DA7675BA-50F5-4CB0-9610-AF60012C4905 at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Nov 22, 2010, at 8:38 PM, joeponzio wrote:
>
> hello r users,
>
> i'm trying to use the apply method on a function with several
> inputs, but
> cannot figure out how to send multiple arguments to the function (not
> multiple runs of the same function, but one run of the function
> including
> two variables - each used within the function).
>
> a <- c(1:10,999,999,999)
> b <- c(11:20,999,999,999)
>
> tfun <- function(x,y){
> if( (x = 1 & y !=999) || (x > 1 & x < 999 & y == 999) )
There is a problem with that first logical test, assigns 1 to x rather
than testing.
> x1 <- 1
> else
> x1 <-0
> }
>
> mapply("tfun", a, b)
[1] 1 1 1 1 1 1 1 1 1 1 0 0 0
(but see above if that were not what you expected.)
> #this doesn't work - gives an error " 'y' is missing
> tfilt <- sapply(data.frame(a,b), tfun)
>
> thanks,
> joe
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/using-the-apply-method-for-functions-with-mult
iple-inputs-tp3054719p3054719.html> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 133
Date: Mon, 22 Nov 2010 19:26:14 -0800 (PST)
To: David Scott <d.scott at auckland.ac.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] How to start default browser on R
Message-ID: <389534.66648.qm at web113215.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi David,
Thanks for your advice.
According to the Example on ?browseURL I tried:
1)
browseURL("file:http://www.r-project.org", browser="C:/Program
Files/Internet
Explorer/iexplore.exe")
It starts a small windows asking for permission to accept ActiveX
-> OK
IE doesn't start
2)
browseURL("file:http://d:/R/R-2.5.1/html/index.html",
browser="C:/Program
Files/Internet Explorer/iexplore.exe")
same result as 1) above
What I have missed? TIA
B.R.
Stephen L
----- Original Message ----
From: David Scott <d.scott at auckland.ac.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Sent: Tue, November 23, 2010 10:16:04 AM
Subject: Re: [R] How to start default browser on R
On 23/11/10 14:20, Stephen Liu wrote:> Hi folks,
>
> Win7 64 bit
> IE 64 bit
>
> How to start IE on R? TIA
>
> B.R.
> Stephen L
>
>
?browseURL
--
_________________________________________________________________
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
------------------------------
Message: 134
Date: Mon, 22 Nov 2010 22:39:15 -0500
From: Ista Zahn <izahn at psych.rochester.edu>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] How to start default browser on R
Message-ID:
<AANLkTik4RKiUwPPDj+TYimm3pdrdxCJ2eoSsiR-0zaaA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Stephen,
I'm not sure if this is the problem, but you almost certainly do not
want the "file:" part. Try
browseURL("http://www.r-project.org")
-Ista
> Hi David,
>
> Thanks for your advice.
>
> According to the Example on ?browseURL I tried:
>
> 1)
> browseURL("file:http://www.r-project.org",
browser="C:/Program
Files/Internet> Explorer/iexplore.exe")
>
> It starts a small windows asking for permission to accept ActiveX
> -> OK
>
> IE doesn't start
>
> 2)
> browseURL("file:http://d:/R/R-2.5.1/html/index.html",
browser="C:/Program
> Files/Internet Explorer/iexplore.exe")
>
> same result as 1) above
>
>
> What I have missed? ?TIA
>
>
> B.R.
> Stephen L
>
>
>
>
> ----- Original Message ----
> From: David Scott <d.scott at auckland.ac.nz>
> Cc: "r-help at r-project.org" <r-help at r-project.org>
> Sent: Tue, November 23, 2010 10:16:04 AM
> Subject: Re: [R] How to start default browser on R
>
> ?On 23/11/10 14:20, Stephen Liu wrote:
>> Hi folks,
>>
>> Win7 64 bit
>> IE 64 bit
>>
>> How to start IE on R? ?TIA
>>
>> B.R.
>> Stephen L
>>
>>
> ?browseURL
>
> --
> _________________________________________________________________
> David Scott ? ?Department of Statistics
> ? ? ? ?The University of Auckland, PB 92019
> ? ? ? ?Auckland 1142, ? ?NEW ZEALAND
> Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
> Email: ? ?d.scott at auckland.ac.nz, ?Fax: +64 9 373 7018
>
> Director of Consulting, Department of Statistics
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
------------------------------
Message: 135
Date: Mon, 22 Nov 2010 22:49:15 -0500
From: Ravi Varadhan <rvaradhan at jhmi.edu>
To: Yogesh Tiwari <yogesh.mpi at googlemail.com>
Cc: r-help <r-help at stat.math.ethz.ch>
Subject: Re: [R] how to calculate derivative
Message-ID: <718097d9ea7a.4ceaf36b at johnshopkins.edu>
Content-Type: text/plain; CHARSET=US-ASCII
Here is a simple approach:
data <- read.table("test-data.txt")
deriv <- diff(data$V2) / diff(data$V1)
times <- (data$V1[-1] + data$V1[-3545])/2
plot(times, deriv, type="l")
Another approach is to smooth the original data and then obtain derivatives
from the smooth
Ravi.
____________________________________________________________________
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvaradhan at jhmi.edu
----- Original Message -----
From: Yogesh Tiwari <yogesh.mpi at googlemail.com>
Date: Monday, November 22, 2010 5:14 pm
Subject: [R] how to calculate derivative
To: r-help <r-help at stat.math.ethz.ch>
> Dear R Users,
>
> I have trend of two time series of CO2 each 10 years of data. One is
> varying
> weekly and another is bi-weekly. I want to calculate Growth rate ppmv
> / year
> of these CO2 trends. Therefore I want to calculate time derivative
> ppmv /
> year.
>
> How to do it in R?
>
> Here I attached example data file, I would appreciate if any one
> kindly can
> help on it.
>
> Thanks,
>
> Regards,
> Yogesh
> ______________________________________________
> R-help at r-project.org mailing list
>
> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 136
Date: Mon, 22 Nov 2010 19:59:02 -0800 (PST)
To: Ista Zahn <izahn at psych.rochester.edu>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] How to start default browser on R
Message-ID: <64349.64091.qm at web113204.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi Ista,
I see. Your advice works. Thanks
even without:
browser="C:/Program Files/Internet Explorer/iexplore.exe")
For non default browser it needs;
browser="C:/Program Files/Mozilla Firefoe/firefox.exe"
What will be "file:" used for?
B.R.
Stephen L
----- Original Message ----
From: Ista Zahn <izahn at psych.rochester.edu>
Cc: David Scott <d.scott at auckland.ac.nz>; "r-help at
r-project.org"
<r-help at r-project.org>
Sent: Tue, November 23, 2010 11:39:15 AM
Subject: Re: [R] How to start default browser on R
Hi Stephen,
I'm not sure if this is the problem, but you almost certainly do not
want the "file:" part. Try
browseURL("http://www.r-project.org")
-Ista
> Hi David,
>
> Thanks for your advice.
>
> According to the Example on ?browseURL I tried:
>
> 1)
> browseURL("file:http://www.r-project.org",
browser="C:/Program
Files/Internet> Explorer/iexplore.exe")
>
> It starts a small windows asking for permission to accept ActiveX
> -> OK
>
> IE doesn't start
>
> 2)
> browseURL("file:http://d:/R/R-2.5.1/html/index.html",
browser="C:/Program
> Files/Internet Explorer/iexplore.exe")
>
> same result as 1) above
>
>
> What I have missed? TIA
>
>
> B.R.
> Stephen L
>
>
>
>
> ----- Original Message ----
> From: David Scott <d.scott at auckland.ac.nz>
> Cc: "r-help at r-project.org" <r-help at r-project.org>
> Sent: Tue, November 23, 2010 10:16:04 AM
> Subject: Re: [R] How to start default browser on R
>
> On 23/11/10 14:20, Stephen Liu wrote:
>> Hi folks,
>>
>> Win7 64 bit
>> IE 64 bit
>>
>> How to start IE on R? TIA
>>
>> B.R.
>> Stephen L
>>
>>
> ?browseURL
>
> --
> _________________________________________________________________
> David Scott Department of Statistics
> The University of Auckland, PB 92019
> Auckland 1142, NEW ZEALAND
> Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
> Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
>
> Director of Consulting, Department of Statistics
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
------------------------------
Message: 137
Date: Tue, 23 Nov 2010 17:00:36 +1300
From: David Scott <d.scott at auckland.ac.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>, Ista
Zahn
<izahn at psych.rochester.edu>
Subject: Re: [R] How to start default browser on R
Message-ID: <4CEB3C64.3000106 at auckland.ac.nz>
Content-Type: text/plain; charset=UTF-8; format=flowed
On 23/11/10 16:59, Stephen Liu wrote:> Hi Ista,
>
> I see. Your advice works. Thanks
>
> even without:
> browser="C:/Program Files/Internet Explorer/iexplore.exe")
>
> For non default browser it needs;
> browser="C:/Program Files/Mozilla Firefoe/firefox.exe"
>
>
> What will be "file:" used for?
>
>
> B.R.
> Stephen L
>
You can use it to open a local file on your machine as well. I use this
all the time with hwriter which writes html reports.
David Scott
--
_________________________________________________________________
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
------------------------------
Message: 138
Date: Mon, 22 Nov 2010 20:23:29 -0800
From: Spencer Graves <spencer.graves at structuremonitoring.com>
To: Ravi Varadhan <rvaradhan at jhmi.edu>
Cc: Yogesh Tiwari <yogesh.mpi at googlemail.com>, r-help
<r-help at stat.math.ethz.ch>
Subject: Re: [R] how to calculate derivative
Message-ID: <4CEB41C1.8070106 at structuremonitoring.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
The "fda" package includes various implementations for
smoothing
data and differentiating the smooth, per Ravi's alternative approach.
This is generally preferable to using first differences of raw data,
because differencing raw data amplifies noise, while appropriate smooths
eliminate much of the noise, leaving you with what you most want.
Ramsay and Silverman (2005) Functional Data Analysis, 2nd ed. (Springer)
suggest that if you want a second derivative, it is often wise to use
quintic splines, because then the second derivative are cubic splines.
(The first derivative of a spline of order k is a spline of order k-1.)
An example is provided in Figure 1.2 of Ramsay, Hooker and Graves (2009)
Functional Data Analysis with R and Matlab (Springer).
However, you don't have to get to book to see that example. Just
work through the script file "fdarm-ch01.R" in
system.file('scripts',
package='fda') on any computer with the 'fda' package installed.
Hope this helps.
Spencer
On 11/22/2010 7:49 PM, Ravi Varadhan wrote:> Here is a simple approach:
>
> data<- read.table("test-data.txt")
>
> deriv<- diff(data$V2) / diff(data$V1)
>
> times<- (data$V1[-1] + data$V1[-3545])/2
>
> plot(times, deriv, type="l")
>
> Another approach is to smooth the original data and then obtain
derivatives from the smooth>
> Ravi.
>
> ____________________________________________________________________
>
> Ravi Varadhan, Ph.D.
> Assistant Professor,
> Division of Geriatric Medicine and Gerontology
> School of Medicine
> Johns Hopkins University
>
> Ph. (410) 502-2619
> email: rvaradhan at jhmi.edu
>
>
> ----- Original Message -----
> From: Yogesh Tiwari<yogesh.mpi at googlemail.com>
> Date: Monday, November 22, 2010 5:14 pm
> Subject: [R] how to calculate derivative
> To: r-help<r-help at stat.math.ethz.ch>
>
>
>> Dear R Users,
>>
>> I have trend of two time series of CO2 each 10 years of data. One is
>> varying
>> weekly and another is bi-weekly. I want to calculate Growth rate ppmv
>> / year
>> of these CO2 trends. Therefore I want to calculate time derivative
>> ppmv /
>> year.
>>
>> How to do it in R?
>>
>> Here I attached example data file, I would appreciate if any one
>> kindly can
>> help on it.
>>
>> Thanks,
>>
>> Regards,
>> Yogesh
>> ______________________________________________
>> R-help at r-project.org mailing list
>>
>> PLEASE do read the posting guide
>> and provide commented, minimal, self-contained, reproducible code.
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San Jos?, CA 95126
ph: 408-655-4567
------------------------------
Message: 139
Date: Mon, 22 Nov 2010 20:29:11 -0800 (PST)
From: David Stoffer <dsstoffer at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] Is it possible to make a matrix to start at row 0?
Message-ID: <1290486551690-3054829.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
bogdanno-2 wrote:>
> I want to make the matrix to be indexed from row (column) 0, not 1
> Can I do that? How?
> Thanks
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
Try the Oarray package... it did have some problems at one time, but maybe
it has been updated since then.
--
View this message in context:
http://r.789695.n4.nabble.com/Is-it-possible-to-make-a-matrix-to-start-at-ro
w-0-tp3054248p3054829.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 140
Date: Mon, 22 Nov 2010 20:41:05 -0800
From: Steve Bellan <sbellan at berkeley.edu>
To: r-help at r-project.org
Subject: [R] overlay histograms on map at map coordinates
Message-ID: <0B1FE6E7-2E3A-4AD0-9199-A1CB88393D10 at berkeley.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi all,
I'm trying to visualize animal movement data characteristics
spatiotemporally by overlaying many different histograms on a map. I
want the histograms to be plotted at coordinates in the map that
matches a region they describe. If I was just doing this once, I'd
fiddle in Illustrator after R and avoid the headache. But I'll be
doing it many many times so it seems worth the elegance & repeatability.
For example, say we have the following data:
covariate <- rep(letters[1:10], each = 100)
shape.pars <- rep(seq(.5,.7, length.out = 10), each = 100)
zz <- rgamma(1000, shape = shape.pars, scale = 2)
map <- data.frame(factor = unique(covariate), xx = rnorm(10), yy =
rnorm(10))
I'd like to be able to have 10 histograms plotted for each level of
the covariate at the coordinates specified in the map data.frame.
Ideally, I'd like to be able to specify whether they were plotted to
the left, right, top, bottom or center of the coordinates similar to
in text() and other graphical functions. Looking around the archives,
all I've come across are the viewport system in library(grid) which
doesn't seem to be able to handle plot() hist() or other such
functions. Otherwise, I could create viewports for each histogram
inside the map's coordinate system.
Any ideas? Thanks!
Steve
Steve Bellan
MPH, Epidemiology
PhD Candidate, Environmental Science, Policy & Management
Getz Lab
University of California, Berkeley
------------------------------
Message: 141
Date: Mon, 22 Nov 2010 21:35:11 -0800 (PST)
From: David Stoffer <dsstoffer at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] Kalman filter
Message-ID: <1290490511301-3054858.post at n4.nabble.com>
Content-Type: text/plain; charset=UTF-8
It sounds like you've looked at the DLM, DSE, and SSPIR packages. If not,
then certainly check them out. Also, we have code for filtering, smoothing
and estimation in our text- go to www.stat.pitt.edu/stoffer/tsa3/ and look
at the code for chapter 6. There's not a package for the text, but all the
code is in a compressed file that you can download. The examples are
discussed in detail in the text, but I think looking at the code (and
Appendix R on the site) will be sufficient to set up your problem.
David
Garten Stuhl wrote:>
> Hello,
>
>
>
> I have completed my kalman filter problem with more details.
>
>
>
> The transition- and the measurement equation is given by
>
>
>
> x[t]=A[t]*x[t-1]+B[t]*epsilon[t]
>
> y[t]=C[t]*x[t]+eta[t]
>
>
>
> A, y, B and C are Matrices. Y[t] is the data input vector with 800
> elements
> (every t has one element)
>
>
>
> My Model is described by the following
>
(discretisation<http://www.dict.cc/englisch-deutsch/discretisation.html>)
> stochastic differential equation
>
>
>
> Lambda[t]=lambda[t-1]+kappa*lambda[t]*delta_t+epsilon_l
>
> R[t]=R[t-1]+mu*delta_t+epsilon_r
>
> epsilon_l=sigma_l*sqroot(delta_t)
>
> epsilon_r=sigma_r*sqroot(delta_t)
>
>
>
> Ln(S[t])=lambda[t]+R[t]
>
>
>
> The paramters for estimation are:
>
> kappa
>
> mu
>
> sigma_l
>
> sigma_r
>
>
>
> The state-space-model for this problem is:
>
>
>
> x[t]=(lambda[t], R[t])?
>
> A[t]=(1-kappa+delta_t, 0; 0, 1+mu)
>
> B[t]=(1,0;0,1)
>
> epsilon[t]=(epsilon_l, epsilon_r)?
>
> C[t]=(1,1)
>
> Eta[t]=0
>
>
>
> I used serveral alternative methods (dlm, kalmanLike, fkf, kfilter) for
> parameter estimation but I don?t understand the syntax and the correct
> input
> for model estimation.
>
>
>
> Can anybody help me, which packed is the most best for my problem and how
> is
> it to control?
>
>
>
> Thanks for helping.
>
>
>
> Best,
>
> Thomas
>
> [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
--
View this message in context:
http://r.789695.n4.nabble.com/Kalman-filter-tp3049591p3054858.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 142
Date: Mon, 22 Nov 2010 23:36:53 -0600
From: Mari Pesek <marifrances at gmail.com>
To: r-help at r-project.org
Subject: [R] (no subject)
Message-ID:
<AANLkTikd0ymrDTzJfjad=2CFJvLZEmZKP4gXDRO_ctGX at mail.gmail.com>
Content-Type: text/plain
Dear R Help -
I am analyzing data from an ecological experiment and am having problems
with the ANOVA functions I've tried thus far. The experiment consists of a
blocked/split-plot design, with plant biomass as the response. The following
is an overview of the treatments applied (nitrogen addition, phosphorus
addition, and seeded/not seeded) and at what level (block, main-plot, and
sub-plot):
- 6 experimental blocks divided into 2 main-plots
- each main-plot divided into 8 sub-plots, for a total of 96 sub-plots (6
blocks * 2 main-plots * 8 sub-plots)
- 16 experimental treatment conditions in a 4 x 2 x 2 factorial design:
- N at 4 levels for each sub-plot
- P at 2 levels for each sub-plot
- Seed at two levels for each block (one level per main-plot)
- response variable = biomass
Block
Main Plot 0 : No Seed
Sub-Plot 0.1 : N0 P0
Sub-Plot 0.2 : N0 P1
Sub-Plot 0.3 : N1 P0
Sub-Plot 0.4 : N1 P1
Sub-Plot 0.5 : N2 P0
Sub-Plot 0.6 : N2 P1
Sub-Plot 0.7 : N3 P0
Sub-Plot 0.8 : N3 P1
Main Plot 1 : Seed
Sub-Plot 1.1 : N0 P0
Sub-Plot 1.2 : N0 P1
Sub-Plot 1.3 : N1 P0
Sub-Plot 1.4 : N1 P1
Sub-Plot 1.5 : N2 P0
Sub-Plot 1.6 : N2 P1
Sub-Plot 1.7 : N3 P0
Sub-Plot 1.8 : N3 P1
I've tried several different approaches to run an ANOVA (lmer, aov, lme) on
this data, trying to use type III SSs and include a random factor, but am
having problems. Any suggestions?
[[elided Yahoo spam]]
-Mari Pesek
--
Dept of Ecology and Evolutionary Biology
University of Kansas
Haworth Hall, 1200 Sunnyside Ave
Lawrence, KS 66045
[[alternative HTML version deleted]]
------------------------------
Message: 143
Date: Mon, 22 Nov 2010 23:39:17 -0600
From: Mari Pesek <marifrances at gmail.com>
To: r-help at r-project.org
Subject: [R] factorial ANOVA for block/split-plot design
Message-ID:
<AANLkTimenMxEoq_WGb6hD_Qifp1Y02dN+T3nh55N8LXP at mail.gmail.com>
Content-Type: text/plain
Dear R Help -
I am analyzing data from an ecological experiment and am having problems
with the ANOVA functions I've tried thus far. The experiment consists of a
blocked/split-plot design, with plant biomass as the response. The following
is an overview of the treatments applied (nitrogen addition, phosphorus
addition, and seeded/not seeded) and at what level (block, main-plot, and
sub-plot):
- 6 experimental blocks divided into 2 main-plots
- each main-plot divided into 8 sub-plots, for a total of 96 sub-plots (6
blocks * 2 main-plots * 8 sub-plots)
- 16 experimental treatment conditions in a 4 x 2 x 2 factorial design:
- N at 4 levels for each sub-plot
- P at 2 levels for each sub-plot
- Seed at two levels for each block (one level per main-plot)
- response variable = biomass
Block
Main Plot 0 : No Seed
Sub-Plot 0.1 : N0 P0
Sub-Plot 0.2 : N0 P1
Sub-Plot 0.3 : N1 P0
Sub-Plot 0.4 : N1 P1
Sub-Plot 0.5 : N2 P0
Sub-Plot 0.6 : N2 P1
Sub-Plot 0.7 : N3 P0
Sub-Plot 0.8 : N3 P1
Main Plot 1 : Seed
Sub-Plot 1.1 : N0 P0
Sub-Plot 1.2 : N0 P1
Sub-Plot 1.3 : N1 P0
Sub-Plot 1.4 : N1 P1
Sub-Plot 1.5 : N2 P0
Sub-Plot 1.6 : N2 P1
Sub-Plot 1.7 : N3 P0
Sub-Plot 1.8 : N3 P1
I've tried several different approaches to run an ANOVA (lmer, aov, lme) on
this data, trying to use type III SSs and include a random factor, but am
having problems. Any suggestions?
[[elided Yahoo spam]]
-Mari Pesek
--
Dept of Ecology and Evolutionary Biology
University of Kansas
Haworth Hall, 1200 Sunnyside Ave
Lawrence, KS 66045
[[alternative HTML version deleted]]
------------------------------
Message: 144
Date: Tue, 23 Nov 2010 00:59:09 -0500
From: "RICHARD M. HEIBERGER" <rmh at temple.edu>
To: Mari Pesek <marifrances at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] factorial ANOVA for block/split-plot design
Message-ID:
<AANLkTimAK7kGT3Lgko+seYu9nKbBcSrnJ7oz4CpA71ib at mail.gmail.com>
Content-Type: text/plain
Please see the maiz example at the end of ?HH::MMC
You will need to all the way to the end of the example.
If you don't yet have HH, you can get it with
install.packages("HH")
If you need to write back to the list, please include your attempts.
Rich
[[alternative HTML version deleted]]
------------------------------
Message: 145
Date: Mon, 22 Nov 2010 21:25:37 -0800 (PST)
From: "dhacademic at gmail.com" <dhacademic at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] question about constraint minimization
Message-ID:
<AANLkTim2AgXLOWcaJ7AbFpO9PACz6=TdNJh3nfZ3iie7 at mail.gmail.com>
Content-Type: text/plain
Dear Prof. Ravi Varadhan,
Many thanks for the reply. In my case, besides x1=x3, x1=x4
("x1=x3=x4" was
used in last post), another constraint is needed, x2+x3+x4+...+x12=1.5. So
there are 9 variables.
I have downloaded your code, but I even do not know how to call your code in
R program. Actually, I know very little about R. I spent lots of time to
read the R help files as well as lots of post on line, and finally prepared
the input file that I pasted in my last post. Unfortunately, it does not
work well. Can you please help to revise the input file that can work by
using the constrOptim function? Or can you plese show me how to call your
code in R and send me the input file?
[[elided Yahoo spam]]
Best,
Hao
On Mon, Nov 22, 2010 at 2:31 PM, Ravi Varadhan [via R] <
ml-node+3054297-1984476990-202837 at
n4.nabble.com<ml-node%2B3054297-1984476990
-202837 at n4.nabble.com>> wrote:
> I do not understand the constraint x1 = x3 = x4. If this is correct, you
> only have 10 unknown parameters.
>
> If you can correctly formulate your problem, you can have a look at the
> packages "alabama" or "BB". The function `auglag'
in "alabama" or the
> function `spg' in "BB" may be useful.
>
> Ravi.
>
> -------------------------------------------------------
> Ravi Varadhan, Ph.D.
> Assistant Professor,
> Division of Geriatric Medicine and Gerontology School of Medicine Johns
> Hopkins University
>
> Ph. (410) 502-2619
> email: [hidden
email]<http://user/SendEmail.jtp?type=node&node=3054297&i=0>>
>
> -----Original Message-----
> From: [hidden
email]<http://user/SendEmail.jtp?type=node&node=3054297&i=1>[mailto:[hidden> email]
<http://user/SendEmail.jtp?type=node&node=3054297&i=2>] On
> Behalf Of [hidden
email]<http://user/SendEmail.jtp?type=node&node=3054297&i=3>> Sent: Monday, November 22, 2010 11:10 AM
> To: [hidden email]
<http://user/SendEmail.jtp?type=node&node=3054297&i=4>
> Subject: Re: [R] question about constraint minimization
>
>
> Hi,
>
> I have struggled on this "bound optimization with equality
constraint" by
> using optim function for two days, but still fail to prepare a good input.
> Can anyone help to prepare the input for my specific case? Many thanks.
>
> Best,
> Hao
>
>
> On Sat, Nov 20, 2010 at 3:17 AM, Hans W Borchers [via R] <
> [hidden email]
<http://user/SendEmail.jtp?type=node&node=3054297&i=5><ml-node%2B3051338-309
339578-2>
> [hidden email]
<http://user/SendEmail.jtp?type=node&node=3054297&i=6>>
> > wrote:
>
> > dhacademic <at> gmail.com <dhacademic <at>
gmail.com> writes:
> >
> > >
> > >
> > > Hi,
> > >
> > > I am a beginner of R. There is a question about constraint
> minimization.
> > A
> > > function, y=f(x1,x2,x3....x12), needs to be minimized. There are
3
> > > requirements for the minimization:
> > >
> > > (1) x2+x3+...+x12=1.5 (x1 is excluded);
> > > (2) x1=x3=x4;
> > > (3) x1, x3 and x5 are in the range of -1~0, respectively. The
rest
> > variables
> > > (x2, x4, x6, x7, ...., x12) are in the range of 0~1,
respectively.
> > >
> > > The "optim" function is used. And part of my input is
as follow, where
> > > "xx1r" represents the x12:
> > >
> > > xx1r=1.5-x[2]-x[1]-x[1]-x[3]-x[4]-x[5]-x[6]-x[7]-x[8]-x[9]
> > > start=rnorm(9)
> > > up=1:9/1:9*1
> > > lo=1:9/1:9*-1
> > >
out=optim(start,f,lower=lo,upper=up,method="L-BFGS-B",hessian=TRUE,
> > > control=list(trace=6,maxit=1000))
> > >
> > > There are two problems in this input. the "up" and
"lo" only define a
> > range
> > > of -1~1 for x1 to x11, which can not meet the requirement (3). In
> > addition,
> > > there is not any constraint imposed on x12. I have no idea how to
> specify
> > a
> > > matrix that can impose different constraints on individual
variables
in>
> a
>
> >
> > > function. Any suggestion is highly appreciated.
> > >
> > > Best,
> > > Hao
> > >
> >
> > I don't see any direct need for real 'constraint'
optimization here,
> > it is a 'bounded' optimization where you are allowed to use
> >
> > lower <- c(-1,0,-1,0,-1,0,0,0,0,0,0,0)
> > upper <- c( 0,1, 0,0, 0,1,1,1,1,1,1,1)
> >
> > Otherwise, your description is confusing:
> > (1) Did you change f to a new function with 9 variables, eliminating
> > x3, x4, and x12 ?
> > (2) x4 (being equal to x1) has to be in [-1, 0] but also in [0, 1]?
> > (3) If you need to restrict x12 to [0, 1] also, you cannot eliminate
> it.
> > Either keep x12 and use an equality constraint, or use
inequality
> > constraints on xxlr.
> >
> > Hans Werner
> >
> > ______________________________________________
> > [hidden email]
> <http://user/SendEmail.jtp?type=node&node=3051338&i=0>mailing
list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> >
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting
-guide.html>> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> > ------------------------------
> > View message @
> >
>
>
http://r.789695.n4.nabble.com/question-about-constraint-minimization-tp30508
<http://r.789695.n4.nabble.com/question-about-constraint-minimization-tp3050
8?by-user=t>> 80p3051338.html
> >
> > To unsubscribe from question about constraint minimization, click
> here<
>
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://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscrib&by-usert>>
e_by_code&node=3050880&code=ZGhhY2FkZW1pY0BnbWFpbC5jb218MzA1MDg4MHwtNjM2Nzc0>
> NA==>.
> >
> >
>
> --
> View this message in context:
>
>
http://r.789695.n4.nabble.com/question-about-constraint-minimization-tp30508
<http://r.789695.n4.nabble.com/question-about-constraint-minimization-tp3050
8?by-user=t>> 80p3053912.html
> Sent from the R help mailing list archive at Nabble.com.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email]
<http://user/SendEmail.jtp?type=node&node=3054297&i=7>mailing
list> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting
-guide.html>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> [hidden email]
<http://user/SendEmail.jtp?type=node&node=3054297&i=8>mailing
list> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting
-guide.html>> and provide commented, minimal, self-contained, reproducible code.
>
>
> ------------------------------
> View message @
>
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> To unsubscribe from question about constraint minimization, click
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e_by_code&node=3050880&code=ZGhhY2FkZW1pY0BnbWFpbC5jb218MzA1MDg4MHwtNjM2Nzc0
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[[alternative HTML version deleted]]
------------------------------
Message: 146
Date: Mon, 22 Nov 2010 21:44:16 -0800 (PST)
From: Shai <shainova at gmail.com>
To: r-help at r-project.org
Subject: [R] Explained GLZ model variation
Message-ID:
<093c0ad4-6426-48be-aaa5-04993054424a at 26g2000yqv.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1
Hello,
I am using the MASS library to create some GLZ models. How can I know
how much (%) of the variation is explained by the model, and if it is
significant? I did not see this in the anova() or summary() tables...
Thanks!
Shai
------------------------------
Message: 147
Date: Mon, 22 Nov 2010 23:11:37 -0700
From: Sarah Berry <escalosobre at gmail.com>
To: r-help at r-project.org
Subject: [R] Lattice and Quartz
Message-ID: <B12499D0-CE15-4C74-9705-BD906D10F956 at gmail.com>
Content-Type: text/plain
I ran this script in a source file on my Mac:
library(lattice)
year <- 1900:2000
dollars <- (year-1899)^2
plot(year,dollars)
quartz("year")
histogram(~dollars)
The first plot appears in Quartz 2. The second quartz window, named year,
opens but the histogram doesn't appear.
However, when I copy and paste this script directly into the R console, both
quartz windows (Quartz 2 and year) open and both plots appear.
As a counter example, the script below run as a source file, works as
expected, and I get two plots in two windows:
library(lattice)
year <- 1900:2000
dollars <- (year-1899)^2
plot(year,dollars)
quartz("year")
plot(year, dollars)
How do I get the lattice package to generate multiple plots in multiple
windows from a script run from a source file?
Thank you ahead of time,
Sarah B.
[[alternative HTML version deleted]]
------------------------------
Message: 148
Date: Mon, 22 Nov 2010 23:20:23 -0700
From: Kayce anderson <kaycelu at gmail.com>
To: r-help at r-project.org
Subject: [R] compare GLM coefficients
Message-ID:
<AANLkTi==4cJTdVKgnw1K18KUq-VVXEGyjx70WOGJvMzi at mail.gmail.com>
Content-Type: text/plain
I have a data set of repeated abundance counts over time. I am
investigating whether count data reduced to presence-absence (presence) data
will reveal similar population trends. I am using a negative binomial
distribution for the glm (package MASS) because the count data contains many
zeros and extreme values. "count" and "presence" are annual
sums for each
metric. I have also included sampling effort (visits) as an independent
variable because sampling varies between 29-33 visits per year. My models
are:
glm.nb(count ~ year + visits) and
glm.nb(presence ~ year + visits)
I would like to test whether the coefficients for "year" are
significantly
different between models. Please advise me on the best method to make such
a comparison.
Thank you,
Kayce
[[alternative HTML version deleted]]
------------------------------
Message: 149
Date: Tue, 23 Nov 2010 17:55:58 +1100
From: Michael Bedward <michael.bedward at gmail.com>
To: Kayce anderson <kaycelu at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] compare GLM coefficients
Message-ID:
<AANLkTinoxyjWnP6WZMqCGc8Yu5aE0+eAvgfG6ZrXUiby at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hello Kayce,
My (very basic) understanding is that you can't directly compare the
coefficients across models that have different response variables, nor
could you use AIC and similar metrics of model goodness of fit.
Instead, I think you have to carefully define what you mean by "reveal
similar population trends".
If you treat the model with the count response as your reference, and
it predicts (for example) population decline of magnitude X over
period T, then you can investigate to what extent this same trend is
retrieved by the presence response model. But the specifics of the
comparison(s) should be closely tied to the population behaviours /
syndromes / critical points that you are most interested in. If there
are multiple behaviours of interest you want to know to what extent
the presence data perform as well as the count data for each of them.
That's my general take on the style of the approach. Hopefully others
here will have more detailed and knowledgable comments for you.
Michael
On 23 November 2010 17:20, Kayce anderson <kaycelu at gmail.com>
wrote:> I have a data set of repeated abundance counts over time. ?I am
> investigating whether count data reduced to presence-absence (presence)
data> will reveal similar population trends. ?I am using a negative binomial
> distribution for the glm (package MASS) because the count data contains
many> zeros and extreme values. ?"count" and "presence" are
annual sums for each
> metric. ?I have also included sampling effort (visits) as an independent
> variable because sampling varies between 29-33 visits per year. ?My models
> are:
>
> glm.nb(count ~ year + visits) and
> glm.nb(presence ~ year + visits)
>
> I would like to test whether the coefficients for "year" are
significantly
> different between models. ?Please advise me on the best method to make
such> a comparison.
>
> Thank you,
> Kayce
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 150
Date: Tue, 23 Nov 2010 14:57:23 +0800
From: gireesh bogu <girishbogu at gmail.com>
To: R-help at r-project.org
Subject: [R] Calculating correlation
Message-ID:
<AANLkTi=_GXE1192XXSwaCg-WcugVDat4Rd1jKu8_GTzk at mail.gmail.com>
Content-Type: text/plain
Hi guys
I have an input file with multiple columns and and rows.
Is it possible to calculate correlation of certain value of certain No (For
example x of S1 = 112) with all other values (for example start with x 112
corr a 3 of S1 = x-a 0.2 )
INPUT
*******
No S1 S2 S3 S4 Sn
a 3 4 45 34 23
x 112 0 12 23 0
b 0 1 23 12 1
n 0 1 0 1 1
OUTPUT
***********
No S1 S2 S3 S4 Sn
x-a 0.2 0.3 ...............
x-x 1 1 ................
x-b 0..........................
x-n 0.9 .......................
[[alternative HTML version deleted]]
------------------------------
Message: 151
Date: Tue, 23 Nov 2010 18:33:59 +1100
From: Jim Lemon <jim at bitwrit.com.au>
To: romzero <romzero at yahoo.it>
Cc: r-help at r-project.org
Subject: Re: [R] Some questione about plot
Message-ID: <4CEB6E67.6050608 at bitwrit.com.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 11/22/2010 10:14 PM, romzero wrote:>
> Q1: How can i draw LSD (Least significant difference) on a plot?
> Like this...
> http://r.789695.n4.nabble.com/file/n3053430/LSD.jpg
>
> Q2: How can i draw the axis secondary scale?
>
Hi romzero,
This is somewhat of a guess, but:
segments(2.3,1.6,2.3,1.6+<value of LSD>)
text(2.2,1.6+<value of LSD>/2,"LSD(P<=0.05)",adj=1)
where <value of LSD> is the length of your line.
For the "secondary scale", I assume you mean the little ticks on the
right side of the plot. Maybe:
plotlim<-par("usr")
par(xpd=TRUE)
segments(plotlim[2],<y values for ticks>,
plotlim[2]+diff(plotlim[1:2])/50),<y values for ticks>)
where <y values for ticks> are the vertical positions for the ticks.
Jim
------------------------------
Message: 152
Date: Mon, 22 Nov 2010 23:31:55 -0800 (PST)
To: David Scott <d.scott at auckland.ac.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>, Ista
Zahn
<izahn at psych.rochester.edu>
Subject: Re: [R] How to start default browser on R
Message-ID: <163783.15789.qm at web113203.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi David,
I see. File: gives the full path to the .html file created/download. Then
the
browser will open that file. Thanks.
I don't have hwriter package installed.
A side question, what will be the corresponding command on R for check
whether a
package already installed?
similar to;
On R (Windows)
Packages - Load package
B.R.
Stephen L
----- Original Message ----
From: David Scott <d.scott at auckland.ac.nz>
Cc: Ista Zahn <izahn at psych.rochester.edu>; "r-help at
r-project.org"
<r-help at r-project.org>
Sent: Tue, November 23, 2010 12:00:36 PM
Subject: Re: [R] How to start default browser on R
On 23/11/10 16:59, Stephen Liu wrote:> Hi Ista,
>
> I see. Your advice works. Thanks
>
> even without:
> browser="C:/Program Files/Internet Explorer/iexplore.exe")
>
> For non default browser it needs;
> browser="C:/Program Files/Mozilla Firefoe/firefox.exe"
>
>
> What will be "file:" used for?
>
>
> B.R.
> Stephen L
>
You can use it to open a local file on your machine as well. I use this
all the time with hwriter which writes html reports.
David Scott
--
_________________________________________________________________
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
------------------------------
Message: 153
Date: Tue, 23 Nov 2010 09:35:57 +0200
From: Tal Galili <tal.galili at gmail.com>
To: gireesh bogu <girishbogu at gmail.com>
Cc: R-help at r-project.org
Subject: Re: [R] Calculating correlation
Message-ID:
<AANLkTi=VQ9N5a96Ytx1QPJJ65JrmeUCtWeDW+6+DJY=r at mail.gmail.com>
Content-Type: text/plain
Hi there,
I'm not sure I understand your question.
What are the two vectors you wish to check their correlation?
Are they the two rows x and a?
Because from your example it seems you are trying to do a correlation
between two singular numbers (so probably I didn't get something straight).
Tal
----------------Contact
Details:-------------------------------------------------------
Contact me: Tal.Galili at gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
----------------------------------------------------------------------------
------------------
On Tue, Nov 23, 2010 at 8:57 AM, gireesh bogu <girishbogu at gmail.com>
wrote:
> Hi guys
>
> I have an input file with multiple columns and and rows.
> Is it possible to calculate correlation of certain value of certain No
(For> example x of S1 = 112) with all other values (for example start with x 112
> corr a 3 of S1 = x-a 0.2 )
>
> INPUT
> *******
>
> No S1 S2 S3 S4 Sn
> a 3 4 45 34 23
> x 112 0 12 23 0
> b 0 1 23 12 1
> n 0 1 0 1 1
>
> OUTPUT
> ***********
>
> No S1 S2 S3 S4 Sn
> x-a 0.2 0.3 ...............
> x-x 1 1 ................
> x-b 0..........................
> x-n 0.9 .......................
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
------------------------------
Message: 154
Date: Tue, 23 Nov 2010 00:05:15 -0800 (PST)
To: r-help at r-project.org
Subject: [R] About available datasets on PC
Message-ID: <835227.40335.qm at web113207.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi folks,
Win7
On running;
data(package = .packages(all.available = TRUE))
it displays a list of datasets under:-
Data sets in package ?AER?:
But I couldn't call/load all of them on the list.
> DJFranses
Error: object 'DJFranses' not found
> CreditCard
Error: object 'CreditCard' not found
But I can call/load;> iris
Whether the list shows all available datasets on repo, NOT the datasets
already
download/installed on PC? If YES how to find the running/available datasets
on
PC?
Packages -> Load Datasets
the list looks different.
Pls advise. TIA
B.R.
Stephen L
------------------------------
Message: 155
Date: Tue, 23 Nov 2010 00:24:42 -0800
From: Noah Silverman <noah at smartmediacorp.com>
To: r-help <r-help at r-project.org>
Subject: [R] More detail in chart axis?
Message-ID: <4CEB7A4A.8040305 at smartmediacorp.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
I have a series of data (about 80,000 pairs of x,y).
Plotting it shows a great chart. However, R has randomly chosen about 6
labels for my x axis. Now, clearly I can't show them all, but would
like some control over the granularity of what is displayed. I can't
find anything in the documentation about controlling the axis data
labels. Is there a way?
Alternately, is there a package that would allow me to zoom into an area
of the chart so I can see more detail?
Thanks,
-N
------------------------------
Message: 156
Date: Tue, 23 Nov 2010 09:26:48 +0100
From: derek eder <derek.eder at lungall.gu.se>
To: r-help at r-project.org
Subject: [R] Error: cannot allocate vector of size x Gb (64-bit ...
yet again)
Message-ID: <4CEB7AC8.6090304 at lungall.gu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello,
I am facing the dreaded "Error: cannot allocate vector of size x Gb"
and
don't understand
enough about R (or operating system) memory management to diagnose and
solve the problem
-- despite studying previous posts and relevant R help -- e.g.:
"Error messages beginning cannot allocate vector of size indicate a
failure to obtain memory,
either because the size exceeded the address-space limit for a process
or, more likely,
because the system was unable to provide the memory.
[...] On all builds of R, the maximum length (number of elements)
of a vector is 2^31 - 1 ~ 2*10^9, as lengths are stored as signed integers.
In addition, the storage space cannot exceed the address limit."
- from Memory-limits {Base}
Simple question: Given 64-bit R (AMD64 Linux) with a ulimit of
"unlimited", can the size of an R object exceed the amount of
availlable RAM
memory?
Empirically my system with 4Gb RAM and ample Swap, is failing:
> x <- integer(10^9)
> object.size(x)
4000000040 bytes
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 121195 6.5 350000 18.7 350000 18.7
Vcells 500124024 3815.7 606849099 4629.9 550124408 4197.2
> matrix(x, ncol=16)
Error: cannot allocate vector of size 3.7 Gb
I don't understand how this operation violates the limits detailed in
the Memory-limit help (above).
Thank you!
Derek Eder
----------------------------------------------------------------------------
---------------------
> version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
derek at papanca:~$ top
top - 09:10:18 up 51 min, 4 users, load average: 0.51, 0.51, 0.45
Tasks: 160 total, 2 running, 158 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.0%us, 25.0%sy, 0.0%ni, 75.0%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Mem: 3796484k total, 3764852k used, 31632k free, 14204k buffers
Swap: 2929660k total, 834240k used, 2095420k free, 94800k cached
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
2854 derek 20 0 239m 9260 5448 S 6 0.2 0:05.53
gnome-terminal
1164 root 20 0 218m 31m 10m S 4 0.8 1:29.71 Xorg
3331 derek 20 0 19276 1324 944 R 1 0.0 0:00.6 top
------------------------------
Message: 157
Date: Tue, 23 Nov 2010 00:41:57 -0800
From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
Cc: r-help at r-project.org
Subject: Re: [R] About available datasets on PC
Message-ID: <4CEB7E55.1090209 at dcn.davis.ca.us>
Content-Type: text/plain; charset=utf-8; format=flowed
You need to load the package and then load the data:
library(AER)
data("DJFranses")
then it will be available for you to work with.
Stephen Liu wrote:> Hi folks,
>
> Win7
>
>
> On running;
> data(package = .packages(all.available = TRUE))
>
> it displays a list of datasets under:-
> Data sets in package ?AER?:
>
> But I couldn't call/load all of them on the list.
>
>
>> DJFranses
>>
> Error: object 'DJFranses' not found
>
>
>> CreditCard
>>
> Error: object 'CreditCard' not found
>
>
> But I can call/load;
>
>> iris
>>
>
> Whether the list shows all available datasets on repo, NOT the datasets
already > download/installed on PC? If YES how to find the running/available
datasets on > PC?
>
>
> Packages -> Load Datasets
> the list looks different.
>
>
> Pls advise. TIA
>
> B.R.
> Stephen L
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 158
Date: Tue, 23 Nov 2010 19:52:47 +1100
From: Jim Lemon <jim at bitwrit.com.au>
To: Noah Silverman <noah at smartmediacorp.com>
Cc: r-help <r-help at r-project.org>
Subject: Re: [R] More detail in chart axis?
Message-ID: <4CEB80DF.7090206 at bitwrit.com.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 11/23/2010 07:24 PM, Noah Silverman wrote:> Hi,
>
> I have a series of data (about 80,000 pairs of x,y).
>
> Plotting it shows a great chart. However, R has randomly chosen about 6
> labels for my x axis. Now, clearly I can't show them all, but would
> like some control over the granularity of what is displayed. I can't
> find anything in the documentation about controlling the axis data
> labels. Is there a way?
>
> Alternately, is there a package that would allow me to zoom into an area
> of the chart so I can see more detail?
>
Hi Noah,
"axis" will let you choose the positions, but may leave some out if it
thinks they are too close. "staxlab" (plotrix) allows you to specify
positions and labels and can stagger or rotate the labels. zoomInPlot is
only one way to show a section of the plot next to the original.
zoomplot (TeachingDemos) allows you to zoom on the same plot. There are
other functions that offer different zooming methods.
Jim
------------------------------
Message: 159
Date: Tue, 23 Nov 2010 09:47:50 +0100
From: Petr PIKAL <petr.pikal at precheza.cz>
To: madr <madrazel at interia.pl>
Cc: r-help at r-project.org
Subject: Re: [R] how to get rid of unused space on all 4 borders in
plot() render
Message-ID:
<OF5F77406D.9CCFFDAC-ONC12577E4.002F5706-C12577E4.00306366 at precheza.
cz>
Content-Type: text/plain; charset="US-ASCII"
Hi
r-help-bounces at r-project.org napsal dne 21.11.2010 19:31:33:
>
> I have looked into par documentation, and only setting for size of the
plot> area was pin. But this setting sets the area as inflexible, that is no
R intro manual
Chapter 12: Graphical procedures page, 71
A typical figure is....
>From that you can find that
pin
The current plot dimensions, (width,height), in inches.
mar
A numerical vector of the form c(bottom, left, top, right) which gives the
number of lines of margin to be specified on the four sides of the plot.
The default is c(5, 4, 4, 2) + 0.1.
So David's remark to look at provided documentation seems to be correct. R
is not Tetris but comes with quite good documentation and you shall use
it. It would help you a lot.
par(mar=c(2,1,1,1)+.1)
Regards
Petr
> matter how I make the window small or big it stays the same. Default
value> has advantage that however it uses plot area that is always smaller than
> device area still this area is changing with the window and able to be
> bigger.
> --
> View this message in context:
http://r.789695.n4.nabble.com/how-to-get-rid-of-> unused-space-on-all-4-borders-in-plot-render-tp3052527p3052631.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 160
Date: Tue, 23 Nov 2010 09:56:25 +0100
From: Ivan Calandra <ivan.calandra at uni-hamburg.de>
To: r-help at r-project.org
Subject: Re: [R] how to loop through variables in R?
Message-ID: <4CEB81B9.8050901 at uni-hamburg.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi!
You haven't got any answer probably because you didn't provide a
reproducible example. You can do it by copy/pasting the output of
dput(d) or dput(df).
Moreover, before this email, I couldn't really understand what you were
trying to do. It's not crystal clear now, but I think I got it.
First, when you read your txt, don't you already have the correct
data.frame? What is the difference between d and df? It looks like your
cbind() step is complicated. You can also index columns by their index
numbers.
So let's say you want in df the columns 1 to 5 and 6 to 8 from d. You
can do it like this:
sel <- c(1:5,6:8) ## creates a vector with the columns indexes you want
to have in df
df <- d[, sel] ## extract these columns from d and assign it into
[[elided Yahoo spam]]
You can also so it in one step of course:
df <- d[, c(1:5,6:8)]
Second, in your loop, you overwrite at each iteration the result from
the previous one. You could do something like this:
result <- numeric(length(df)) ## shouldn't it be length(df)-1?
for (i in 1:(length(df)-1)) {
result[i] <- chisq.test(table(df[[i]], df[[i+1]])) ## each
computation will be stored in a different element of result
}
Next, chisq.test() returns a list, so it's not really a good idea to
store the output in a vector.
Take a look at
str(chisq.test(table(df[[1]], df[[2]])))
to know which element(s) you want to keep.
You would probably want something like this:
chisq.test(table(df[[1]], df[[2]]))[1:3]
[[elided Yahoo spam]]
result <- vector(mode="list", length=length(df)) ## create a list,
shouldn't it here also be length(df)-1?
names(result) <- paste("chisq_df[[", 1:length(df),
"]]_df[[",
(1:length(df))+1, "]]", sep="") ## that way, your list is
named, which
is easier to remember what is
## what if you have lots of columns
for (i in 1:(length(df)-1)) {
result[[i]] <- chisq.test(table(df[[i]], df[[i+1]]))[1:3] ## each
computation will be stored in a different element of the list
}
Is it what you're looking for?
HTH,
Ivan
Le 11/23/2010 03:11, watashi at post.com a ?crit :>
> d<-read.table("D:\\Working\\Statics.txt")
>
> df<- cbind("Q1", "Q2", "Q3",
"Q4", "Q5", "Q5A", "Q5B",
"Q5C", "Q5D",
"Q5E", "Q5F", "Q5G", "Q6",
"Q6A", "Q6B", "Q6C", "Q6D",
"Q6E", "Q6F", "Q7",
"Q8", "Q9")> #Than you can loop through them simply by doing:
> result<- numeric(length(df))
> for (i in 1:(length(df)-1)) {
> result<- chisq.test(table(df[[i]], df[[i+1]]))
> }
>
> and then this error comes out:
>
> Error: unexpected '}' in "}"
>
>
> and how can I redirect the output of the chi-square test to a file instead
of console output?>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
Abt. S?ugetiere
Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231
ivan.calandra at uni-hamburg.de
**********
http://www.for771.uni-bonn.de
http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php
------------------------------
Message: 161
Date: Tue, 23 Nov 2010 10:13:18 +0100
From: Petr PIKAL <petr.pikal at precheza.cz>
To: "Ni, Melody Zhifang" <z.ni at imperial.ac.uk>
Cc: "'r-help at r-project.org'" <r-help at
r-project.org>
Subject: [R] Odp: save a regression model that can be used later
Message-ID:
<OF688B8342.0757530D-ONC12577E4.0032343E-C12577E4.0032B81A at precheza.
cz>
Content-Type: text/plain; charset="US-ASCII"
Hi
r-help-bounces at r-project.org napsal dne 22.11.2010 16:02:20:
> Hi everyone
>
> I have a question about how to save a regression model in R and how to
> retrieve it for making predictions in a new session.
>
> To be more specific, I fitted a multilevel logistic regression model
using the> lmer from the "lme4" package. I then successfully make
predictions
using > fitted(mymodel).
>
> Since data are complex (three levels, nested, numerous categorical and
> continuous data describing types of laparoscopic surgery), the computer
takes > quite a while to fit the MLM model. I wonder whether it's possible to
save > the fitted model so that I don't have to fit it again for making
predictions > every time I start a new R session.
When you quit R session with option save =Yes you get a file .Rdata.
Whenever you start R with this file you get saved environment back,
together with your "mymodel".
I recommend for each bigger task to create separate directory in which you
can save your .Rhelp and .Rdata file without interfering other tasks.
Regards
Petr
>
> I searched the mailing-list archive. Suggestions include using save ()
to save> the model as "mymodel.rda" and then use load(mymodel.rda) into
the
workspace. > I tried without success (in Windows), returning the error message:
"Error in > object$fitted : $ operator is invalid for atomic vectors"
>
> Did I do anything wrong? Any help on this topic is much appreciated
1.11 Data permanency and removing objects
from R-intro
Regards
Petr
>
> BW, Melody
>
> --
> Dr Melody Ni
> Imperial College
> Department of Surgery and Cancer
> 10th floor, QEQM Building
> St. Mary's Hospital
> London W2 1NY
> Tel/Fax: +44 (0) 20 331 27657/26309
> z.ni at imperial.ac.uk<mailto:z.ni at imperial.ac.uk>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 162
Date: Tue, 23 Nov 2010 01:14:03 -0800
From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
To: Dimitri Shvorob <dimitri.shvorob at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Lost in POSIX
Message-ID: <4CEB85DB.8010203 at dcn.davis.ca.us>
Content-Type: text/plain; charset=us-ascii; format=flowed
Dimitri Shvorob wrote:>> Nor would I call this much of an improvement in clarity... what about
>>
> "min"? You want to know the minimum?
>
> LOL. (And apologies for the insensitivity). Thank you for help, Jeff. This
> works, but I am still curious to see a solution based on "trunc",
if
anyone> can find it.
>
You mean like
trunc(df$t,units="mins")
?
See ?trunc.POSIXt for hints on arguments to "units" parameter...
------------------------------
Message: 163
Date: Tue, 23 Nov 2010 01:21:29 -0800 (PST)
To: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
Cc: r-help at r-project.org
Subject: Re: [R] About available datasets on PC
Message-ID: <976004.93861.qm at web113205.mail.gq1.yahoo.com>
Content-Type: text/plain; charset=utf-8
Hi Jeff,
Tks for your advice. I got it
B.R.
satimis
----- Original Message ----
From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
Cc: r-help at r-project.org
Sent: Tue, November 23, 2010 4:41:57 PM
Subject: Re: [R] About available datasets on PC
You need to load the package and then load the data:
library(AER)
data("DJFranses")
then it will be available for you to work with.
Stephen Liu wrote:> Hi folks,
>
> Win7
>
>
> On running;
> data(package = .packages(all.available = TRUE))
>
> it displays a list of datasets under:-
> Data sets in package ?AER?:
>
> But I couldn't call/load all of them on the list.
>
>
>> DJFranses
>>
> Error: object 'DJFranses' not found
>
>
>> CreditCard
>>
> Error: object 'CreditCard' not found
>
>
> But I can call/load;
>
>> iris
>>
>
> Whether the list shows all available datasets on repo, NOT the datasets
already >
> download/installed on PC? If YES how to find the running/available
datasets on >
> PC?
>
>
> Packages -> Load Datasets
> the list looks different.
>
>
> Pls advise. TIA
>
> B.R.
> Stephen L
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 164
Date: Tue, 23 Nov 2010 12:16:36 +0200
From: Tal Galili <tal.galili at gmail.com>
To: gireesh bogu <girishbogu at gmail.com>
Cc: R-help at r-project.org
Subject: Re: [R] Calculating correlation
Message-ID:
<AANLkTi=0fzzzrZ5kCf6thcVyDSzm2+2c=qEGr_pW1rVZ at mail.gmail.com>
Content-Type: text/plain
Hi Gireesh,
I seem to be missing something.
Could you give me the formula you think should be used to calculate this?
I don't get how you wish to get a "correlation" for only one pair
of
numbers.
(or maybe I didn't understood what you explained - please try a simpler
example)
----------------Contact
Details:-------------------------------------------------------
Contact me: Tal.Galili at gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
----------------------------------------------------------------------------
------------------
On Tue, Nov 23, 2010 at 10:03 AM, gireesh bogu <girishbogu at gmail.com>
wrote:
> in one output
>
> x - S1 i.e. 112 with all combinations ex:
>
>
> 112 vs 3 [ x-S1 vs a -S1]
>
> 112 vs 4 [ x-S1 vs a- S2 ]
>
> 112 vs 45
>
> 112 vs 34
>
> 112 vs 23
>
> 112 vs 112
>
> .
>
> ..
>
> 112 vs 1
>
>
> in second output
>
> x - S2 i.e. 0 with all . ex:
>
> 0 vs 3
>
> 0 vs 4
>
>
>
>
>
> 0 vs 1
>
>
> in next output
>
> x-S3 i.e. 12 with all and so on
>
>
> Probably in the given input I should get 5 outputs because of 5 samples
> S1,2,3,4,n.
>
> If they are more like 69 or some thing then I should get 69 outputs or
> everything in one output if possible.
>
>
> Please let me know if it is still confusing.
>
>
> thanx
>
> On Tue, Nov 23, 2010 at 3:35 PM, Tal Galili <tal.galili at gmail.com>
wrote:
>
>> Hi there,
>> I'm not sure I understand your question.
>>
>> What are the two vectors you wish to check their correlation?
>> Are they the two rows x and a?
>> Because from your example it seems you are trying to do a correlation
>> between two singular numbers (so probably I didn't get something
straight).>>
>> Tal
>>
>>
>>
>> ----------------Contact
>> Details:-------------------------------------------------------
>> Contact me: Tal.Galili at gmail.com | 972-52-7275845
>> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew)
|
>> www.r-statistics.com (English)
>>
>>
----------------------------------------------------------------------------
------------------>>
>>
>>
>>
>> On Tue, Nov 23, 2010 at 8:57 AM, gireesh bogu
<girishbogu at gmail.com>wrote:>>
>>> Hi guys
>>>
>>> I have an input file with multiple columns and and rows.
>>> Is it possible to calculate correlation of certain value of certain
No
>>> (For
>>> example x of S1 = 112) with all other values (for example start
with x
>>> 112
>>> corr a 3 of S1 = x-a 0.2 )
>>>
>>> INPUT
>>> *******
>>>
>>> No S1 S2 S3 S4 Sn
>>> a 3 4 45 34 23
>>> x 112 0 12 23 0
>>> b 0 1 23 12 1
>>> n 0 1 0 1 1
>>>
>>> OUTPUT
>>> ***********
>>>
>>> No S1 S2 S3 S4 Sn
>>> x-a 0.2 0.3 ...............
>>> x-x 1 1 ................
>>> x-b 0..........................
>>> x-n 0.9 .......................
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>
>
> --
> Regards
>
> Gireesh
> #HP#8375-9256
>
[[alternative HTML version deleted]]
------------------------------
_______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
End of R-help Digest, Vol 93, Issue 23
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