Sharma, Dhruv
2010-Dec-11 22:45 UTC
[R] is there a packge or code to generate markov chains in R
Hi,
if i have data in the following time series format:
time, amount, state
1 2222 A
1 333 B
2 45 A
2 77 B
where states could be n and time periods t is there a package in R that would
calculate the transition probabilities in a markov chain.
for each t except t=0 to generate
A B
A
B
perhaps the best structure might be t, AA, AB, BA, BB.
is there already a package for this ? i know i could hard code a solution but i
was hoping there is a package for this so if thre are t time windows then t-1
markov chains could be generated.
hope this makes sense.
thanks
Dhruv
-----Original Message-----
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Today's Topics:
1. Need help on nnet (jothy)
2. Re: How to enable Arial font for postcript/pdf figure on
Windows? (Camille)
3. [R-pkgs] pgfSweave 1.1.1 Released (Cameron Bracken)
4. Compare one level of a factor with *all* other non-missing
levels (deriK2000)
5. subset with two factors (Martin Spindler)
6. Re: [lattice xyplot] Help needed in help in customizing the
panel.abline() function (Felix Andrews)
7. Re: subset with two factors (Michael Bedward)
8. Re: [lattice xyplot] Help needed in help in customizing the
panel.abline() function (Girish A.R.)
9. New Installs, Same Trouble Loading doBy and coin Packages
(Adam Carr)
10. Help..Neural Network (sadanandan)
11. Re: subset with two factors (Martin Spindler)
12. Re: ReadWrite.xls problem (Hans-Peter Suter)
13. Re: New Installs, Same Trouble Loading doBy and coin Packages
(Peter Ehlers)
14. Re: Using Lagsarlm (Roger Bivand)
15. Re: Projecting data on a world map using long/lat (Michael Sumner)
16. Adding numbers in Outputs (Amelia Vettori)
17. Re: Compare one level of a factor with *all* other
non-missing levels (Peter Ehlers)
18. Re: Sweave: Setting options with SweaveOpts{} when using
driver=RweaveHTML (Duncan Murdoch)
19. Re: Adding numbers in Outputs (jim holtman)
20. Re: Adding numbers in Outputs (Peter Ehlers)
21. Re: Adding numbers in Outputs (Jinyan Huang)
22. Re: Compare one level of a factor with *all* other
non-missing levels (deriK2000)
23. Re: Adding numbers in Outputs (Amelia Vettori)
24. (no subject) (andrija djurovic)
25. Re: (no subject) (jim holtman)
26. melt causes errors when characters and values are used
(Daniel Brewer)
27. Re: ReadWrite.xls problem (haruo0409)
28. Re: Adding numbers in Outputs (jim holtman)
29. Re: (no subject) (David L Lorenz)
30. Textwrangler Languages Folder (Scott Chamberlain)
31. Re: Minimization of the distance (bluesky)
32. [r] overlap different line in a xyplot (lattice)
(Francesco Nutini)
33. Re: survival: ridge log-likelihood workaround (Terry Therneau)
34. Re: Textwrangler Languages Folder (Ben Tupper)
35. Remove 100 years from a date object (Daniel Brewer)
36. help requested (profaar)
37. 45 Degree labels on barplot? Help understanding code
previously posted. (Simon Kiss)
38. Re: Remove 100 years from a date object (Barry Rowlingson)
39. Re: help requested (Jinyan Huang)
40. Re: help requested (Henrique Dallazuanna)
41. survreg vs. aftreg (eha) - the relationship between fitted
coefficients? (Eleni Rapsomaniki)
42. Re: Remove 100 years from a date object (Clint Bowman)
43. Re: Remove 100 years from a date object (Gabor Grothendieck)
44. Stricter read.table? (Stavros Macrakis)
45. Re: Remove 100 years from a date object (Daniel Brewer)
46. Re: Perl "cut" equivalent in R (Martin Maechler)
47. Re: Projecting data on a world map using long/lat (mathijsdevaan)
48. Re: Perl "cut" equivalent in R (William Dunlap)
49. new edition of R Companion to Applied Regression (John Fox)
50. Re: help requested (Mike Marchywka)
51. Re: Perl "cut" equivalent in R (Duncan Murdoch)
52. Re: [r] overlap different line in a xyplot (lattice)
(Peter Ehlers)
53. Could concurrent R sessions mix up variables? (Anthony Damico)
54. help with RSQLite adding a new column (Michael D)
55. Re: help requested (Petr Savicky)
56. Re: 45 Degree labels on barplot? Help understanding code
previously posted. (David Winsemius)
57. Re: Could concurrent R sessions mix up variables? (Duncan Murdoch)
58. Re: Could concurrent R sessions mix up variables? (Phil Spector)
59. survival package - calculating probability to survive a given
time (Andreas Wittmann)
60. Re: Compare one level of a factor with *all* other
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61. Re: survival package - calculating probability to survive a
given time (David Winsemius)
62. Reorder factor and address embedded escapes (Rob James)
63. Time Series Row Label (dreadgazebo)
64. Re: Reorder factor and address embedded escapes (Erik Iverson)
65. Re: Reorder factor and address embedded escapes (David Winsemius)
66. Re: Encoding problem - I fails to read Hebrew text from
online (Tal Galili)
67. spatial clusters (dorina.lazar)
68. Re: Time Series Row Label (Gabor Grothendieck)
69. WriteXLS error:Error in get(x, envir = envir) : variable
names are limited to 256 bytes (Patrick McKann)
70. How to print colorful R output?? (casperyc)
71. Re: WriteXLS error:Error in get(x, envir = envir) : variable
names are limited to 256 bytes (David Winsemius)
72. Re: WriteXLS error:Error in get(x, envir = envir) : variable
names are limited to 256 bytes (David Winsemius)
73. Re: Stricter read.table? (Ben Bolker)
74. Quantile with discrete types (Stavros Macrakis)
75. Re: [r] overlap different line in a xyplot (lattice) (Ben Bolker)
76. locfit weights not working as expected (Layla Parast)
77. R question: memory usage (simon lu)
78. randomForest: help with combine() function (Dennis Duro)
79. Re: How to print colorful R output?? (Yihui Xie)
80. Re: WriteXLS error:Error in get(x, envir = envir) : variable
names are limited to 256 bytes (Marc Schwartz)
81. Re: How to print colorful R output?? (Liviu Andronic)
82. Re: help with RSQLite adding a new column (Michael Bedward)
83. Re: 45 Degree labels on barplot? Help understanding code
previously posted. (Jim Lemon)
84. Re: Adding numbers in Outputs (Petr PIKAL)
----------------------------------------------------------------------
Message: 1
Date: Fri, 10 Dec 2010 02:56:13 -0800 (PST)
From: jothy <gnanajothyk at gmail.com>
To: r-help at r-project.org
Subject: [R] Need help on nnet
Message-ID:
<AANLkTikK7qyrFZPyuSZMqDZV17GQhZMYdU0pZjhcbL8m at mail.gmail.com>
Content-Type: text/plain
Hi,
Am working on neural network.
Below is the coding and the output
> library (nnet)
> uplift.nn<-nnet (PVU~ConsumerValue+Duration+PromoVolShare,y,size=3)
# weights: 16
initial value 4068.052704
final value 3434.194253
converged
> summary (uplift.nn)
a 3-3-1 network with 16 weights
options were -
b->h1 i1->h1 i2->h1 i3->h1
16.64 6.62 149.93 2.24
b->h2 i1->h2 i2->h2 i3->h2
-42.79 -17.40 -507.50 -5.14
b->h3 i1->h3 i2->h3 i3->h3
3.45 1.87 18.89 0.61
b->o h1->o h2->o h3->o
402.81 41.29 236.76 6.06
I have few questions, please i need help
Q1: How to interpret the above output
Q2: My objective is to know the contribution of each independent variable.
Q3: Which package of neural network provides the AIC or BIC values
Regards
jothy
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------------------------------
Message: 2
Date: Fri, 10 Dec 2010 03:20:23 -0800 (PST)
From: Camille <c.pelat at imperial.ac.uk>
To: r-help at r-project.org
Subject: Re: [R] How to enable Arial font for postcript/pdf figure on
Windows?
Message-ID: <1291980023177-3081774.post at n4.nabble.com>
Content-Type: text/plain; charset=UTF-8
Hi Agnes,
I converted the Arial font files from ttf to afm using ttf2afm from MikTex
complete installation.
When used in R with the line recommended by Plos, they seem to give correct
Arial font graphics: I checked by opening the ps file with a viewer
(gsview), a text editor (notepad++) and Adobe illustrator.
However I did not try (but hopefully will do soon) the ultimate test:
submission to Plos.
Here is a way to do it: (Mind the trick at step 5)
1) Download ttf2afm.exe (available for ex in the install directory of MikTex
complete installation)
2) Fetch the arial ttf files in C:\Windows\Fonts
3) Place ttf2afm.exe and the ttf files in a directory (eg C:/ttf2afm/)
4) Open a DOS window (using cmd). Place yourself into the created directory
(using cd). Then type
ttf2afm.exe arial.ttf > arial.afm
ttf2afm.exe arialbd.ttf > arial-Bold.afm
ttf2afm.exe ariali.ttf > arial-Oblique.afm
ttf2afm.exe arialbi.ttf > arial-BoldOblique.afm
5) Now, if you used ttf2afm.exe from MikTex you should open the created afm
files with a text editor (ex Notepad++) and correct the following things:
? Remove the copyright line (or make it start zith comment and get rid of
the (c) copyright symbol )
? At the beginning of 4 of the first lines, the variable name is missing, so
add it. Eg in arial.afm:
o FontName ArialMT
o FullName Arial
o FamilyName Arial
o Weight Normal
Now you can use these fonts with the postscript function in R with the
following line:
postscript(file="try.ps", horizontal=F, onefile=F, width=4, height=4,
pointsize=12,
family=c (
?C:/ttf2afm/arial.afm",
?C:/ttf2afm/arial-Bold.afm ",
?C:/ttf2afm/arial-Oblique.afm ",
?C:/ttf2afm/arial-BoldOblique.afm "
)
)
hist( rnorm(100) )
dev.off()
Cheers,
Camille
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------------------------------
Message: 3
Date: Tue, 7 Dec 2010 16:26:40 -0700
From: Cameron Bracken <cameron.bracken at gmail.com>
To: R-Packages <r-packages at r-project.org>
Subject: [R] [R-pkgs] pgfSweave 1.1.1 Released
Message-ID:
<AANLkTikApA4_FpOi=PGsHZD8GM=UScK0ZRCo92dgEC++ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
The next release of?pgfSweave?is now on CRAN! pgfSweave has seen some
significant changes in the past couple of months.
The main new features are:
- Automatic code highlighting via the?highlight?package. This can be
turned off with the new `highlight`?option.
- "Tidying" of source code output via the?tidy?option.
- Access to?tikzDevice?sanitization through a code chunk option?`sanitize`
- Automatic addition of the?\pgfrealjobname?command if it does not
exist similarly to the addition of the?\usepackage{Sweave}?line.
- Setting tex.driver=latex will now (in addition to working) generate
an eps file
And of course bug fixes:
- Fixes for bunches of issues related to the changes in Sweave in R
2.12. I think these issues are now resolved (fingers crossed)
- keep.source?actually works now.
See the?NEWS?file for the complete list of changes and the?vignette
for information on now to use the new options.
Cheers!
-Cameron
_______________________________________________
R-packages mailing list
R-packages at r-project.org
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------------------------------
Message: 4
Date: Fri, 10 Dec 2010 03:24:33 -0800 (PST)
From: deriK2000 <derik2000 at yahoo.de>
To: r-help at r-project.org
Subject: [R] Compare one level of a factor with *all* other
non-missing levels
Message-ID: <1291980273092-3081777.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Dear list,
I try to compare the mean of a variable given a value of a factor with the
mean of the same variable for all K-1 other non-missing values of this
factor. This procedure I want to repeat for each level of the factor.
Having read the recommendations of this list I want to avoid creating K-1
dummy variables and searched for options of the pairwise.t.test. But
couldn't find a solution. Anyone with a suggestion how to do the
comparisions?
Cheers,
Derik
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------------------------------
Message: 5
Date: Fri, 10 Dec 2010 12:25:13 +0100
From: "Martin Spindler" <Martin.Spindler at gmx.de>
To: r-help at R-project.org
Subject: [R] subset with two factors
Message-ID: <20101210112513.214200 at gmx.net>
Content-Type: text/plain; charset="utf-8"
Dear all,
I have a dataframe of the following strucutre
numacc_b coverage_b Geschlecht GG
1 0 1 W A
2 0 1 M A
3 0 1 M B
4 0 1 M B
5 0 1 W A
6 0 1 M B
I would like to form a subset consisting of all entries with Geschlecht=M and
GG=A.
Using
>T1 <- subset(daten1, Geschlecht=="M", GG=="A")
delievers
data frame with 0 columns and 6 rows
> T1 <- subset(daten1, Geschlecht=="M")
delievers
numacc_b coverage_b Geschlecht GG
2 0 1 M A
3 0 1 M B
4 0 1 M B
6 0 1 M B
9 0 1 M B
10 0 1 M B
But I want to select the dataframe according to both factos.
What can I do?
[[elided Yahoo spam]]
Best,
Martin
--
GMX DSL Doppel-Flat ab 19,99 €/mtl.! Jetzt auch mit
gratis Notebook-Flat! http://portal.gmx.net/de/go/dsl
------------------------------
Message: 6
Date: Fri, 10 Dec 2010 22:33:11 +1100
From: Felix Andrews <felix at nfrac.org>
To: "Girish A.R." <garamach at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] [lattice xyplot] Help needed in help in customizing
the panel.abline() function
Message-ID:
<AANLkTimD6dRUkkjEhW4-sB8CBDcFVASRRKkF6Xex+cb9 at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Girish,
Try this:
disc <- xyplot(cnt_gt50pct_disc ~ week_num|sku_num, data=DF,type
"h",lwd=2,panel = function(x, y, ...) {
panel.abline(v = x[which.max(y)], lty = 2)
panel.xyplot(x, y, ...)
})
-Felix
On 9 December 2010 17:35, Girish A.R. <garamach at gmail.com>
wrote:>
> Hi folks,
>
> I need some help in customizing the abline() function to be used in a
> lattice plot. I have attached a reproducible example below.
>
> I need help in the following snippet:
> disc <- xyplot(cnt_gt50pct_disc ~ week_num|sku_num, data=DF,type >
"h",lwd=2,panel = function(...) {
> ? ? ? ? ? panel.abline(v = 8, lty = 2)
> ? ? ? ? ? panel.xyplot(...)
> ? ? ? })
>
> Is there a way I can give panel.abline() input from a which.max() function?
> Essentially I need the vertical line to be drawn at the week_num
> corresponding to the max (cnt_gt50pct_disc).
>
> Thanks in advance,
>
> -Girish
>
> ==========================================> Lines <- "sku_num
week_num ? ?pct_inv_left ? ?cnt_gt50pct_disc
> 1 ? 1 ? 99.88 ? 47
> 1 ? 2 ? 99.54 ? 109
> 1 ? 3 ? 98.7 ? ?260
> 1 ? 4 ? 97.83 ? 202
> 1 ? 5 ? 96.53 ? 389
> 1 ? 6 ? 94.11 ? 450
> 1 ? 7 ? 90.42 ? 459
> 1 ? 8 ? 86.63 ? 448
> 1 ? 9 ? 83.39 ? 411
> 1 ? 10 ?77 ?478
> 1 ? 11 ?71.65 ? 476
> 1 ? 12 ?67.3 ? ?463
> 1 ? 13 ?62.45 ? 472
> 1 ? 14 ?52.47 ? 488
> 1 ? 15 ?40.86 ? 486
> 1 ? 16 ?31.34 ? 484
> 1 ? 17 ?23.2 ? ?472
> 1 ? 18 ?17 ?458
> 1 ? 19 ?12.66 ? 423
> 1 ? 20 ?10.18 ? 364
> 1 ? 21 ?7.6 343
> 1 ? 22 ?3.09 ? ?343
> 1 ? 23 ?1.05 ? ?211
> 2 ? 1 ? 99.94 ? 30
> 2 ? 2 ? 99.4 ? ?151
> 2 ? 3 ? 98.85 ? 146
> 2 ? 4 ? 97.92 ? 274
> 2 ? 5 ? 97.03 ? 204
> 2 ? 6 ? 95.59 ? 378
> 2 ? 7 ? 92.81 ? 452
> 2 ? 8 ? 89.07 ? 470
> 2 ? 9 ? 85.11 ? 454
> 2 ? 10 ?81.68 ? 421
> 2 ? 11 ?75.34 ? 479
> 2 ? 12 ?70.05 ? 476
> 2 ? 13 ?66.11 ? 456
> 2 ? 14 ?61.85 ? 465
> 2 ? 15 ?53.2 ? ?485
> 2 ? 16 ?42.75 ? 486
> 2 ? 17 ?33.58 ? 481
> 2 ? 18 ?25 ?477
> 2 ? 19 ?18.13 ? 450
> 2 ? 20 ?12.97 ? 416
> 2 ? 21 ?10.03 ? 343
> 2 ? 22 ?7.03 ? ?293
> 2 ? 23 ?2.33 ? ?283
> 2 ? 24 ?0.77 ? ?116
> "
>
> DF <- read.table(con<- textConnection(Lines), skip = 1);
> names(DF) <- scan(textConnection(Lines), what = "", nlines =
1) ;
> close(con);
>
> require(latticeExtra)
> DF$sku_num <- as.factor(DF$sku_num)
> disc <- xyplot(cnt_gt50pct_disc ~ week_num|sku_num, data=DF,type >
"h",lwd=2,panel = function(...) {
> ? ? ? ? ? panel.abline(v = 8, lty = 2)
> ? ? ? ? ? panel.xyplot(...)
> ? ? ? })
> sales <- xyplot(pct_inv_left ?~ week_num|sku_num, data=swtop16,type >
"l",lwd=2,panel = function(...) {
> ? ? ? ? ? panel.abline(h = 75, lty = 2)
> ? ? ? ? ? panel.xyplot(...)
> ? ? ? })
> doubleYScale(disc, sales, style1 = 0, style2 = 2, add.ylab2 = TRUE,text
> c("# stores with gt 50pct disc", "% Unsold"))
> --
> View this message in context:
http://r.789695.n4.nabble.com/lattice-xyplot-Help-needed-in-help-in-customizing-the-panel-abline-function-tp3079656p3079656.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.
>
--
Felix Andrews / ???
http://www.neurofractal.org/felix/
------------------------------
Message: 7
Date: Fri, 10 Dec 2010 22:35:56 +1100
From: Michael Bedward <michael.bedward at gmail.com>
To: Martin Spindler <Martin.Spindler at gmx.de>
Cc: r-help at r-project.org
Subject: Re: [R] subset with two factors
Message-ID:
<AANLkTikspbP6oyxaxTYAf6ua_eW3-DkfYk4KWWUcb3bW at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hello Martin,
You were almost there :)
T1 <- subset(daten1, Geschlecht=="M" & GG=="A")
Hope this helps.
Michael
On 10 December 2010 22:25, Martin Spindler <Martin.Spindler at gmx.de>
wrote:> Dear all,
>
> I have a dataframe of the following strucutre
>
> ?numacc_b coverage_b Geschlecht GG
> 1 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?W ?A
> 2 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?A
> 3 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> 4 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> 5 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?W ?A
> 6 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
>
> I would like to form a subset consisting of all entries with Geschlecht=M
and GG=A.
>
> Using
>
>>T1 <- subset(daten1, Geschlecht=="M", GG=="A")
>
> delievers
>
> data frame with 0 columns and 6 rows
>
>> T1 <- subset(daten1, Geschlecht=="M")
>
> delievers
>
> ?numacc_b coverage_b Geschlecht GG
> 2 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?A
> 3 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> 4 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> 6 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> 9 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> 10 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
>
> But I want to select the dataframe according to both factos.
>
> What can I do?
>
[[elided Yahoo spam]]>
> Best,
>
> Martin
> --
> GMX DSL Doppel-Flat ab 19,99 €/mtl.! Jetzt auch mit
> gratis Notebook-Flat! http://portal.gmx.net/de/go/dsl
>
> ______________________________________________
> 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: 8
Date: Fri, 10 Dec 2010 03:38:03 -0800 (PST)
From: "Girish A.R." <garamach at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] [lattice xyplot] Help needed in help in customizing
the panel.abline() function
Message-ID: <1291981083178-3081792.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Thanks, Felix! That works.
best,
-Girish
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Message: 9
Date: Fri, 10 Dec 2010 03:43:18 -0800 (PST)
From: Adam Carr <adamlcarr at yahoo.com>
To: r-help at r-project.org
Subject: [R] New Installs, Same Trouble Loading doBy and coin Packages
Message-ID: <539652.57795.qm at web35307.mail.mud.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
I tried Tal's suggestion of deleting the doBy and coin packages and then
reinstalling them from a different mirror. The first install was from the
Harvard mirror and the second was from the Case Western Univ. mirror. The new
packages generate the same errors when I call them using the library() command.
Also, I tried to load these packages using R and its script editor thinking that
the problem may have something to do with Tinn-R, but the same errors are
generated on the R terminal when I use the library() function.
Any help would be appreciated.
Again, the errors for these two packages:
Error in length(label) : could not find function ".extendsForS3"
Error: package/namespace load failed for 'doBy'
> library(coin)
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4? #This is odd. I cannot find any reference for
this package. AC
Error in length(sig) : could not find function ".extendsForS3"
Error: package 'stats4' could not be loaded
----- Forwarded Message ----
From: Adam Carr <adamlcarr at yahoo.com>
To: Tal Galili <tal.galili at gmail.com>
Cc: r-help at r-project.org
Sent: Thu, December 9, 2010 1:12:21 PM
Subject: Re: [R] Trouble Loading doBy and coin Packages
Hi Tal:
No I have not tried this. I will do it this evening and we'll see what
happens.
Thanks for the suggestion.
Adam
________________________________
From: Tal Galili <tal.galili at gmail.com>
Cc: r-help at r-project.org
Sent: Thu, December 9, 2010 12:29:20 PM
Subject: Re: [R] Trouble Loading doBy and coin Packages
I Adam,
Have you tried deleting the package files and then reinstalling them from a
different CRAN mirror?
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)
----------------------------------------------------------------------------------------------
Good Evening R-Help Community:>
>I have attached a file that contains the output from sessionInfo() and a
summary>of my Win XP system. I am?running R 2.12.0 and using Tinn-R 2.3.6.2 as my
>interface. When I attempt to call either the doBy or coin packages R
generates
>an error that I do not understand and have so far not been able to resolve
by
>searching R resources.
>
>I exchanged a couple of emails with Soren Hojsgaard who does not think the
doBy
>error is directly related to the package itself, and he suggested that I
post
>this problem for input from others.
>
>When the doBy package is loaded, the following error appears in the Tinn-R
log:
>
>Error in length(label) : could not find function ".extendsForS3"
>Error: package/namespace load failed for 'doBy'
>
>When the coin package is called, this error appears in the Tinn-R log:
>
>Error in length(sig) : could not find function ".extendsForS3"
>Error: package 'stats4' could not be loaded
>
>No functions in either package work, and when I attempt to call them the
same
>errors are generated in the log.
>
>Any help or direction would be appreciated.
>
>Thanks very much,
>
>Adam
>
>
>? ? ?
>______________________________________________
>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]]
-------------- next part --------------
______________________________________________
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: 10
Date: Fri, 10 Dec 2010 03:45:46 -0800 (PST)
From: sadanandan <sudeesh.sadanandan at gmail.com>
To: r-help at r-project.org
Subject: [R] Help..Neural Network
Message-ID: <1291981546611-3081800.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi all,
I am trying to develop a neural network with single target variable and 5
input variables to predict the importance of input variables using R. I used
the packages nnet and RSNNS. But unfortunately I could not interpret the out
put properly and the documentation of that packages also not giving proper
direction. Please help me to find a good package with a proper documentation
for neural network.
Advance thanks
s.sadanand
--
View this message in context:
http://r.789695.n4.nabble.com/Help-Neural-Network-tp3081800p3081800.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 11
Date: Fri, 10 Dec 2010 12:47:27 +0100
From: "Martin Spindler" <Martin.Spindler at gmx.de>
To: r-help at r-project.org
Subject: Re: [R] subset with two factors
Message-ID: <20101210114727.128910 at gmx.net>
Content-Type: text/plain; charset="utf-8"
Hey Michael,
[[elided Yahoo spam]]
Best,
Martin
-------- Original-Nachricht --------> Datum: Fri, 10 Dec 2010 22:35:56 +1100
> Von: Michael Bedward <michael.bedward at gmail.com>
> An: Martin Spindler <Martin.Spindler at gmx.de>
> CC: r-help at r-project.org
> Betreff: Re: [R] subset with two factors
> Hello Martin,
>
> You were almost there :)
>
> T1 <- subset(daten1, Geschlecht=="M" & GG=="A")
>
> Hope this helps.
>
> Michael
>
> On 10 December 2010 22:25, Martin Spindler <Martin.Spindler at
gmx.de> wrote:
> > Dear all,
> >
> > I have a dataframe of the following strucutre
> >
> > ?numacc_b coverage_b Geschlecht GG
> > 1 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?W ?A
> > 2 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?A
> > 3 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> > 4 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> > 5 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?W ?A
> > 6 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> >
> > I would like to form a subset consisting of all entries with
> Geschlecht=M and GG=A.
> >
> > Using
> >
> >>T1 <- subset(daten1, Geschlecht=="M",
GG=="A")
> >
> > delievers
> >
> > data frame with 0 columns and 6 rows
> >
> >> T1 <- subset(daten1, Geschlecht=="M")
> >
> > delievers
> >
> > ?numacc_b coverage_b Geschlecht GG
> > 2 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?A
> > 3 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> > 4 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> > 6 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> > 9 ? ? ? ? 0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> > 10 ? ? ? ?0 ? ? ? ? ?1 ? ? ? ? ?M ?B
> >
> > But I want to select the dataframe according to both factos.
> >
> > What can I do?
> >
[[elided Yahoo spam]]> >
> > Best,
> >
> > Martin
> > --
> > GMX DSL Doppel-Flat ab 19,99 €/mtl.! Jetzt auch mit
> > gratis Notebook-Flat! http://portal.gmx.net/de/go/dsl
> >
> > ______________________________________________
> > 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.
> >
--
GRATIS! Movie-FLAT mit ?ber 300 Videos.
--
GMX DSL Doppel-Flat ab 19,99 €/mtl.! Jetzt auch mit
gratis Notebook-Flat! http://portal.gmx.net/de/go/dsl
------------------------------
Message: 12
Date: Fri, 10 Dec 2010 12:56:59 +0100
From: Hans-Peter Suter <gchappi at gmail.com>
To: tkdweber <tkd.weber at gmail.com>, eixcxisx at bca.bai.ne.jp
Cc: r-help at r-project.org
Subject: Re: [R] ReadWrite.xls problem
Message-ID:
<AANLkTi=qon_=O+4so7Au-_gRYjGOouEbPnnQ954G+qqw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Toby, haruo0409,
2010/12/8 tkdweber <tkd.weber at gmail.com>:> This is my Error-Message in its German original:
> Fehler in .Call("ReadXls", file, colNames, sheet, type, from,
rowNames, ?:
> ?Falsche Anzahl von Argumenten (11), erwarte 10 f?r ReadXls
There was a wrong DLL for a short while in the old 1.5.2 version (I
fixed a R2.12.0 related issue and unfortunately introduced this
error). If you delete the old xlsReadWrite package and re-install the
package (either from CRAN or see www.swissr.org/download) it really
should work.
2010/12/10 haruo0409 <eixcxisx at bca.bai.ne.jp>:> I'm also annoyed at same problem.
> I installed xlsReadWriter today and entered
> x <- read.xls("data.xls",sheet=1)
> But I got Error Message:
> ?????? .Call("ReadXls", file, colNames, sheet, type, from,
rowNames, :
> ?????(11)??????10 ?? ReadXls ?????????
> (It's Japanese.Its English translation is the same as yours)
What's the 'library(xlsReadWrite)' startup message? For the current
version it should be: 'xlsReadWrite version 1.5.3 (0b78c1)'. Could you
please give more details about 'I installed xlsReadWriter today'
(which CRAN mirror, 'R.version' and '.Platform' output, is there
only
one 'xlsReadWrite.dll' file on your system). It is supposed to work
[[elided Yahoo spam]]
2010/12/8 tkdweber <tkd.weber at gmail.com>:>Without being able to read data, the
> programme renders pointless for me :-(
There are many ways to read/write data in R:
* Other than load/save you could use read.table/write.table (see R
Data Import/Export).
* Using Excel files is not the recommended way. However when you
want/need it, there are several options (see
http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windows)
Cheers,
Hans-Peter
PS. not that I mind to discuss things here, but as these are package
specific problems I'd suggest to switch to the xlsReadWrite forum
(http://dev.swissr.org/projects/xlsreadwrite/boards). You also can
create an issue
(http://dev.swissr.org/projects/xlsreadwrite/issues/new) or just send
an email to 'support' at 'swissr.org').
------------------------------
Message: 13
Date: Fri, 10 Dec 2010 04:13:17 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
To: Adam Carr <adamlcarr at yahoo.com>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] New Installs, Same Trouble Loading doBy and coin
Packages
Message-ID: <4D02195D.6070500 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-12-10 03:43, Adam Carr wrote:> I tried Tal's suggestion of deleting the doBy and coin packages and
then
> reinstalling them from a different mirror. The first install was from the
> Harvard mirror and the second was from the Case Western Univ. mirror. The
new
> packages generate the same errors when I call them using the library()
command.
>
> Also, I tried to load these packages using R and its script editor thinking
that
> the problem may have something to do with Tinn-R, but the same errors are
> generated on the R terminal when I use the library() function.
>
> Any help would be appreciated.
>
> Again, the errors for these two packages:
>
> Error in length(label) : could not find function ".extendsForS3"
> Error: package/namespace load failed for 'doBy'
>
>
>> library(coin)
> Loading required package: mvtnorm
> Loading required package: modeltools
> Loading required package: stats4 #This is odd. I cannot find any reference
for
> this package. AC
> Error in length(sig) : could not find function ".extendsForS3"
> Error: package 'stats4' could not be loaded
>
I would remove and re-install R. 'stats4' is a base package
and if that can't be loaded, your installation may be broken.
Try
require(stats4)
or
help(package=stats4)
Peter Ehlers
>
>
>
>
> ----- Forwarded Message ----
> From: Adam Carr<adamlcarr at yahoo.com>
> To: Tal Galili<tal.galili at gmail.com>
> Cc: r-help at r-project.org
> Sent: Thu, December 9, 2010 1:12:21 PM
> Subject: Re: [R] Trouble Loading doBy and coin Packages
>
> Hi Tal:
>
> No I have not tried this. I will do it this evening and we'll see what
happens.
> Thanks for the suggestion.
>
> Adam
>
>
>
>
> ________________________________
> From: Tal Galili<tal.galili at gmail.com>
>
> Cc: r-help at r-project.org
> Sent: Thu, December 9, 2010 12:29:20 PM
> Subject: Re: [R] Trouble Loading doBy and coin Packages
>
>
> I Adam,
> Have you tried deleting the package files and then reinstalling them from a
> different CRAN mirror?
>
>
> 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)
>
----------------------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
> Good Evening R-Help Community:
>>
>> I have attached a file that contains the output from sessionInfo() and
a
> summary
>> of my Win XP system. I am running R 2.12.0 and using Tinn-R 2.3.6.2 as
my
>> interface. When I attempt to call either the doBy or coin packages R
generates
>> an error that I do not understand and have so far not been able to
resolve by
>> searching R resources.
>>
>> I exchanged a couple of emails with Soren Hojsgaard who does not think
the doBy
>> error is directly related to the package itself, and he suggested that
I post
>> this problem for input from others.
>>
>> When the doBy package is loaded, the following error appears in the
Tinn-R log:
>>
>> Error in length(label) : could not find function
".extendsForS3"
>> Error: package/namespace load failed for 'doBy'
>>
>> When the coin package is called, this error appears in the Tinn-R log:
>>
>> Error in length(sig) : could not find function
".extendsForS3"
>> Error: package 'stats4' could not be loaded
>>
>> No functions in either package work, and when I attempt to call them
the same
>> errors are generated in the log.
>>
>> Any help or direction would be appreciated.
>>
>> Thanks very much,
>>
>> Adam
>>
>>
>>
>> ______________________________________________
>> 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: 14
Date: Fri, 10 Dec 2010 04:16:31 -0800 (PST)
From: Roger Bivand <Roger.Bivand at nhh.no>
To: r-help at r-project.org
Subject: Re: [R] Using Lagsarlm
Message-ID: <1291983391495-3081833.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
This has been answered offlist (the poster also wrote directly to me as
package maintainer, but did not post on the R-sig-geo list, as would have
seemed natural). The resolution was to read ?formula, and to use either
errorsarlm() or lagsarlm() in spdep with formula=y ~ 1. Apparently an
insurance analyst in a hurry ...
Roger
Saswati Neogi wrote:>
>
>
> I'm trying to use the spdep package to calculate this:
>
> y = rho W y + e
>
> I don't want to use explanatory variables, just the lag from the
dependent
> variable.
>
> How would I code this?
>
> ______________________________________________
> 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.
>
>
-----
Roger Bivand
Economic Geography Section
Department of Economics
Norwegian School of Economics and Business Administration
Helleveien 30
N-5045 Bergen, Norway
--
View this message in context:
http://r.789695.n4.nabble.com/Using-Lagsarlm-tp3080368p3081833.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 15
Date: Sat, 11 Dec 2010 00:01:38 +1100
From: Michael Sumner <mdsumner at gmail.com>
To: Barry Rowlingson <b.rowlingson at lancaster.ac.uk>
Cc: r-help at r-project.org, mathijsdevaan <mathijsdevaan at gmail.com>
Subject: Re: [R] Projecting data on a world map using long/lat
Message-ID:
<AANLkTi=079ZiWJSZnhLfvoTneO6x=JLhtGKqNTG6my=+ at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Oh, whoops I was looking for the "vote up" button and accidentally hit
"Reply All".
On Fri, Dec 10, 2010 at 8:25 PM, Barry Rowlingson
<b.rowlingson at lancaster.ac.uk> wrote:> On Fri, Dec 10, 2010 at 2:21 AM, mathijsdevaan <mathijsdevaan at
gmail.com> wrote:
>>
>> Hi,
>>
>> I have a dataset (CSV) with some counts of firms located around the
globe.
>> Each count is assigned to the longitude and latitude of the specific
>> location. Now I want to plot these counts on a world map using dots
(size of
>> dots represent the count). I have been unable to find any info on
whether
[[elided Yahoo spam]]>>
>
> ?Plotting points is trivial - plot(data$x,data$y,pch=19,cex=data$size)
> will do for a start. i'm guessing your real problem is when you say
> 'on a world map'.
>
> ?How detailed a world map do you need? There's an outline one in the
> 'maps' package, or you should be able to find a shapefile of the
world
> on the web somewhere and use that via the rgdal package.
>
> ?Other options include making a KML file of your points and overlaying
> on google earth. Or getting google map tiles and overlaying on
> that.... Or exporting your data to a GIS format and doing the pretty
> map in something like Quantum GIS. What are you trying to do exactly?
>
> also, you might want to post to r-sig-geo
>
>
>
> Barry
>
> ______________________________________________
> 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.
>
--
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsumner at gmail.com
------------------------------
Message: 16
Date: Fri, 10 Dec 2010 02:41:12 -0800 (PST)
From: Amelia Vettori <amelia_vettori at yahoo.co.nz>
To: r-help at r-project.org
Subject: [R] Adding numbers in Outputs
Message-ID: <533730.19296.qm at web121402.mail.ne1.yahoo.com>
Content-Type: text/plain
two OutputsHello!
I am Amelia from Auckland and work for a bank. I am new to R and I have started
my venture with R just a couple of weeks back and this is my first mail to
R-forum. I need following assistance
Suppose my R code generates following outputs as
> X
[[1]]
[1] 40
[[2]]
[1] 80??? 160
[[3]]
[1] 160?? 80? 400
> Y
[[1]]
[1] 10
[[2]]
[1] 10??? 30
[[3]]
[1] 5? 18? 20
and suppose
Z = c(1, 2, 3)
I need to perform the calculation where I will be multiplying corresponding
terms of X and Y individually and multiplying their sum by Z and store these
results in a dataframe.
I.e. I need to calculate
(40*10) * 1 ??????????????????????????????? # (first element of X + First
element of Y) * Z[1] = 400
((80*10)+(160*30)) * 2???????????????? # 2 row of X and 2nd row of Y = 11200
((160*5)+(80*18)+(400*20)) * 3???? # 3rd row of X and 3 row of Y and Z[3] =?
30720
So the final output should be
400
11200
30720
One way of doing it is write R code for individual rows and
arrive at the result e.g.
([[X]][1]*[[Y]][1])*1 will result in 400. However, I was just trying to know
some smart way of doing it as there could be number of rows and writing code for
each row will be a cumbersome job. So is there any better way to do it?
Please guide me.
I thank you in advance.
Thanking
all
Amelia ????
?
[[alternative HTML version deleted]]
------------------------------
Message: 17
Date: Fri, 10 Dec 2010 05:06:39 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] Compare one level of a factor with *all* other
non-missing levels
Message-ID: <4D0225DF.40705 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-12-10 03:24, deriK2000 wrote:>
> Dear list,
>
> I try to compare the mean of a variable given a value of a factor with the
> mean of the same variable for all K-1 other non-missing values of this
> factor. This procedure I want to repeat for each level of the factor.
>
> Having read the recommendations of this list I want to avoid creating K-1
> dummy variables and searched for options of the pairwise.t.test. But
> couldn't find a solution. Anyone with a suggestion how to do the
> comparisions?
Sounds like you want the Dunnett test procedure which seems
to be implemented in a number of packages: multcomp, asd, MCPAN
and others.
It would probably be a good idea to install package 'sos' and
learn how to search with it.
Peter Ehlers
>
> Cheers,
>
> Derik
------------------------------
Message: 18
Date: Fri, 10 Dec 2010 08:31:56 -0500
From: Duncan Murdoch <murdoch.duncan at gmail.com>
To: S?ren H?jsgaard <Soren.Hojsgaard at agrsci.dk>
Cc: "r-help at stat.math.ethz.ch" <r-help at stat.math.ethz.ch>
Subject: Re: [R] Sweave: Setting options with SweaveOpts{} when using
driver=RweaveHTML
Message-ID: <4D022BCC.9020805 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 10/12/2010 3:40 AM, S?ren H?jsgaard wrote:> When using Sweave in connection with the driver RweaveLatex(), global
options can be set with \SweaveOpts{}, e.g.
> \SweaveOpts{keep.source=T}.
> Does anybody know if it is possible to set global options in the same way
when using Sweave with the driver RweaveHTML().
>
>
> I haven't used R2HTML, but it looks from the SweaveSyntaxHTML variable
that the same syntax should work there.
> Regards
> S?ren
>
> [[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: 19
Date: Fri, 10 Dec 2010 08:43:37 -0500
From: jim holtman <jholtman at gmail.com>
To: Amelia Vettori <amelia_vettori at yahoo.co.nz>
Cc: r-help at r-project.org
Subject: Re: [R] Adding numbers in Outputs
Message-ID:
<AANLkTikPfKZ56JcpaX5yRE29TYBdzE4n_Rw1DVh28dzS at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
try this:
> x <- list(40, c(80,160), c(160,80,400))
> y <- list(10, c(10,30), c(5,18,20))
> z <- c(1,2,3)
> mapply(function(a1,a2,a3){
+ a3 * sum(a1 * a2)
+ }
+ , x
+ , y
+ , z
+ )
[1] 400 11200 30720
On Fri, Dec 10, 2010 at 5:41 AM, Amelia Vettori
<amelia_vettori at yahoo.co.nz> wrote:> two OutputsHello!
>
> I am Amelia from Auckland and work for a bank. I am new to R and I have
started my venture with R just a couple of weeks back and this is my first mail
to R-forum. I need following assistance
>
> Suppose my R code generates following outputs as
>
>
>> X
> [[1]]
> [1] 40
>
> [[2]]
> [1] 80??? 160
>
> [[3]]
> [1] 160?? 80? 400
>
>
>> Y
>
> [[1]]
>
> [1] 10
>
>
>
> [[2]]
>
> [1] 10??? 30
>
>
>
> [[3]]
>
> [1] 5? 18? 20
>
> and suppose
>
> Z = c(1, 2, 3)
>
> I need to perform the calculation where I will be multiplying corresponding
terms of X and Y individually and multiplying their sum by Z and store these
results in a dataframe.
>
> I.e. I need to calculate
>
> (40*10) * 1 ??????????????????????????????? # (first element of X + First
element of Y) * Z[1] = 400
>
> ((80*10)+(160*30)) * 2???????????????? # 2 row of X and 2nd row of Y =
11200
>
> ((160*5)+(80*18)+(400*20)) * 3???? # 3rd row of X and 3 row of Y and Z[3]
=? 30720
>
>
>
> So the final output should be
>
> 400
> 11200
> 30720
>
>
> One way of doing it is write R code for individual rows and
> ?arrive at the result e.g.
>
> ([[X]][1]*[[Y]][1])*1 will result in 400. However, I was just trying to
know some smart way of doing it as there could be number of rows and writing
code for each row will be a cumbersome job. So is there any better way to do it?
>
> Please guide me.
>
> I thank you in advance.
>
> Thanking
> ?all
>
> Amelia
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ? ? ? ?[[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.
>
>
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
------------------------------
Message: 20
Date: Fri, 10 Dec 2010 05:50:56 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
To: Amelia Vettori <amelia_vettori at yahoo.co.nz>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] Adding numbers in Outputs
Message-ID: <4D023040.2030106 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-12-10 02:41, Amelia Vettori wrote:> two OutputsHello!
>
> I am Amelia from Auckland and work for a bank. I am new to R and I have
started my venture with R just a couple of weeks back and this is my first mail
to R-forum. I need following assistance
>
> Suppose my R code generates following outputs as
>
>
>> X
> [[1]]
> [1] 40
>
> [[2]]
> [1] 80 160
>
> [[3]]
> [1] 160 80 400
>
>
>> Y
>
> [[1]]
>
> [1] 10
>
>
>
> [[2]]
>
> [1] 10 30
>
>
>
> [[3]]
>
> [1] 5 18 20
>
> and suppose
>
> Z = c(1, 2, 3)
>
> I need to perform the calculation where I will be multiplying corresponding
terms of X and Y individually and multiplying their sum by Z and store these
results in a dataframe.
>
> I.e. I need to calculate
>
> (40*10) * 1 # (first element of X + First
element of Y) * Z[1] = 400
>
> ((80*10)+(160*30)) * 2 # 2 row of X and 2nd row of Y =
11200
>
> ((160*5)+(80*18)+(400*20)) * 3 # 3rd row of X and 3 row of Y and Z[3] =
30720
>
>
>
> So the final output should be
>
> 400
> 11200
> 30720
>
>
> One way of doing it is write R code for individual rows and
> arrive at the result e.g.
>
> ([[X]][1]*[[Y]][1])*1 will result in 400. However, I was just trying to
know some smart way of doing it as there could be number of rows and writing
code for each row will be a cumbersome job. So is there any better way to do it?
>
> Please guide me.
>
Why not just write a function to do what
you've done by hand:
f <- function(x, y, z){
len <- length(x)
res <- rep(NA, len)
for(i in 1:len){
res[i] <- sum(x[[i]] * y[[i]]) * z[i]
}
res
}
f(X, Y, Z)
Peter Ehlers
> I thank you in advance.
>
> Thanking
> all
>
> Amelia
>
------------------------------
Message: 21
Date: Fri, 10 Dec 2010 14:57:17 +0100
From: Jinyan Huang <jinyan.fr at gmail.com>
To: Peter Ehlers <ehlers at ucalgary.ca>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] Adding numbers in Outputs
Message-ID:
<AANLkTik+2=5EOEcM-bnz4st-Pcrv=q9dqVnQjTE0MjUB at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
X<-list(40,c(80,160),c(160,80,400))
Y<-list(10,c(10,30),c(5,18,20))
Z<-c(1,2,3)
as.data.frame(do.call("rbind",X))->x
as.data.frame(do.call("rbind",Y))->y
x*y*Z->r
r[upper.tri(r)] <- 0
rowSums(r)
------------------------------
Message: 22
Date: Fri, 10 Dec 2010 05:58:30 -0800 (PST)
To: r-help at r-project.org
Subject: Re: [R] Compare one level of a factor with *all* other
non-missing levels
Message-ID: <1291989510070-3082005.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Peter Ehlers wrote:>
>
> Sounds like you want the Dunnett test procedure which seems
> to be implemented in a number of packages: multcomp, asd, MCPAN
> and others.
>
> It would probably be a good idea to install package 'sos' and
> learn how to search with it.
>
> Peter Ehlers
>
>
[[elided Yahoo spam]]
Unfortunately, Dunnett compares the mean(x) for a factor level with the
means(x) of all single K-1 other levels resulting in K-1 comparisions for
each level (printed in a lower triangular matrix for the results). Instead,
I just want to compare this one mean(x) with one other mean(x) of all the
K-1 other levels (printed in a vector of length K for the results).
[[elided Yahoo spam]]
Cheers,
Derik
--
View this message in context:
http://r.789695.n4.nabble.com/Compare-one-level-of-a-factor-with-all-other-non-missing-levels-tp3081777p3082005.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 23
Date: Fri, 10 Dec 2010 06:00:12 -0800 (PST)
From: Amelia Vettori <amelia_vettori at yahoo.co.nz>
To: jim holtman <jholtman at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Adding numbers in Outputs
Message-ID: <762099.6806.qm at web121409.mail.ne1.yahoo.com>
Content-Type: text/plain
Dear Mr Holtman Sir,
Thanks a lot for your great solution. This certainly is helping me achieve what
I need to get. However, I shall be hugely thankful to you if you can guide me in
one respect.
Sir, you have used following commands to assign values to x and y.?
> x <- list(40, c(80,160), c(160,80,400))
> y <- list(10, c(10,30), c(5,18,20))
> z <- c(1,2,3)
But Sir, the problem is these values are basically outputs of some other process
which I am running and chances are these will vary. Sir, it will be a great help
if you can guide me to convert the output (which I am getting)
X
[[1]]
[1] 40
[[2]]
[1] 80??? 160
[[3]]
[1] 160?? 80? 400
to what you have suggested
x <- list(40, c(80,160), c(160,80,400))
So, in that case once I get output in my format, I will convert that output as
provided by you.
I apologize for taking the liberty of writing to you, but I shall be really
grateful to you, as I have just started getting the feel of 'R' and I
know I need to take lots of efforts to begin with.
Thanks and eagerly waiting for your guidance.
Amelia Vettori
--- On Fri, 10/12/10, jim holtman <jholtman at gmail.com> wrote:
From: jim holtman <jholtman at gmail.com>
Subject: Re: [R] Adding numbers in Outputs
To: "Amelia Vettori" <amelia_vettori at yahoo.co.nz>
Cc: r-help at r-project.org
Received: Friday, 10 December, 2010, 1:43 PM
try this:
> x <- list(40, c(80,160), c(160,80,400))
> y <- list(10, c(10,30), c(5,18,20))
> z <- c(1,2,3)
> mapply(function(a1,a2,a3){
+? ???a3 * sum(a1 * a2)
+? ???}
+? ???, x
+? ???, y
+? ???, z
+ )
[1]???400 11200 30720
On Fri, Dec 10, 2010 at 5:41 AM, Amelia Vettori
<amelia_vettori at yahoo.co.nz> wrote:> two OutputsHello!
>
> I am Amelia from Auckland and work for a bank. I am new to R and I have
started my venture with R just a couple of weeks back and this is my first mail
to R-forum. I need following assistance
>
> Suppose my R code generates following outputs as
>
>
>> X
> [[1]]
> [1] 40
>
> [[2]]
> [1] 80??? 160
>
> [[3]]
> [1] 160?? 80? 400
>
>
>> Y
>
> [[1]]
>
> [1] 10
>
>
>
> [[2]]
>
> [1] 10??? 30
>
>
>
> [[3]]
>
> [1] 5? 18? 20
>
> and suppose
>
> Z = c(1, 2, 3)
>
> I need to perform the calculation where I will be multiplying corresponding
terms of X and Y individually and multiplying their sum by Z and store these
results in a dataframe.
>
> I.e. I need to calculate
>
> (40*10) * 1 ??????????????????????????????? # (first element of X + First
element of Y) * Z[1] = 400
>
> ((80*10)+(160*30)) * 2???????????????? # 2 row of X and 2nd row of Y =
11200
>
> ((160*5)+(80*18)+(400*20)) * 3???? # 3rd row of X and 3 row of Y and Z[3]
=? 30720
>
>
>
> So the final output should be
>
> 400
> 11200
> 30720
>
>
> One way of doing it is write R code for individual rows and
> ?arrive at the result e.g.
>
> ([[X]][1]*[[Y]][1])*1 will result in 400. However, I was just trying to
know some smart way of doing it as there could be number of rows and writing
code for each row will be a cumbersome job. So is there any better way to do it?
>
> Please guide me.
>
> I thank you in advance.
>
> Thanking
> ?all
>
> Amelia
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ? ? ? ?[[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.
>
>
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
------------------------------
Message: 24
Date: Fri, 10 Dec 2010 15:18:41 +0100
From: andrija djurovic <djandrija at gmail.com>
To: r-help at r-project.org
Subject: [R] (no subject)
Message-ID:
<AANLkTinMTKS-Jr1x5WwXXV3A-WFEaHoxmBpVpRL5T+=K at mail.gmail.com>
Content-Type: text/plain
Hi R-help,
I am trying to find a way to select five highest values in data frame
according some variable. I will demonstrate:
c
X1 X2
1 1 1
2 1 2
3 1 3
4 1 4
5 1 5
6 1 6
7 1 7
8 1 8
9 1 9
10 1 10
11 2 11
12 2 12
13 2 13
14 2 14
15 2 15
16 2 16
17 2 17
18 2 18
19 2 19
20 2 20
21 2 21
22 2 22
23 2 23
24 2 24
25 2 25
So I would like to select a rows with higest values of X2 inside X1.
Expected result should be:
X1 X2
1 10
1 9
1 8
1 7
1 6
2 25
2 24
2 23
2 22
2 21
I first oreded the data frame using
c=c[with(c,order(X1,-X2)),]
but I need a help to select highes five. It is easy to select when I have
just 2 unique values of X1 but what is if I have 500 unique values in X1?
Thanks
Andrija
[[alternative HTML version deleted]]
------------------------------
Message: 25
Date: Fri, 10 Dec 2010 09:42:44 -0500
From: jim holtman <jholtman at gmail.com>
To: andrija djurovic <djandrija at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] (no subject)
Message-ID:
<AANLkTik+Ssu45gg2PvGF5r0di46pEnEgmHQr_7pAHYWV at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
try this:
> do.call(rbind, lapply(split(x, x$X1), function(.grp){
+ .ord <- .grp[order(.grp$X2, decreasing = TRUE),]
+ .ord[seq(min(5, nrow(.grp))),]
+ }))
X1 X2
1.10 1 10
1.9 1 9
1.8 1 8
1.7 1 7
1.6 1 6
2.25 2 25
2.24 2 24
2.23 2 23
2.22 2 22
2.21 2 21
On Fri, Dec 10, 2010 at 9:18 AM, andrija djurovic <djandrija at gmail.com>
wrote:> Hi R-help,
>
>
>
> I am trying to find a way to select five highest values in data frame
> according some variable. I will demonstrate:
>
> c
>
> ? X1 X2
>
> 1 ? 1 ?1
>
> 2 ? 1 ?2
>
> 3 ? 1 ?3
>
> 4 ? 1 ?4
>
> 5 ? 1 ?5
>
> 6 ? 1 ?6
>
> 7 ? 1 ?7
>
> 8 ? 1 ?8
>
> 9 ? 1 ?9
>
> 10 ?1 10
>
> 11 ?2 11
>
> 12 ?2 12
>
> 13 ?2 13
>
> 14 ?2 14
>
> 15 ?2 15
>
> 16 ?2 16
>
> 17 ?2 17
>
> 18 ?2 18
>
> 19 ?2 19
>
> 20 ?2 20
>
> 21 ?2 21
>
> 22 ?2 22
>
> 23 ?2 23
>
> 24 ?2 24
>
> 25 ?2 25
>
>
>
> So I would like to select a rows with higest values of X2 inside X1.
> Expected result should be:
>
> X1 X2
>
> ? 1 ?10
>
> ? 1 ?9
>
> ? 1 ?8
>
> ? 1 ?7
>
> ? 1 ?6
>
> ? 2 ?25
>
> ? 2 ?24
>
> ? 2 ?23
>
> ? 2 ?22
>
> ? 2 ?21
>
>
>
> I first oreded the data frame using
>
> c=c[with(c,order(X1,-X2)),]
>
> but I need a help to select highes five. It is easy to select when I have
> just 2 unique values of X1 but what is if I have 500 unique values in X1?
>
>
>
> Thanks
>
> Andrija
>
> ? ? ? ?[[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.
>
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
------------------------------
Message: 26
Date: Fri, 10 Dec 2010 14:47:24 +0000
From: Daniel Brewer <daniel.brewer at icr.ac.uk>
To: r-help at stat.math.ethz.ch
Subject: [R] melt causes errors when characters and values are used
Message-ID: <4D023D7C.1080607 at icr.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
Hello,
I am finding that the melt function from the reshape library causes
errors when applied to a data.frame that contains numeric and character
columns. For example,
melt(id.vars="ID",data.frame(ID=1:3,date=c("a","b","c"),value=c(1,4,5)))
ID variable value
1 1 date a
2 2 date b
3 3 date c
4 1 value <NA>
5 2 value <NA>
6 3 value <NA>
Warning message:
In `[<-.factor`(`*tmp*`, ri, value = c(1, 4, 5)) :
invalid factor level, NAs generated
It would be useful in this situation that the numerical column got
converted to a character column in this situation. Any ways round this?
In actual fact I have got a situation where it is more like this
ID Date_1 Value_1 Date_2 Value_2 ...
and I would like to convert it to a data.frame of ID, Date & Value but I
thought the above would be an appropriate middle step.
Thanks
Dan
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
------------------------------
Message: 27
Date: Fri, 10 Dec 2010 06:54:56 -0800 (PST)
From: haruo0409 <eixcxisx at bca.bai.ne.jp>
To: r-help at r-project.org
Subject: Re: [R] ReadWrite.xls problem
Message-ID: <1291992896890-3082108.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hans-Peter
I have checked the 'library(xlsReadWrite)' startup message.
I found that I just failed to 'xls.getshlib()'.
Entering 'xls.getshlib()', read.xls() works regularly.
Thank you.
--
View this message in context:
http://r.789695.n4.nabble.com/ReadWrite-xls-problem-tp3078348p3082108.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 28
Date: Fri, 10 Dec 2010 09:31:21 -0500
From: jim holtman <jholtman at gmail.com>
To: Amelia Vettori <amelia_vettori at yahoo.co.nz>
Cc: r-help at r-project.org
Subject: Re: [R] Adding numbers in Outputs
Message-ID:
<AANLkTi=Von-bjo0XgXQqkxJcuGAg-TyK2Ny3XeYsVEm5 at mail.gmail.com>
Content-Type: text/plain
You should be able to use whatever values you are getting from your script
right now. I just did the assignment to match what you were showing on the
output. The easiest thing to do is to do 'str(X)' from your data and
compare it to the 'x' I created -- str(x).
Here is what 'str(x)' gives:
> x <- list(40, c(80,160), c(160,80,400))
> str(x)
List of 3
$ : num 40
$ : num [1:2] 80 160
$ : num [1:3] 160 80 400
When providing sample data, it is probably best to use 'dput' to it can
be
reconstructed by the reader:
> dput(x)
list(40, c(80, 160), c(160, 80, 400))
This gives back what I was using and hopefully it compares with your
current output.
On Fri, Dec 10, 2010 at 9:00 AM, Amelia Vettori
<amelia_vettori at yahoo.co.nz>wrote:
> Dear Mr Holtman Sir,
>
> Thanks a lot for your great solution. This certainly is helping me achieve
> what I need to get. However, I shall be hugely thankful to you if you can
> guide me in one respect.
>
> Sir, you have used following commands to assign values to x and y.
>
> > x <- list(40, c(80,160), c(160,80,400))
> > y <- list(10, c(10,30), c(5,18,20))
> > z <- c(1,2,3)
>
> But Sir, the problem is these values are basically outputs of some other
> process which I am running and chances are these will vary. Sir, it will be
> a great help if you can guide me to convert the output (which I am getting)
>
>
> X
> [[1]]
> [1] 40
>
> [[2]]
> [1] 80 160
>
> [[3]]
> [1] 160 80 400
>
> to what you have suggested
>
> x <- list(40, c(80,160), c(160,80,400))
>
> So, in that case once I get output in my format, I will convert that output
> as provided by you.
>
> I apologize for taking the liberty of writing to you, but I shall be really
> grateful to you, as I have just started getting the feel of 'R' and
I know I
> need to take lots of efforts to begin with.
>
> Thanks and eagerly waiting for your guidance.
>
> Amelia Vettori
>
> --- On *Fri, 10/12/10, jim holtman <jholtman at gmail.com>* wrote:
>
>
> From: jim holtman <jholtman at gmail.com>
> Subject: Re: [R] Adding numbers in Outputs
> To: "Amelia Vettori" <amelia_vettori at yahoo.co.nz>
> Cc: r-help at r-project.org
> Received: Friday, 10 December, 2010, 1:43 PM
>
>
> try this:
>
> > x <- list(40, c(80,160), c(160,80,400))
> > y <- list(10, c(10,30), c(5,18,20))
> > z <- c(1,2,3)
> > mapply(function(a1,a2,a3){
> + a3 * sum(a1 * a2)
> + }
> + , x
> + , y
> + , z
> + )
> [1] 400 11200 30720
>
>
> On Fri, Dec 10, 2010 at 5:41 AM, Amelia Vettori
> <amelia_vettori at yahoo.co.nz<http://mc/compose?to=amelia_vettori at
yahoo.co.nz>>
> wrote:
[[elided Yahoo spam]]> >
> > I am Amelia from Auckland and work for a bank. I am new to R and I
have
> started my venture with R just a couple of weeks back and this is my first
> mail to R-forum. I need following assistance
> >
> > Suppose my R code generates following outputs as
> >
> >
> >> X
> > [[1]]
> > [1] 40
> >
> > [[2]]
> > [1] 80 160
> >
> > [[3]]
> > [1] 160 80 400
> >
> >
> >> Y
> >
> > [[1]]
> >
> > [1] 10
> >
> >
> >
> > [[2]]
> >
> > [1] 10 30
> >
> >
> >
> > [[3]]
> >
> > [1] 5 18 20
> >
> > and suppose
> >
> > Z = c(1, 2, 3)
> >
> > I need to perform the calculation where I will be multiplying
> corresponding terms of X and Y individually and multiplying their sum by Z
> and store these results in a dataframe.
> >
> > I.e. I need to calculate
> >
> > (40*10) * 1 # (first element of X +
First
> element of Y) * Z[1] = 400
> >
> > ((80*10)+(160*30)) * 2 # 2 row of X and 2nd row of Y
> 11200
> >
> > ((160*5)+(80*18)+(400*20)) * 3 # 3rd row of X and 3 row of Y and
Z[3]
> = 30720
> >
> >
> >
> > So the final output should be
> >
> > 400
> > 11200
> > 30720
> >
> >
> > One way of doing it is write R code for individual rows and
> > arrive at the result e.g.
> >
> > ([[X]][1]*[[Y]][1])*1 will result in 400. However, I was just trying
to
> know some smart way of doing it as there could be number of rows and
writing
> code for each row will be a cumbersome job. So is there any better way to
do
> it?
> >
> > Please guide me.
> >
> > I thank you in advance.
> >
> > Thanking
> > all
> >
> > Amelia
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> >
> > ______________________________________________
> > R-help at r-project.org <http://mc/compose?to=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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
>
>
>
> --
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
>
>
>
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
------------------------------
Message: 29
Date: Fri, 10 Dec 2010 08:57:55 -0600
From: David L Lorenz <lorenz at usgs.gov>
To: andrija djurovic <djandrija at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] (no subject)
Message-ID:
<OF0496E27C.59EA4F61-ON862577F5.00517845-862577F5.00523549 at usgs.gov>
Content-Type: text/plain
Andrija,
You should be able to extract the data that you want using a call like
this (AD substituted for your c)
with(AD, tapply(X2, X1, function(x) sort(x, dec=T)[1:5]))
That returns a list like this:
$`1`
[1] 10 9 8 7 6
$`2`
[1] 25 24 23 22 21
Just package it the way that you want.
Dave
From:
andrija djurovic <djandrija at gmail.com>
To:
r-help at r-project.org
Date:
12/10/2010 08:21 AM
Subject:
[R] (no subject)
Sent by:
r-help-bounces at r-project.org
Hi R-help,
I am trying to find a way to select five highest values in data frame
according some variable. I will demonstrate:
c
X1 X2
1 1 1
2 1 2
3 1 3
4 1 4
5 1 5
6 1 6
7 1 7
8 1 8
9 1 9
10 1 10
11 2 11
12 2 12
13 2 13
14 2 14
15 2 15
16 2 16
17 2 17
18 2 18
19 2 19
20 2 20
21 2 21
22 2 22
23 2 23
24 2 24
25 2 25
So I would like to select a rows with higest values of X2 inside X1.
Expected result should be:
X1 X2
1 10
1 9
1 8
1 7
1 6
2 25
2 24
2 23
2 22
2 21
I first oreded the data frame using
c=c[with(c,order(X1,-X2)),]
but I need a help to select highes five. It is easy to select when I have
just 2 unique values of X1 but what is if I have 500 unique values in X1?
Thanks
Andrija
[[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: 30
Date: Fri, 10 Dec 2010 08:27:23 -0600
From: Scott Chamberlain <schamber at rice.edu>
To: r-help <r-help at r-project.org>
Subject: [R] Textwrangler Languages Folder
Message-ID:
<AANLkTikUF+4B3krpbePb5Oym_ni3H9FN1scx8FzF4y9g at mail.gmail.com>
Content-Type: text/plain
Dear R Community,
I recently switched to a Mac (10.6.5), and have installed Textwrangler to
run code to R. However, I can't install the syntax highlighting file because
I can't find the directory: "~Users/username/Library/Application
Support/TextWrangler/Language Modules/". Is there a different location I
can
place the syntax highlighting file?
Scott
[[alternative HTML version deleted]]
------------------------------
Message: 31
Date: Fri, 10 Dec 2010 04:55:14 -0800 (PST)
From: bluesky <yooyoodd at yahoo.com.cn>
To: r-help at r-project.org
Subject: Re: [R] Minimization of the distance
Message-ID: <1291985714124-3081900.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
its really help,thanks a lot
--
View this message in context:
http://r.789695.n4.nabble.com/Minimization-of-the-distance-tp3081345p3081900.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 32
Date: Fri, 10 Dec 2010 15:04:41 +0000
From: Francesco Nutini <nutini.francesco at gmail.com>
To: "[R] help" <r-help at r-project.org>
Subject: [R] [r] overlap different line in a xyplot (lattice)
Message-ID: <BAY156-w3AAC96CF0EA9ACD3137FEDF2F0 at phx.gbl>
Content-Type: text/plain
dear [R] users,
is there a way to plot different data (but with the same x-variables) in the
same xyplot window?
There are already a similar question, but the answer is not enought
explanatory...
Thanks a lot,
Francesco
[[alternative HTML version deleted]]
------------------------------
Message: 33
Date: Fri, 10 Dec 2010 09:07:42 -0600
From: Terry Therneau <therneau at mayo.edu>
To: r-help at r-project.org, Damjan Krstajic <dkrstajic at hotmail.com>
Subject: Re: [R] survival: ridge log-likelihood workaround
Message-ID: <1291993662.26439.22.camel at punchbuggy>
Content-Type: text/plain
------ begin inclusion ---------
Dear all,
I need to calculate likelihood ratio test for ridge regression. In
February I have reported a bug where coxph returns unpenalized
log-likelihood for final beta estimates for ridge coxph regression. In
high-dimensional settings ridge regression models usually fail for lower
values of lambda. As the result of it, in such settings the ridge
regressions have higher values of lambda (e.g. over 100) which means
that the difference between unpenalized log-likelihood and penalized
log-likelihood is not insignificant. I would be grateful if someone can
confirm that the below code is correct workaround.
--- end included message ----
First, the "bug" you report is not a bug. The log partial likelihood
from a Cox model LPL(beta) is well defined for any vector of
coefficients beta, whether they are result of a maximization or taken
from your daily horoscope. The loglik component of coxph is the LPL for
the reported coefficients.
For a ridge regression the coxph function maximizes LPL(beta) -
penalty(beta) = penalized partial likelihood = PPL(beta). You have
correctly recreated the PPL.
Second: how do you do formal tests on such a model? This is hard. The
difference LPL1- LPL2 is a chi-square when each is the result of
maximizing the Cox LPL over a set of coefficients; when using a PPL we
are maximizing over something else. The distribution of the difference
of constrained LPL values can be argued to be a weighed sum of squared
normals where the weights are in (0,1), which is something more complex
than a chisq distribution. In a world with infinite free time I'd have
pursued this, worked it all out, and added appropriate code to coxph.
What about the difference in PPL values, which is the test you propose?
I'm not aware of any theory showing that these have any relation to a
chi-square distribution. (Said theory may well exist, and I'd be happy
for pointers.)
Terry Therneau
------------------------------
Message: 34
Date: Fri, 10 Dec 2010 10:13:22 -0500
From: Ben Tupper <btupper at bigelow.org>
To: r-help <r-help at r-project.org>
Cc: Scott Chamberlain <schamber at rice.edu>
Subject: Re: [R] Textwrangler Languages Folder
Message-ID: <B9A94995-291A-4A4F-9092-21318D042EDC at bigelow.org>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi,
On Dec 10, 2010, at 9:27 AM, Scott Chamberlain wrote:
> Dear R Community,
>
> I recently switched to a Mac (10.6.5), and have installed
> Textwrangler to
> run code to R. However, I can't install the syntax highlighting file
> because
> I can't find the directory: "~Users/username/Library/Application
> Support/TextWrangler/Language Modules/". Is there a different
> location I can
> place the syntax highlighting file?
>
I don't have OSX 10.6 and I happen to use SubEthaEdit, but I suspect
that you are really looking for something like the following:
/Users/ben/Library/Application Support/TextWrangler/Language Modules/
Note that you would place your user name in the place where mine
("ben") appears. If the "TextWrangler/Language Modules"
directory
doesn't exist in the Application Support directory you can create it.
Cheers,
Ben
Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine 04575-0475
http://www.bigelow.org/
------------------------------
Message: 35
Date: Fri, 10 Dec 2010 15:27:53 +0000
From: Daniel Brewer <daniel.brewer at icr.ac.uk>
To: r-help at stat.math.ethz.ch
Subject: [R] Remove 100 years from a date object
Message-ID: <4D0246F9.8070907 at icr.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
Hello,
I have some data that has dates in the form 27.02.37. I convert them to
a date object as follows:
as.Date(data$date,format="%d.%m.%y")
But this gives me years such as 2037 when I would like them to be 1937.
I thought of trying to take off some time i.e.
as.Date(camCD$DoB,format="%d.%m.%y") - 100*365
But that doesn't seem to work out correctly. Any ideas how to do this?
Thanks
Dan
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
------------------------------
Message: 36
Date: Fri, 10 Dec 2010 07:20:55 -0800 (PST)
From: profaar <profaar at live.com>
To: r-help at r-project.org
Subject: [R] help requested
Message-ID: <1291994455364-3082147.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
HI friends,
I have very lengthy graph data in edge list format. I want to convert it
into node list format.
example:
EDGE LIST FORMAT
1 2
1 3
1 4
1 5
2 3
2 4
3 2
4 1
4 3
4 5
5 2
5 4
ITS NODE LIST FORMAT SHOULD BE LIKE:
1 2 3 4 5
2 3 4
3 2
4 1 3
5 2 4
Kindly suggest me which package in R provides the support to do my task.
Thank u friends in advance.
--
View this message in context:
http://r.789695.n4.nabble.com/help-requested-tp3082147p3082147.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 37
Date: Fri, 10 Dec 2010 10:25:48 -0500
From: Simon Kiss <simonjkiss at yahoo.ca>
To: r-help at r-project.org
Subject: [R] 45 Degree labels on barplot? Help understanding code
previously posted.
Message-ID: <6EC1F9BA-28EF-4052-9F54-CD8E38B06E79 at yahoo.ca>
Content-Type: text/plain; charset=us-ascii
Dear colleagues,
i found a line or two of code in the help archives from Uwe Ligges about
creating slanted x-labels for a barplot and it works well for my purposes (code
below). However, I was hoping someone could explain to me precisely what the
code is doing.
I'm aware it's invoking the text command, and I know the first ttwo
arguments to text are x and y co-ordinates. I'm also aware that
par("usr")[3] is grabbing the third element of the vector of plotting
co-ordinates. But I tried replacing par("usr")[3] with just
"0" and that didn't work; all the labels got bunched up on the
left. Is it necessary to create a new object via "barplot" and then
quote that in the x,y coordinates of text?
Like I said, the code works great, but I'm trying to actually understand the
rationale behind the elements so I can apply it in future.
Yours, Simon Kiss
#Reproducible Code
mydat<-data.frame(countries=c("Canada", "Denmark",
"Framce", "United Kingdom", "Germany",
"Australia", "New Zealand", "Switzerland",
"Belgium", "Netherlands"), stories_total=c(429, 25,
239, 99, 100, 96, 18, 21, 0, 6), avg=c(4.165048544, 6.25, 6.459459459,
0.908256881, 1.923076923, 1.103448276, 1.058823529, 1.615384615, 0,
0.107142857), steps=c(2, 2, 2, 0,1, 1, 1, 0,0,0),
newspapers=c(103, 4, 37, 109, 52, 87, 17, 13, 10, 56))
mydat.sort1<-mydat[order(-mydat$avg), ]
myplot<-barplot(mydat.sort1$avg, col=c("black", "black",
"black", "grey", "white", "grey",
"grey", "white", "white", "white"),
ylim=c(0,7), main="Regulatory Action On Bisphenol A By Newspaper
Coverage")
col.vec=c("black", "grey", "white")
legend("topright", col=col.vec, fill=c("black",
"grey", "white"), legend=c("Meaningful Ban",
"Recommendations To Withdraw", "No Legislative Action"))
labels=mydat.sort1$countries
#These lines create the labels
text(myplot, par("usr")[3], labels=labels, srt=35, offset=1, adj=1,
xpd=TRUE)
axis(2)
par("usr")[3]
*********************************
Simon J. Kiss, PhD
Assistant Professor, Wilfrid Laurier University
73 George Street
Brantford, Ontario, Canada
N3T 2C9
Cell: +1 519 761 7606
------------------------------
Message: 38
Date: Fri, 10 Dec 2010 16:17:42 +0000
From: Barry Rowlingson <b.rowlingson at lancaster.ac.uk>
To: Daniel Brewer <daniel.brewer at icr.ac.uk>
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Remove 100 years from a date object
Message-ID:
<AANLkTiksEzwdCwM1JCeN3c8JAkohcMAchxy7qRS8kkD+ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Fri, Dec 10, 2010 at 3:27 PM, Daniel Brewer <daniel.brewer at
icr.ac.uk> wrote:> Hello,
>
> I have some data that has dates in the form 27.02.37. ?I convert them to
> a date object as follows:
> as.Date(data$date,format="%d.%m.%y")
>
> But this gives me years such as 2037 when I would like them to be 1937.
> ?I thought of trying to take off some time i.e.
> as.Date(camCD$DoB,format="%d.%m.%y") - 100*365
> But that doesn't seem to work out correctly. ?Any ideas how to do this?
Normally to adjust dates you can use as.difftime() and do arithmetic,
but a year is a variable thing (can be 365 or 366 days) so you cant
make a difftime of years. Days are variable things if you worry about
leap seconds...
Also, you could end up with an invalid date if you have 29-Feb-2000
and 29-Feb-1900. One wasn't a leap year...
A solution minus those caveats is to convert to POSIXlt and adjust the
$year element:
> dob="27.02.37"
> as.Date(dob,format="%d.%m.%y")
[1] "2037-02-27"
> dobp = as.POSIXlt(as.Date(dob,format="%d.%m.%y"))
> dobp$year = dobp$year - 100
> dobp
[1] "1937-02-27 UTC"
> as.Date(dobp)
[1] "1937-02-27"
although it might be easier to paste a '19' into your character variable
> paste(substr(dob,1,6),"19",substr(dob,7,9),sep="")
[1] "27.02.1937"
and then do it the way you started. Assumes you have leading zeroes on
all fields though.
Barry
------------------------------
Message: 39
Date: Fri, 10 Dec 2010 17:20:00 +0100
From: Jinyan Huang <jinyan.fr at gmail.com>
To: profaar <profaar at live.com>
Cc: r-help at r-project.org
Subject: Re: [R] help requested
Message-ID:
<AANLkTi=e+XhReMP8p+LaLG3Mibwjq_bzkhEBvGVAjRVN at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
awk '{arr[$1]=arr[$1] " " $2}END{for( i in arr){print
i,arr[i]}}'
edgelist.txt | sort -k1
On Fri, Dec 10, 2010 at 4:20 PM, profaar <profaar at live.com>
wrote:> 1 2
> 1 3
> 1 4
> 1 5
> 2 3
> 2 4
> 3 2
> 4 1
> 4 3
> 4 ?5
> 5 2
> 5 4
------------------------------
Message: 40
Date: Fri, 10 Dec 2010 14:23:48 -0200
From: Henrique Dallazuanna <wwwhsd at gmail.com>
To: profaar <profaar at live.com>
Cc: r-help at r-project.org
Subject: Re: [R] help requested
Message-ID:
<AANLkTineF+bDByVa0vRP2X8ak29_dUmNT+kq7eSWaE6g at mail.gmail.com>
Content-Type: text/plain
Try this:
> DF
V1 V2
1 1 2
2 1 3
3 1 4
4 1 5
5 2 3
6 2 4
7 3 2
8 4 1
9 4 3
10 4 5
11 5 2
12 5 4
> aggregate(V2 ~ V1, DF, paste, collapse = ' ')
V1 V2
1 1 2 3 4 5
2 2 3 4
3 3 2
4 4 1 3 5
5 5 2 4
On Fri, Dec 10, 2010 at 1:20 PM, profaar <profaar at live.com> wrote:
>
> HI friends,
> I have very lengthy graph data in edge list format. I want to convert it
> into node list format.
>
> example:
> EDGE LIST FORMAT
> 1 2
> 1 3
> 1 4
> 1 5
> 2 3
> 2 4
> 3 2
> 4 1
> 4 3
> 4 5
> 5 2
> 5 4
>
> ITS NODE LIST FORMAT SHOULD BE LIKE:
> 1 2 3 4 5
> 2 3 4
> 3 2
> 4 1 3
> 5 2 4
>
> Kindly suggest me which package in R provides the support to do my task.
> Thank u friends in advance.
> --
> View this message in context:
> http://r.789695.n4.nabble.com/help-requested-tp3082147p3082147.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.
>
--
Henrique Dallazuanna
Curitiba-Paran?-Brasil
25? 25' 40" S 49? 16' 22" O
[[alternative HTML version deleted]]
------------------------------
Message: 41
Date: Fri, 10 Dec 2010 16:21:29 -0000
From: "Eleni Rapsomaniki" <er339 at medschl.cam.ac.uk>
To: <r-help at r-project.org>
Subject: [R] survreg vs. aftreg (eha) - the relationship between
fitted coefficients?
Message-ID:
<807B01905E122642ACFED8271250B0C306129AF8 at me-mail1.medlan.cam.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"
Dear R-users,
I need to use the aftreg function in package 'eha' to estimate failure
times for left truncated survival data. Apparently, survreg still cannot fit
such models. Both functions should be fitting the accelerated failure time
(Weibull) model. However, as G?ran Brostr?m points out in the help file for
aftreg, the parameterisation is different giving rise to different coefficients.
The betas for adjusted covariates are opposite in sign but otherwise identical,
whereas the intercept is quite different in a non-obvious way. The
log-likelihoods are similar also, but not identical. I would like to find out
how I can convert one set of coefficients to the other so as to obtain the same
linear predictors using either model. Any ideas???
#the example below uses right-censored data for simplicity (the principle should
be the same with left truncation I hope)
library(survival)
library(eha)
# COMPARE coefs between survreg ('survival' pkg) and aftreg
('eha' pkg)
#Fitting NULL models (no covariates) results in (approximately) the same coefs
(which is good!)
m1_NULL=survreg(Surv(futime/365, status==1) ~ 1, data=pbcseq)
m2_NULL=aftreg(Surv(futime/365, status==1) ~ 1, data=pbcseq)
c(m1_NULL$coef, 1/m1_NULL$scale) #--> intercept= 3.878656 , shape =
1.478177
c(m2_NULL$coef[1], exp(m2_NULL$coef[2])) #--> intercept= 3.878859 ,
shape=1.478150
# NOW I adjust for covariates
m1=survreg(Surv(futime/365, status==1) ~ chol+stage, data=pbcseq)
m2= aftreg(Surv(futime/365, status==1) ~ chol+stage, data=pbcseq)
### m2 #######
#Coefficients:
# (Intercept) chol stage
# 5.944641913 -0.001692574 -0.470861324
#Scale= 0.6416744
#Loglik(model)= -483.9 Loglik(intercept only)= -506.8
# Chisq= 45.91 on 2 degrees of freedom, p= 1.1e-10
#n=1124 (821 observations deleted due to missingness)
### m2 #######
#Covariate W.mean Coef Exp(Coef) se(Coef) Wald p
#chol 303.777 0.002 1.002 0.000 0.000
#stage 3.298 0.460 1.584 0.119 0.000
#
#log(scale) 5.029 152.807 0.477 0.000
#log(shape) 0.467 1.595 0.095 0.000
#
#Events 92
#Total time at risk 9017
#Max. log. likelihood -484.31
#LR test statistic 45.0
#Degrees of freedom 2
#Overall p-value 1.64669e-10
Many thanks for any help you may be able to provide.
Eleni Rapsomaniki
Research Associate
University of Cambridge
Institute of Primary and Public Health
------------------------------
Message: 42
Date: Fri, 10 Dec 2010 08:27:33 -0800 (PST)
From: Clint Bowman <clint at ecy.wa.gov>
To: Barry Rowlingson <b.rowlingson at lancaster.ac.uk>
Cc: r-help at stat.math.ethz.ch, Daniel Brewer <daniel.brewer at
icr.ac.uk>
Subject: Re: [R] Remove 100 years from a date object
Message-ID: <alpine.LRH.2.02.1012100824120.8321 at aeolus.ecy.wa.gov>
Content-Type: text/plain; charset="iso-8859-1";
Format="flowed"
There still may be a problem if the dates go back far enough, e.g.,
1909. Is '09' 1909 or 2009? No matter what, you have to decide
which values need 1900 added and which need 2000. I'd split the
date on the delimiter '.', decide whether to add 1900 or 2000, and
then paste them together and then as.Date().
Clint
--
Clint Bowman INTERNET: clint at ecy.wa.gov
Air Quality Modeler INTERNET: clint at math.utah.edu
Department of Ecology VOICE: (360) 407-6815
PO Box 47600 FAX: (360) 407-7534
Olympia, WA 98504-7600
USPS: PO Box 47600, Olympia, WA 98504-7600
Parcels: 300 Desmond Drive, Lacey, WA 98503-1274
On Fri, 10 Dec 2010, Barry Rowlingson wrote:
> On Fri, Dec 10, 2010 at 3:27 PM, Daniel Brewer <daniel.brewer at
icr.ac.uk> wrote:
>> Hello,
>>
>> I have some data that has dates in the form 27.02.37. ?I convert them
to
>> a date object as follows:
>> as.Date(data$date,format="%d.%m.%y")
>>
>> But this gives me years such as 2037 when I would like them to be 1937.
>> ?I thought of trying to take off some time i.e.
>> as.Date(camCD$DoB,format="%d.%m.%y") - 100*365
>> But that doesn't seem to work out correctly. ?Any ideas how to do
this?
>
> Normally to adjust dates you can use as.difftime() and do arithmetic,
> but a year is a variable thing (can be 365 or 366 days) so you cant
> make a difftime of years. Days are variable things if you worry about
> leap seconds...
>
> Also, you could end up with an invalid date if you have 29-Feb-2000
> and 29-Feb-1900. One wasn't a leap year...
>
> A solution minus those caveats is to convert to POSIXlt and adjust the
> $year element:
>
> > dob="27.02.37"
> > as.Date(dob,format="%d.%m.%y")
> [1] "2037-02-27"
> > dobp = as.POSIXlt(as.Date(dob,format="%d.%m.%y"))
> > dobp$year = dobp$year - 100
>
> > dobp
> [1] "1937-02-27 UTC"
> > as.Date(dobp)
> [1] "1937-02-27"
>
> although it might be easier to paste a '19' into your character
variable
>
> > paste(substr(dob,1,6),"19",substr(dob,7,9),sep="")
> [1] "27.02.1937"
>
> and then do it the way you started. Assumes you have leading zeroes on
> all fields though.
>
> Barry
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
------------------------------
Message: 43
Date: Fri, 10 Dec 2010 11:38:11 -0500
From: Gabor Grothendieck <ggrothendieck at gmail.com>
To: Daniel Brewer <daniel.brewer at icr.ac.uk>
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Remove 100 years from a date object
Message-ID:
<AANLkTik9sDts866P12KifkC4WWKVu_2qAoGJx4q+OTKF at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Fri, Dec 10, 2010 at 10:27 AM, Daniel Brewer <daniel.brewer at
icr.ac.uk> wrote:> Hello,
>
> I have some data that has dates in the form 27.02.37. ?I convert them to
> a date object as follows:
> as.Date(data$date,format="%d.%m.%y")
>
> But this gives me years such as 2037 when I would like them to be 1937.
> ?I thought of trying to take off some time i.e.
> as.Date(camCD$DoB,format="%d.%m.%y") - 100*365
> But that doesn't seem to work out correctly. ?Any ideas how to do this?
>
The easiest is just to use chron dates since it uses a cut.off of 30
by default. That is, if yy is less than that then 2000+yy is used
and if greater than that then 1900+yy is used.
Thus try this:
library(chron)
d <- "27.02.37"
as.Date(dates(d, format = "d.m.y")) # "1937-02-27"
as.Date(d, format = "%d.%m.%y") # "2037-02-27"
Also if that is not good enough and you want a different value for the
cut.off then note that the default in chron is to use the year.expand
function to expand two digit dates but you can change that via
something like this:
options(chron.year.expand = function(..., cut.off = 25)
year.expand(..., cut.off = cut.off))
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
------------------------------
Message: 44
Date: Fri, 10 Dec 2010 11:38:53 -0500
From: Stavros Macrakis <macrakis at alum.mit.edu>
To: r-help <r-help at r-project.org>
Subject: [R] Stricter read.table?
Message-ID:
<AANLkTikJm=VtsYcigvcMhVW4ru6nwBN7N32j_qkcQ=0a at mail.gmail.com>
Content-Type: text/plain
read.table gives idiosyncratic results when the input is formatted
strangely, for example:
read.table(textConnection("a'b\nc'd\n"),header=FALSE,fill=TRUE,sep="",quote="'")
=> "c'd" "a'b" "c'd"
read.table(textConnection("a'b\nc'd\nf'\n'\n"),header=FALSE,fill=TRUE,sep="",quote="'")
=> "f'" "\na" "b" "c'd"
"f'" "\n"
Though read.table doesn't specify the syntax of its input precisely, these
results don't seem particularly useful or consistent.
Is there a stricter version of read.table (perhaps in a package) that gives
errors or warnings if it finds quotation marks in the middle of fields or
encounters other such peculiar situations?
Thanks,
-s
[[alternative HTML version deleted]]
------------------------------
Message: 45
Date: Fri, 10 Dec 2010 16:40:39 +0000
From: Daniel Brewer <daniel.brewer at icr.ac.uk>
To: Barry Rowlingson <b.rowlingson at lancaster.ac.uk>
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Remove 100 years from a date object
Message-ID: <4D025807.9030400 at icr.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
On 10/12/2010 4:17 PM, Barry Rowlingson wrote:> On Fri, Dec 10, 2010 at 3:27 PM, Daniel Brewer <daniel.brewer at
icr.ac.uk> wrote:
>> Hello,
>>
>> I have some data that has dates in the form 27.02.37. I convert them
to
>> a date object as follows:
>> as.Date(data$date,format="%d.%m.%y")
>>
>> But this gives me years such as 2037 when I would like them to be 1937.
>> I thought of trying to take off some time i.e.
>> as.Date(camCD$DoB,format="%d.%m.%y") - 100*365
>> But that doesn't seem to work out correctly. Any ideas how to do
this?
>
> Normally to adjust dates you can use as.difftime() and do arithmetic,
> but a year is a variable thing (can be 365 or 366 days) so you cant
> make a difftime of years. Days are variable things if you worry about
> leap seconds...
>
> Also, you could end up with an invalid date if you have 29-Feb-2000
> and 29-Feb-1900. One wasn't a leap year...
>
> A solution minus those caveats is to convert to POSIXlt and adjust the
> $year element:
>
> > dob="27.02.37"
> > as.Date(dob,format="%d.%m.%y")
> [1] "2037-02-27"
> > dobp = as.POSIXlt(as.Date(dob,format="%d.%m.%y"))
> > dobp$year = dobp$year - 100
>
> > dobp
> [1] "1937-02-27 UTC"
> > as.Date(dobp)
> [1] "1937-02-27"
>
> although it might be easier to paste a '19' into your character
variable
>
> >
paste(substr(dob,1,6),"19",substr(dob,7,9),sep="")
> [1] "27.02.1937"
>
> and then do it the way you started. Assumes you have leading zeroes on
> all fields though.
>
> Barry
Many thanks. Thats great
Dan
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
------------------------------
Message: 46
Date: Fri, 10 Dec 2010 17:53:45 +0100
From: Martin Maechler <maechler at stat.math.ethz.ch>
To: Steve Lianoglou <mailinglist.honeypot at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Perl "cut" equivalent in R
Message-ID: <19714.23321.622897.948731 at lynne.math.ethz.ch>
Content-Type: text/plain; charset=iso-8859-1
>>>>> "SL" == Steve Lianoglou <mailinglist.honeypot
at gmail.com>
>>>>> on Mon, 6 Dec 2010 14:21:59 -0500 writes:
>>> if(FALSE) { stuff your don't want executed ? ? ? ? ?}
>>>
>> > Switching a block of code off/on with editing a single
>> character may be done using 0/1 instead of FALSE/TRUE.
SL> Or even F/T
Bad Idea:
F <- 1
------------------------------
Message: 47
Date: Fri, 10 Dec 2010 08:53:46 -0800 (PST)
From: mathijsdevaan <mathijsdevaan at gmail.com>
To: r-help at r-project.org
Subject: Re: [R] Projecting data on a world map using long/lat
Message-ID: <1292000026484-3082305.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Thanks for the suggestions, but I am not there yet (I'm a real novice). In
the code provided by Patrick (see below), I changed the shape input (from
sids to world) which I downloaded here:
http://thematicmapping.org/downloads/world_borders.php. As a result I also
need to change the "CNTY_ID" and "id" in the code, but I
have no idea what
[[elided Yahoo spam]]
Mathijs
library(maptools)
library(ggplot2)
gpclibPermit()
myshp<- readShapeSpatial(system.file("shapes/sids.shp",
package="maptools"))
## see licence, not GPL
myshp.points<- fortify.SpatialPolygonsDataFrame(myshp,
region="CNTY_ID")
shpm<- merge(myshp.points, myshp, by.x="id",
by.y="CNTY_ID")
head(shpm)
p <- ggplot(shpm, aes(long, lat, group=group, fill=NWBIR74))
p <- p + geom_polygon() + geom_path(color="white") + coord_equal()
## Add some locations
cities <- read.table(textConnection("
long lat city val
-78.644722 35.818889 Raleigh 323
-80.843333 35.226944 Charlotte 510
-82.555833 35.58 Asheville 400"), header = TRUE)
p <- p + geom_point(aes( fill=NULL, group = NULL, size=val),
data = cities, color= 'black')
p
--
View this message in context:
http://r.789695.n4.nabble.com/Projecting-data-on-a-world-map-using-long-lat-tp3081298p3082305.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 48
Date: Fri, 10 Dec 2010 09:05:24 -0800
From: "William Dunlap" <wdunlap at tibco.com>
To: "Martin Maechler" <maechler at stat.math.ethz.ch>,
"Steve Lianoglou"
<mailinglist.honeypot at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Perl "cut" equivalent in R
Message-ID:
<77EB52C6DD32BA4D87471DCD70C8D70003B9AB1D at NA-PA-VBE03.na.tibco.com>
Content-Type: text/plain; charset="iso-8859-1"
> -----Original Message-----
> From: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] On Behalf Of Martin Maechler
> Sent: Friday, December 10, 2010 8:54 AM
> To: Steve Lianoglou
> Cc: r-help at r-project.org
> Subject: Re: [R] Perl "cut" equivalent in R
>
> >>>>> "SL" == Steve Lianoglou
<mailinglist.honeypot at gmail.com>
> >>>>> on Mon, 6 Dec 2010 14:21:59 -0500 writes:
>
> >>> if(FALSE) { stuff your don't want executed ? ? ? ? ?}
> >>>
> >>
> > Switching a block of code off/on with editing a single
> >> character may be done using 0/1 instead of FALSE/TRUE.
>
> SL> Or even F/T
>
> Bad Idea:
>
> F <- 1
Another approach is to write the following function
dontRun <- function(expr) {}
and replace that
if (FALSE) { ... questionable code ... }
with
dontRun( {... questionable code ...} )
If you do want the questionable code to run,
redefine dontRun to be
dontRun <- function(expr) { expr }
You can use this approach to put assertion tests
into your code that only get run when the assertion
function is defined to do something.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.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: Fri, 10 Dec 2010 12:18:03 -0500
From: "John Fox" <jfox at mcmaster.ca>
To: <r-help at r-project.org>
Subject: [R] new edition of R Companion to Applied Regression
Message-ID: <005f01cb988e$345736e0$9d05a4a0$@ca>
Content-Type: text/plain; charset="us-ascii"
Dear all,
Sandy Weisberg and I would like to announce the publication of the second
edition of An R Companion to Applied Regression (Sage, 2011).
As is immediately clear, the book now has two authors and S-PLUS is gone
from the title (and the book). The R Companion has also been thoroughly
rewritten, covering developments in the nearly 10 years since the first
edition was written and expanding coverage of topics such as R graphics and
R programming. As before, however, the R Companion provides a general
introduction to R in the context of applied regression analysis, broadly
construed. It is available from the publisher at
<http://www.sagepub.com/books/Book233899?> (US) or
<http://www.uk.sagepub.com/books/Book233899?> (UK), and from Amazon at
<http://www.amazon.ca/R-Companion-Applied-Regression/dp/141297514X/ref=sr_1_
3?s=books&ie=UTF8&qid=1291995545&sr=1-3>.
The book is augmented by a web site
<http://socserv.mcmaster.ca/jfox/Books/Companion/> with data sets,
appendices on a variety of topics, and more, and it associated with the car
package on CRAN, which has recently undergone an overhaul.
Regards,
John and Sandy
--------------------------------
John Fox
Senator William McMaster
Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
web: socserv.mcmaster.ca/jfox
------------------------------
Message: 50
Date: Fri, 10 Dec 2010 12:55:32 -0500
From: Mike Marchywka <marchywka at hotmail.com>
To: <jinyan.fr at gmail.com>, <profaar at live.com>
Cc: r-help at r-project.org
Subject: Re: [R] help requested
Message-ID: <BLU113-W7141585491F2E4027F5C6BE2F0 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
----------------------------------------> From: jinyan.fr at gmail.com
> Date: Fri, 10 Dec 2010 17:20:00 +0100
> To: profaar at live.com
> CC: r-help at r-project.org
> Subject: Re: [R] help requested
>
> awk '{arr[$1]=arr[$1] " " $2}END{for( i in arr){print
i,arr[i]}}'
> edgelist.txt | sort -k1
My first thought PERL hash but I guess my answer would
still be to consider any R hash-like structures. I guess any array
that accepts arbitrary subscripts amounts to a hash.
>
>
>
> On Fri, Dec 10, 2010 at 4:20 PM, profaar wrote:
> > 1 2
> > 1 3
> > 1 4
> > 1 5
> > 2 3
> > 2 4
> > 3 2
> > 4 1
> > 4 3
> > 4 5
> > 5 2
> > 5 4
>
> ______________________________________________
> 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: 51
Date: Fri, 10 Dec 2010 13:09:10 -0500
From: Duncan Murdoch <murdoch.duncan at gmail.com>
To: William Dunlap <wdunlap at tibco.com>
Cc: r-help at r-project.org, Martin Maechler <maechler at
stat.math.ethz.ch>
Subject: Re: [R] Perl "cut" equivalent in R
Message-ID: <4D026CC6.8010804 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 10/12/2010 12:05 PM, William Dunlap wrote:> > -----Original Message-----
> > From: r-help-bounces at r-project.org
> > [mailto:r-help-bounces at r-project.org] On Behalf Of Martin Maechler
> > Sent: Friday, December 10, 2010 8:54 AM
> > To: Steve Lianoglou
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Perl "cut" equivalent in R
> >
> > >>>>> "SL" == Steve
Lianoglou<mailinglist.honeypot at gmail.com>
> > >>>>> on Mon, 6 Dec 2010 14:21:59 -0500 writes:
> >
> > >>> if(FALSE) { stuff your don't want executed
}
> > >>>
> > >>
> > > Switching a block of code off/on with editing a single
> > >> character may be done using 0/1 instead of FALSE/TRUE.
> >
> > SL> Or even F/T
> >
> > Bad Idea:
> >
> > F<- 1
>
> Another approach is to write the following function
> dontRun<- function(expr) {}
> and replace that
> if (FALSE) { ... questionable code ... }
> with
> dontRun( {... questionable code ...} )
> If you do want the questionable code to run,
> redefine dontRun to be
> dontRun<- function(expr) { expr }
>
> You can use this approach to put assertion tests
> into your code that only get run when the assertion
> function is defined to do something.
That's a nice idea!
Duncan Murdoch
------------------------------
Message: 52
Date: Fri, 10 Dec 2010 10:13:00 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
To: Francesco Nutini <nutini.francesco at gmail.com>
Cc: "\[R\] help" <r-help at r-project.org>
Subject: Re: [R] [r] overlap different line in a xyplot (lattice)
Message-ID: <4D026DAC.6070701 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-12-10 07:04, Francesco Nutini wrote:>
> dear [R] users,
> is there a way to plot different data (but with the same x-variables) in
the same xyplot window?
> There are already a similar question, but the answer is not enought
explanatory...
Something like this?
x <- rep(1:10, 2)
y1 <- rnorm(10); y2 <- rnorm(10) + 2
y <- c(y1, y2)
g <- gl(2, 10)
xyplot( y ~ x, groups = g, type = 'b')
Peter Ehlers
>
>
> Thanks a lot,
> Francesco
>
------------------------------
Message: 53
Date: Fri, 10 Dec 2010 13:13:32 -0500
From: Anthony Damico <ajdamico at gmail.com>
To: r-help at r-project.org
Subject: [R] Could concurrent R sessions mix up variables?
Message-ID:
<AANLkTi=mqRZqf1zSkg1L=xmEDub_VeiN+9pYQ=nDAak_ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi, I'm working in R 2.11.1 x64 on Windows x86_64-pc-mingw32.
I'm experiencing a strange problem in R that I'm not even sure how to
begin to fix.
I've got a huge (forty-pages printed) simulation written in R that I'd
like to run multiple times. When I open up R and run it on its own,
it works fine. At the beginning of the program, there's a variable X
that I set to 1, 5, 10, 20, depending on how sensitive I want the
simulation to be to a certain parameter. When I just run one instance
of R, the X variable stays the same throughout the program.
I have a quad-core machine, so I'd like to take advantage of all four
processors.
If I open up four sessions and set X to 1, 5, 10, and 20 in those
different sessions, then run all four simulations all the way through
(about eighteen hours of processing time) at the same time, the
variable X ends up being 20 at the end of all four sessions. It's as
if R mixed up the variable setting between the four concurrent
sessions. I can't figure out why else my variable X would ever get
changed to 20 in the three simulations that I set it to 1, 5, and 10,
respeectively (it doesn't get updated anywhere during the simulation).
When I have all four of these simulations running concurrently, I am
absolutely maxing out my computer. All four processors are at 100%,
and my Windows Task Manager says I'm using almost 100% of my 16 GB of
RAM. Is it possible that intense resource use would cause a variable
conflict like this? I have no idea where to start troubleshooting
this error, so any advice would be appreciated.
Thanks!
Anthony Damico
Kaiser Family Foundation
------------------------------
Message: 54
Date: Fri, 10 Dec 2010 13:18:21 -0500
From: Michael D <mike409 at gmail.com>
To: r-help at r-project.org
Subject: [R] help with RSQLite adding a new column
Message-ID:
<AANLkTikL9tqK=RZphOVs8FCPYKCXF2CMAiXfWQtuEsGt at mail.gmail.com>
Content-Type: text/plain
I'm new to using sql so I'm having difficulties (and worries) in adding
a
new column of data to a table I have. Its a very large file (around 5 Gb)
which is why I'm having to use SQL
I have a table with variables ID, IDrec and IDdes and the variables IDrec
and IDdes give a mapping of some other values but the other values are
associated with the ID variable (think of IDrec and IDdes being character
strings and ID being numeric)
(Imagine the transposed)
Table1:
ID: 1,2,3,4,...
IDrec: A,B,C,D...
IDdes: B,C,A,E...
So I've created a table with the final form I need it to be in
dbGetQuery(db, "CREATE TABLE Map
(ID int, IDrec int, IDrec1 int,
IDdes int, IDdes1 int)")
And the finished table would look something like:
Map:
ID: 1, 2, 3, 4,...
IDrec: 1, 2, 3, 4,...
IDrec1: A, B, C, D,...
IDdes: 2, 3, 1, 5,....
IDdes1: B, C, A, E,...
So I copy in the first set of values easily:
dbGetQuery(db, "INSERT INTO Map(ID, IDrec, IDrec1, IDdes1)
SELECT ID, ID, IDrec, IDdes FROM Ntemp")
Giving me a table that looks like:
Map:
ID: 1, 2, 3, 4,...
IDrec: 1, 2, 3, 4,...
IDrec1: A, B, C, D,...
IDdes: NA,NA,NA,NA,...
IDdes1: B, C, A, E,...
Then I create a new table with just the IDdes values I need:
dbGetQuery(db, "Create table temp2 as
SELECT temp.ID
FROM Ntemp, temp
WHERE Ntemp.IDdes1 = temp.IDrec1")
Giving me temp2 (not sure what the variable name is)
V1: 2, 3, 1, 5,...
But when I try to copy in the new data:
dbGetQuery(db, "INSERT INTO Map(IDdes)
SELECT * FROM temp2")
My map table isn't updated:
Map:
ID: 1, 2, 3, 4,...
IDrec: 1, 2, 3, 4,...
IDrec1: A, B, C, D,...
IDdes: NA,NA,NA,NA,...
IDdes1: B, C, A, E,...
Is there something I'm missing? Or am I just going about inserting the IDdes
variables the wrong way?
Thanks for the help.
Michael
[[alternative HTML version deleted]]
------------------------------
Message: 55
Date: Fri, 10 Dec 2010 19:31:04 +0100
From: Petr Savicky <savicky at cs.cas.cz>
To: r-help at r-project.org
Subject: Re: [R] help requested
Message-ID: <20101210183104.GA24654 at cs.cas.cz>
Content-Type: text/plain; charset=utf-8
On Fri, Dec 10, 2010 at 07:20:55AM -0800, profaar wrote:>
> HI friends,
> I have very lengthy graph data in edge list format. I want to convert it
> into node list format.
>
> example:
> EDGE LIST FORMAT
> 1 2
> 1 3
> 1 4
> 1 5
> 2 3
> 2 4
> 3 2
> 4 1
> 4 3
> 4 5
> 5 2
> 5 4
>
> ITS NODE LIST FORMAT SHOULD BE LIKE:
> 1 2 3 4 5
> 2 3 4
> 3 2
> 4 1 3
> 5 2 4
>
> Kindly suggest me which package in R provides the support to do my task.
How long the list of egdes is? For not too large lists, consider also
library(graph)
G <- new("graphNEL", edgemode="directed")
G <- addNode(as.character(1:5), G)
edges <- read.table(file=stdin(), colClasses="character")
1 2
1 3
1 4
1 5
2 3
2 4
3 2
4 1
4 3
4 5
5 2
5 4
G <- addEdge(from=edges[, 1], to=edges[, 2], G)
edgeL(G)
$`1`
$`1`$edges
[1] 2 3 4 5
$`2`
$`2`$edges
[1] 3 4
$`3`
$`3`$edges
[1] 2
$`4`
$`4`$edges
[1] 1 3 5
$`5`
$`5`$edges
[1] 2 4
Very large lists can be handled by unix/linux sort command (if not sorted
already) and by extracting the end-nodes of the edges starting in each node.
In a sorted file, they form blocks of consecutive lines, so a simple text
processing with perl is sufficient.
Petr Savicky.
------------------------------
Message: 56
Date: Fri, 10 Dec 2010 13:41:38 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: Simon Kiss <simonjkiss at yahoo.ca>
Cc: r-help at r-project.org
Subject: Re: [R] 45 Degree labels on barplot? Help understanding code
previously posted.
Message-ID: <F3071826-3CCB-4396-B85D-7BCADF1D3FEE at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Dec 10, 2010, at 10:25 AM, Simon Kiss wrote:
> Dear colleagues,
> i found a line or two of code in the help archives from Uwe Ligges
> about creating slanted x-labels for a barplot and it works well for
> my purposes (code below). However, I was hoping someone could
> explain to me precisely what the code is doing.
> I'm aware it's invoking the text command, and I know the first ttwo
> arguments to text are x and y co-ordinates. I'm also aware that
> par("usr")[3] is grabbing the third element of the vector of
> plotting co-ordinates.
More accurately the limits of the plot area in plot dimensions.
> But I tried replacing par("usr")[3] with just "0" and
that didn't
> work; all the labels got bunched up on the left.
That was the "y" argument, not the rotation argument. (Which means I
am surprised that it bunched things to the side ... and for me it did
nothing at all... same graphic.) It is the srt argument that controls
the angle.
> Is it necessary to create a new object via "barplot"
That gives you appropriate positions for the labels in plot coordinate
terms and the xpd argument allows these locations to be used outside
the plot area.
> and then quote that in the x,y coordinates of text?
What do you mean by "then quote it in the x,y,coordinates"? I
don't
see any quotes. You could of course just look at the plot area and
supply your own locations. You would need to figure out what the
unlabeled x-axis scale really was, but that too is documented.
--
David.
> Like I said, the code works great, but I'm trying to actually
> understand the rationale behind the elements so I can apply it in
> future.
> Yours, Simon Kiss
>
> #Reproducible Code
> mydat<-data.frame(countries=c("Canada", "Denmark",
"Framce", "United
> Kingdom", "Germany", "Australia", "New
Zealand", "Switzerland",
> "Belgium", "Netherlands"), stories_total=c(429, 25,
> 239, 99, 100, 96, 18, 21, 0, 6), avg=c(4.165048544, 6.25,
> 6.459459459, 0.908256881, 1.923076923, 1.103448276, 1.058823529,
> 1.615384615, 0, 0.107142857), steps=c(2, 2, 2, 0,1, 1, 1, 0,0,0),
> newspapers=c(103, 4, 37, 109, 52, 87, 17, 13, 10, 56))
> mydat.sort1<-mydat[order(-mydat$avg), ]
> myplot<-barplot(mydat.sort1$avg, col=c("black",
"black", "black",
> "grey", "white", "grey", "grey",
"white", "white", "white"),
> ylim=c(0,7), main="Regulatory Action On Bisphenol A By Newspaper
> Coverage")
> col.vec=c("black", "grey", "white")
> legend("topright", col=col.vec, fill=c("black",
"grey", "white"),
> legend=c("Meaningful Ban", "Recommendations To
Withdraw", "No
> Legislative Action"))
> labels=mydat.sort1$countries
> #These lines create the labels
> text(myplot, par("usr")[3], labels=labels, srt=35, offset=1,
adj=1,
> xpd=TRUE)
> axis(2)
> par("usr")[3]
>
> *********************************
> Simon J. Kiss, PhD
> Assistant Professor, Wilfrid Laurier University
> 73 George Street
> Brantford, Ontario, Canada
> N3T 2C9
> Cell: +1 519 761 7606
>
> ______________________________________________
> 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: 57
Date: Fri, 10 Dec 2010 13:50:45 -0500
From: Duncan Murdoch <murdoch.duncan at gmail.com>
To: Anthony Damico <ajdamico at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Could concurrent R sessions mix up variables?
Message-ID: <4D027685.5050700 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 10/12/2010 1:13 PM, Anthony Damico wrote:> Hi, I'm working in R 2.11.1 x64 on Windows x86_64-pc-mingw32.
>
> I'm experiencing a strange problem in R that I'm not even sure how
to
> begin to fix.
>
> I've got a huge (forty-pages printed) simulation written in R that
I'd
> like to run multiple times. When I open up R and run it on its own,
> it works fine. At the beginning of the program, there's a variable X
> that I set to 1, 5, 10, 20, depending on how sensitive I want the
> simulation to be to a certain parameter. When I just run one instance
> of R, the X variable stays the same throughout the program.
>
> I have a quad-core machine, so I'd like to take advantage of all four
> processors.
>
> If I open up four sessions and set X to 1, 5, 10, and 20 in those
> different sessions, then run all four simulations all the way through
> (about eighteen hours of processing time) at the same time, the
> variable X ends up being 20 at the end of all four sessions. It's as
> if R mixed up the variable setting between the four concurrent
> sessions. I can't figure out why else my variable X would ever get
> changed to 20 in the three simulations that I set it to 1, 5, and 10,
> respeectively (it doesn't get updated anywhere during the simulation).
>
> When I have all four of these simulations running concurrently, I am
> absolutely maxing out my computer. All four processors are at 100%,
> and my Windows Task Manager says I'm using almost 100% of my 16 GB of
> RAM. Is it possible that intense resource use would cause a variable
> conflict like this? I have no idea where to start troubleshooting
> this error, so any advice would be appreciated.
If you are running something that takes 18 hours to complete, a common
practice is to save intermediate results to disk occasionally. Have you
(or whoever wrote the simulation) done this and forgotten about it? If
all 4 processes are saving to the same place, then reading results back,
you'd see something like you describe.
If all calculations are held in memory, you shouldn't.
A simple approach that might debug this is to create a new variables
initX, set equal to X. Then sprinkle statements
stopifnot(X == initX)
through your simulation code. That should quit when the change happens,
and you can try to figure out why it happened.
Duncan Murdoch
------------------------------
Message: 58
Date: Fri, 10 Dec 2010 10:58:01 -0800 (PST)
From: Phil Spector <spector at stat.berkeley.edu>
To: Anthony Damico <ajdamico at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Could concurrent R sessions mix up variables?
Message-ID:
<alpine.DEB.2.00.1012101047210.20652 at springer.Berkeley.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Anthony -
I would advise you to use the multicore or snowfall packages
to utilize multiple CPUs. As an example using multicore:
> library(multicore)
> sim = function(mu)max(replicate(100000,max(rnorm(100,mu))))
> library(multicore)
> unlist(mclapply(c(1,5,10,20),sim))
[1] 6.569332 10.268091 15.335847 25.291502
Using snowfall:
> library(snowfall)
> sim = function(mu)max(replicate(100000,max(rnorm(100,mu))))
> sfInit(cpus=4,type='SOCK',parallel=TRUE)
> sfSapply(c(1,5,10,20),sim)
[1] 6.200161 10.307807 15.271581 25.055950
Hope this helps.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spector at stat.berkeley.edu
On Fri, 10 Dec 2010, Anthony Damico wrote:
> Hi, I'm working in R 2.11.1 x64 on Windows x86_64-pc-mingw32.
>
> I'm experiencing a strange problem in R that I'm not even sure how
to
> begin to fix.
>
> I've got a huge (forty-pages printed) simulation written in R that
I'd
> like to run multiple times. When I open up R and run it on its own,
> it works fine. At the beginning of the program, there's a variable X
> that I set to 1, 5, 10, 20, depending on how sensitive I want the
> simulation to be to a certain parameter. When I just run one instance
> of R, the X variable stays the same throughout the program.
>
> I have a quad-core machine, so I'd like to take advantage of all four
> processors.
>
> If I open up four sessions and set X to 1, 5, 10, and 20 in those
> different sessions, then run all four simulations all the way through
> (about eighteen hours of processing time) at the same time, the
> variable X ends up being 20 at the end of all four sessions. It's as
> if R mixed up the variable setting between the four concurrent
> sessions. I can't figure out why else my variable X would ever get
> changed to 20 in the three simulations that I set it to 1, 5, and 10,
> respeectively (it doesn't get updated anywhere during the simulation).
>
> When I have all four of these simulations running concurrently, I am
> absolutely maxing out my computer. All four processors are at 100%,
> and my Windows Task Manager says I'm using almost 100% of my 16 GB of
> RAM. Is it possible that intense resource use would cause a variable
> conflict like this? I have no idea where to start troubleshooting
> this error, so any advice would be appreciated.
>
> Thanks!
>
> Anthony Damico
> Kaiser Family Foundation
>
> ______________________________________________
> 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: 59
Date: Fri, 10 Dec 2010 20:07:40 +0100
From: Andreas Wittmann <andreas_wittmann at gmx.de>
To: r-help <r-help at r-project.org>
Subject: [R] survival package - calculating probability to survive a
given time
Message-ID: <4D027A7C.2020804 at gmx.de>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear R users,
i try to calculate the probabilty to survive a given time by using the
estimated survival curve by kaplan meier.
What is the right way to do that? as far as is see i cannot use the
predict-methods from the survival package?
library(survival)
set.seed(1)
time <- cumsum(rexp(1000)/10)
status <- rbinom(1000, 1, 0.5)
## kaplan meier estimates
fit <- survfit(Surv(time, status) ~ 1)
s <- summary(fit)
## 1. possibility to get the probability for surviving 20 units of time
ind <- findInterval(20, s$time)
cbind(s$surv[ind], s$time[ind])
## 2. possibility to get the probability for surviving 20 units of time
ind <- s$time >= 20
sum(ind) / length(ind)
Thanks and best regards
Andreas
------------------------------
Message: 60
Date: Fri, 10 Dec 2010 11:16:26 -0800
From: Peter Ehlers <ehlers at ucalgary.ca>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] Compare one level of a factor with *all* other
non-missing levels
Message-ID: <4D027C8A.8080902 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2010-12-10 05:58, deriK2000 wrote:>
>
> Peter Ehlers wrote:
>>
>>
>> Sounds like you want the Dunnett test procedure which seems
>> to be implemented in a number of packages: multcomp, asd, MCPAN
>> and others.
>>
>> It would probably be a good idea to install package 'sos' and
>> learn how to search with it.
>>
>> Peter Ehlers
>>
>>
>
>
[[elided Yahoo spam]]>
> Unfortunately, Dunnett compares the mean(x) for a factor level with the
> means(x) of all single K-1 other levels resulting in K-1 comparisions for
> each level (printed in a lower triangular matrix for the results). Instead,
> I just want to compare this one mean(x) with one other mean(x) of all the
> K-1 other levels (printed in a vector of length K for the results).
>
Okay, I misunderstood; should have read more carefully.
I would just use a loop (I'm not as loop-averse as
some R users).
x <- rnorm(20)
f <- gl(4, 5, lab = letters[1:4])
lev <- levels(f)
len <- length(lev)
pv <- numeric(len)
for(i in 1:len){
pv[i] <- t.test(x[f == lev[i]], x[f != lev[i]])$p.value
}
pv
For pvalue adjustment (if you think that's needed),
see ?p.adjust.
[[elided Yahoo spam]]
Yes, it's an excellent tool.
Peter Ehlers
>
> Cheers,
>
> Derik
------------------------------
Message: 61
Date: Fri, 10 Dec 2010 15:11:47 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: Andreas Wittmann <andreas_wittmann at gmx.de>
Cc: r-help <r-help at r-project.org>
Subject: Re: [R] survival package - calculating probability to survive
a given time
Message-ID: <FBE2BF70-878C-46FE-BFCE-19BAFAC3107C at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Dec 10, 2010, at 2:07 PM, Andreas Wittmann wrote:
> Dear R users,
>
> i try to calculate the probabilty to survive a given time by using
> the estimated survival curve by kaplan meier.
>
> What is the right way to do that? as far as is see i cannot use the
> predict-methods from the survival package?
>
> library(survival)
> set.seed(1)
> time <- cumsum(rexp(1000)/10)
> status <- rbinom(1000, 1, 0.5)
>
> ## kaplan meier estimates
> fit <- survfit(Surv(time, status) ~ 1)
> s <- summary(fit)
>
> ## 1. possibility to get the probability for surviving 20 units of
> time
> ind <- findInterval(20, s$time)
> cbind(s$surv[ind], s$time[ind])
See if this helps:
> head(which(s$surv < 0.5))
[1] 368 369 370 371 372 373
> plot(fit)
> abline(h=0.5)
> abline(v=s$time[368])
>
> ## 2. possibility to get the probability for surviving 20 units of
> time
> ind <- s$time >= 20
> sum(ind) / length(ind)
--
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 62
Date: Fri, 10 Dec 2010 12:14:04 -0800
From: Rob James <rob at aetiologic.ca>
To: r-help at r-project.org
Subject: [R] Reorder factor and address embedded escapes
Message-ID: <4D028A0C.3010801 at aetiologic.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
I am trying to reorder a factor variable that has embedded escape
characters. The data begins as a csv file with a factor that includes
embedded new line characters. By the time read.table has rendered it
into a data frame, the variable now has an extra backslash.
e.g.
"This\nLabel" in the csv becomes "This\\nLabel" in the data
frame.
So, I am trying to reorder the factor and deal with the introduction of
a secondary \ . Here's a small example:
A = c("A\\nB", "C\\nD")
test <-data.frame(A)
str(test)
test$reorderA <-factor(test$A, c("C\\nD", "A\\nB"))
str(test)
test$reorderB <-sub("\\\\n", "\n", test$reorderA)
str(test)
When sub is applied to the now-correctly ordered factor, it returns to
the default ordering.
Suggestions?
------------------------------
Message: 63
Date: Fri, 10 Dec 2010 12:16:23 -0800 (PST)
From: dreadgazebo <ernie.tedeschi at gmail.com>
To: r-help at r-project.org
Subject: [R] Time Series Row Label
Message-ID: <1292012183267-3082639.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Simple question...
I know that when referencing data in a multivariate time series matrix, I
can use the variable name instead of the column number (such as
budget.ts[4,"incometax"]). Is there a way I can use the time unit
(say, the
year in an annual time series) instead of the row number?
--
View this message in context:
http://r.789695.n4.nabble.com/Time-Series-Row-Label-tp3082639p3082639.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 64
Date: Fri, 10 Dec 2010 14:20:33 -0600
From: Erik Iverson <eriki at ccbr.umn.edu>
To: Rob James <rob at aetiologic.ca>
Cc: r-help at r-project.org
Subject: Re: [R] Reorder factor and address embedded escapes
Message-ID: <4D028B91.5050408 at ccbr.umn.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Does the following help?
A = c("A\\nB", "C\\nD")
test <-data.frame(A)
#access levels directly to change names
levels(test$A) <- sub("\\\\n", "\n", levels(test$A))
#re-order levels of the factor
test$A <- relevel(test$A, "C\nD")
Rob James wrote:> I am trying to reorder a factor variable that has embedded escape
> characters. The data begins as a csv file with a factor that includes
> embedded new line characters. By the time read.table has rendered it
> into a data frame, the variable now has an extra backslash.
>
> e.g.
> "This\nLabel" in the csv becomes "This\\nLabel" in the
data frame.
>
> So, I am trying to reorder the factor and deal with the introduction of
> a secondary \ . Here's a small example:
>
>
> A = c("A\\nB", "C\\nD")
> test <-data.frame(A)
> str(test)
> test$reorderA <-factor(test$A, c("C\\nD", "A\\nB"))
> str(test)
> test$reorderB <-sub("\\\\n", "\n", test$reorderA)
> str(test)
>
> When sub is applied to the now-correctly ordered factor, it returns to
> the default ordering.
>
> Suggestions?
>
> ______________________________________________
> 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: 65
Date: Fri, 10 Dec 2010 15:31:21 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: Rob James <rob at aetiologic.ca>
Cc: r-help at r-project.org
Subject: Re: [R] Reorder factor and address embedded escapes
Message-ID: <A25DDB11-1027-47F8-89C2-41AB1D7DA30B at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Dec 10, 2010, at 3:14 PM, Rob James wrote:
> I am trying to reorder a factor variable that has embedded escape
> characters. The data begins as a csv file with a factor that
> includes embedded new line characters. By the time read.table has
> rendered it into a data frame, the variable now has an extra
> backslash.
>
> e.g.
> "This\nLabel" in the csv becomes "This\\nLabel" in the
data frame.
>
> So, I am trying to reorder the factor and deal with the introduction
> of a secondary \ . Here's a small example:
>
>
> A = c("A\\nB", "C\\nD")
> test <-data.frame(A)
> str(test)
> test$reorderA <-factor(test$A, c("C\\nD", "A\\nB"))
> str(test)
> test$reorderB <-sub("\\\\n", "\n", test$reorderA)
> str(test)
>
> When sub is applied to the now-correctly ordered factor, it returns
> to the default ordering.
Actually it returns a character vector rather than a factor.
>
> Suggestions?
Perhaps you should ask a question.
--
David Winsemius, MD
West Hartford, CT
------------------------------
Message: 66
Date: Fri, 10 Dec 2010 22:34:23 +0200
From: Tal Galili <tal.galili at gmail.com>
To: Matt Shotwell <shotwelm at musc.edu>
Cc: "r-help at r-project.org" <r-help at r-project.org>
Subject: Re: [R] Encoding problem - I fails to read Hebrew text from
online
Message-ID:
<AANLkTikb1HeF+5LwWqBkvav59eZLkpHx6=T6eR_sygBL at mail.gmail.com>
Content-Type: text/plain
Hi Matt and everyone else,
Thanks for the help so far.
I ended up using the tips provided to create a "dirty hack" based on a
translation table between the code and the Hebrew letters.
For the future (and for any suggestions), I am attaching this code bellow:
Best,
Tal
# the translation table:
translation.table.Hebrew <- structure(list(V1 = structure(1:27, .Label
c("05D0", "05D1",
"05D2", "05D3", "05D4", "05D5",
"05D6", "05D7", "05D8",
"05D9", "05DA", "05DB", "05DC",
"05DD", "05DE", "05DF",
"05E0", "05E1", "05E2", "05E3",
"05E4", "05E5", "05E6",
"05E7", "05E8", "05E9", "05EA"), class =
"factor"), V2 = structure(1:27,
.Label = c("??",
"?'", "?'", "?"",
"?"", "?.", "?-", "?-",
"?~", "?T", "?s", "?>",
"?o", "??",
"?z", "?Y", "??", "??", "??",
"??", "??", "??", "??", "??",
"??", "??", "??"
), class = "factor")), .Names = c("CODE",
"HEBREW"), class = "data.frame",
row.names = c(NA,
-27L))
# translation.table
# STRING = inp
turn_nohash <- function(STRING)
{
require(stringr)
nohash <- str_replace(STRING, "#", "0") # cvrt # to 0
nohash <- str_replace(nohash, ";", "") # cvrt # to 0
nohash <- str_replace(nohash, "&", "") # cvrt # to
0
nohash <- str_replace(nohash, "x", "") # cvrt # to 0
return(nohash)
}
translate.all.chars <- function(STRING, TABLE = translation.table.Hebrew)
{
# TABLE is of the form:
# CODE HEBREW
# 1 05D0 ??
# 2 05D1 ?'
# 3 05D2 ?'
require(stringr)
i.chars.to.check <- seq_len(dim(TABLE)[1])
for(i in i.chars.to.check)
{
STRING <- str_replace(STRING, as.character(TABLE[i,1]),
as.character(TABLE[i,2]))
}
return(STRING)
}
HTML_heb_decode <- function(STRING, TABLE = translation.table.Hebrew)
{
STRING <- turn_nohash(STRING)
STRING <- translate.all.chars(STRING, TABLE)
return(STRING)
}
# example of use:
inp <- "שלום"
HTML_heb_decode(inp)
inp <- "שלום
חנוך\ "
HTML_heb_decode(inp)
ourput:
> HTML_heb_decode(inp)
Loading required package: stringr
Loading required package: plyr
[1] "???o?.??"> inp <- "שלום
חנוך\ "
> HTML_heb_decode(inp)
[1] "???o?.?? ?-???.?s "
----------------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, Dec 10, 2010 at 12:00 AM, Matt Shotwell <shotwelm at musc.edu>
wrote:
> Tal,
>
> OK, let me clarify my understanding. The original and decoded file are
> text, encoded by UTF-8. In the original file, there are HTML `entities'
> that represent UTF-8 Hebrew characters. In the decoded file, the
> entities are converted to UTF-8 characters. The question is how to
> convert these entities within R. It's not the same as converting
between
> character encodings, otherwise iconv() might offer a solution.
>
> I'll have a look around to find a solution, and I hope others will too.
> My first idea is to check RCurl, XML, and the related utils::URLdecode.
> If there really is no existing solution, I think it might be worthwhile
> to look at how PHP and Python do it (and maybe borrow some code :) ).
>
> -Matt
>
>
> On Thu, 2010-12-09 at 14:27 -0500, Tal Galili wrote:
> > Hi Matt,
> > Thanks for having a look at this.
> > I just spent some time looking around and couldn't find any R
function
> > to decode decimal HTML code.
> >
> >
> > Do you (or someone else on the list) knows how to program this sort of
> > thing? (is there a formula for the translation?
> >
> >
> >
> >
> > p.s:
> > For it to work on my end I added the encoding parameter:
> > readLines("http://biostatmatt.com/temp/Hebrew-decoded",
warn=FALSE,
> > encoding= "UTF-8")
> >
> >
> > p.p.s: The Hebrew word I used means "peace"
> >
> >
> > Cheers,
> > 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 Thu, Dec 9, 2010 at 8:38 PM, Matt Shotwell <shotwelm at
musc.edu>
> > wrote:
> > Tal,
> >
> > It looks like the data you received has HTML special hex
> > characters.
> > That is, 'ש' is just an ASCII HTML
representation of a
> > hex
> > character. It's not encoded in a special manner.
> >
> > The trick is to substitute the HTML encoded hex character for
> > its binary
> > representation, or "decode" the character. I
don't know of any
> > R
> > function that does this, but there are web services, for
> > example:
> > http://www.hashemian.com/tools/html-url-encode-decode.php
> >
> > I decoded your file using this service and posted it on my
> > website. You
> > can see the difference by running:
> >
> >
readLines("http://biostatmatt.com/temp/Hebrew-original",
> > warn=FALSE)
> >
> >
readLines("http://biostatmatt.com/temp/Hebrew-decoded",
> > warn=FALSE)
> >
> > The second should display the Hebrew characters correctly (it
> > does in my
> > terminal). The next thing to think about is how to automate
> > this in R
> > without using the web service... We may need to write an
> > HTMLDecode
> > function if there isn't one already.
> >
> > By the way, what's the Hebrew text in English?
> >
> > Best,
> > Matt
> >
> >
> >
> > On Thu, 2010-12-09 at 12:21 -0500, Tal Galili wrote:
> > > I am bumping this question in the hopes that someone
might
> > be able to
> > > advise.
> > > This Hebrew and R business is not as smooth as I had
> > hoped...
> > >
> > > Thanks,
> > > Tal
> > >
> > > Older massage:
> > >
> > > On Tue, Dec 7, 2010 at 2:30 PM, Tal Galili
> > <tal.galili at gmail.com> wrote:
> > >
> > > > Hello all,
> > > >
> > > > # I am trying to read the text in this URL:
> > > > u <-
> > > >
http://google.com/complete/search?output=toolbar&q=%d7%a9%
> > d7%9c%d7%95%d7%9d
> > > > # By using this command:
> > > > readLines(u)
> > > >
> > > > And no matter what variation I tried, I keep getting
this
> > output:
> > > > [1] "<?xml version=\"1.0
> >
\"?><toplevel><CompleteSuggestion><suggestion
> > > >
data=\"שלום\"/><
(etc...)
> > > >
> > >
> > >
> > > > Instead of this output:
> > > > <?xml
> >
version="1.0"?><toplevel><CompleteSuggestion><suggestion
> > data="???o?.??
> > > > "/><num_queries
> >
>
int="16800000"/></CompleteSuggestion><CompleteSuggestion><suggestion
> > > > data="???o?.??
?-???.?s"/><num_queries
> > int="232000"/></CompleteSuggestion>
> > > > <CompleteSuggestion><suggestion
data="???o?.?? ???o?T?>??"/
> > > > (etc....)
> > > >
> > > >
> > >
> > > > I tried:
> > > > readLines(u, encoding= "latin1")
> > > > readLines(u, encoding= "UTF-8")
> > > > And also changing Sys.setlocale:
> > > > Sys.setlocale("LC_ALL",
"Hebrew") # must be done for
> > Hebrew to work.
> > > > Sys.setlocale("LC_ALL",
"English") # must be done for
> > Hebrew to work.
> > > >
> > > > Are there any more options I could try to get this
text
> > properly encoded?
> > > >
[[elided Yahoo spam]]> > > > 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)
> > > >
> > > >
> >
>
----------------------------------------------------------------------------------------------
> > > >
> > > >
> > > >
> > >
> >
> > > [[alternative HTML version deleted]]
> > >
> >
> > --
> > Matthew S. Shotwell
> > Graduate Student
> > Division of Biostatistics and Epidemiology
> > Medical University of South Carolina
> >
> >
> >
>
> --
> Matthew S. Shotwell
> Graduate Student
> Division of Biostatistics and Epidemiology
> Medical University of South Carolina
>
>
[[alternative HTML version deleted]]
------------------------------
Message: 67
Date: Fri, 10 Dec 2010 23:26:28 +0200
From: "dorina.lazar" <dorina.lazar at econ.ubbcluj.ro>
To: <r-help at r-project.org>
Subject: [R] spatial clusters
Message-ID: <7aad2cfb7a3d00c107ecb37cecea9f7d at econ.ubbcluj.ro>
Content-Type: text/plain; charset=UTF-8
Dear all,
I am looking for a clustering method usefull to classify the countries in
some clusters taking account of: a) the geographical distance (in km)
between countries and b) of some macroeconomic indicators (gdp, life
expectancy...).
Are there some packages in R usefull for this?
Thanks a lot for your help,
Dorina
------------------------------
Message: 68
Date: Fri, 10 Dec 2010 16:31:32 -0500
From: Gabor Grothendieck <ggrothendieck at gmail.com>
To: dreadgazebo <ernie.tedeschi at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Time Series Row Label
Message-ID:
<AANLkTikYh1iFRCBAeDyUoAhO+ETP3KOrFBuzpSH8q1fX at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Fri, Dec 10, 2010 at 3:16 PM, dreadgazebo <ernie.tedeschi at gmail.com>
wrote:>
> Simple question...
>
> I know that when referencing data in a multivariate time series matrix, I
> can use the variable name instead of the column number (such as
> budget.ts[4,"incometax"]). Is there a way I can use the time unit
(say, the
> year in an annual time series) instead of the row number?
You can use window(), e.g.
tt <- ts(1:4, start = 2000)
window(tt, start = 2001, end = 2002)
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
------------------------------
Message: 69
Date: Fri, 10 Dec 2010 13:39:33 -0800
From: Patrick McKann <pcmckann at gmail.com>
To: r-help at r-project.org
Subject: [R] WriteXLS error:Error in get(x, envir = envir) : variable
names are limited to 256 bytes
Message-ID:
<AANLkTim5tFDvcu9hRj3jGMOqK8cNzqg8WhveSbpB67WG at mail.gmail.com>
Content-Type: text/plain
Hello all,
I don't understand why this won't work. I have entered:
WriteXLS(alldata,'test.xls')
and I get this error message:
Error in get(x, envir = envir) : variable names are limited to 256 bytes.
My variable names are not very long, and are accepted by write.csv.
alldata is a list containing 4 dataframes, with each dataframe having the
the same variable names, which are:
> names(avg8302)
[1] "ID" "cluster" "rec.unit"
"int.hib"
"yr.hib" "yr0309.hib" "int.hib.se"
"yr.hib.se" "
yr0309.hib.se" "int.cl"
[11] "yr.cl" "yr0309.cl" "int.cl.se"
"yr.cl.se" "
yr0309.cl.se" "int.ru" "yr.ru"
"yr0309.ru" "int.ru.se"
"yr.ru.se"
[21] "yr0309.ru.se" "int.sp" "yr.sp"
"yr0309.sp" "
int.sp.se" "yr.sp.se"
"yr0309.sp.se">
Does anybody know how I can fix this? Or another way to write a multi-sheet
xls?
Thank you.
[[alternative HTML version deleted]]
------------------------------
Message: 70
Date: Fri, 10 Dec 2010 13:53:08 -0800 (PST)
From: casperyc <casperyc at hotmail.co.uk>
To: r-help at r-project.org
Subject: [R] How to print colorful R output??
Message-ID: <1292017988649-3082750.post at n4.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi All,
I wonder if there is a way to print the R output with COLOR?
Not the color plots, but the outputs in the console.
Thank.
casper
--
View this message in context:
http://r.789695.n4.nabble.com/How-to-print-colorful-R-output-tp3082750p3082750.html
Sent from the R help mailing list archive at Nabble.com.
------------------------------
Message: 71
Date: Fri, 10 Dec 2010 17:02:43 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: Patrick McKann <pcmckann at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] WriteXLS error:Error in get(x, envir = envir) :
variable names are limited to 256 bytes
Message-ID: <2C68E697-86FF-4D7C-ABC0-5667437E548F at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Dec 10, 2010, at 4:39 PM, Patrick McKann wrote:
> Hello all,
> I don't understand why this won't work. I have entered:
>
> WriteXLS(alldata,'test.xls')
I have gotten tripped up by the argument syntax in WriteXLS myself,
many times. Please check the help page for argument names and use
them, especially paying attention to the fact that the first argument
needs to be a character _vector_ (and I suspect that passing it a list
may not qualify) and I always use the name for the Excel file
argument. I suspect that this may work:
WriteXLS('alldata','test.xls')
--
David.
>
> and I get this error message:
>
> Error in get(x, envir = envir) : variable names are limited to 256
> bytes.
>
> My variable names are not very long, and are accepted by write.csv.
>
> alldata is a list containing 4 dataframes, with each dataframe
> having the
> the same variable names, which are:
>
>> names(avg8302)
> [1] "ID" "cluster"
"rec.unit" "int.hib"
> "yr.hib" "yr0309.hib" "int.hib.se"
"yr.hib.se" "
> yr0309.hib.se" "int.cl"
> [11] "yr.cl" "yr0309.cl"
"int.cl.se" "yr.cl.se" "
> yr0309.cl.se" "int.ru" "yr.ru"
"yr0309.ru"
> "int.ru.se"
> "yr.ru.se"
> [21] "yr0309.ru.se" "int.sp" "yr.sp"
"yr0309.sp" "
> int.sp.se" "yr.sp.se" "yr0309.sp.se"
>>
>
> Does anybody know how I can fix this? Or another way to write a
> multi-sheet
> xls?
>
> Thank you.
>
> [[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: 72
Date: Fri, 10 Dec 2010 17:14:38 -0500
From: David Winsemius <dwinsemius at comcast.net>
To: David Winsemius <dwinsemius at comcast.net>
Cc: r-help at r-project.org, Patrick McKann <pcmckann at gmail.com>
Subject: Re: [R] WriteXLS error:Error in get(x, envir = envir) :
variable names are limited to 256 bytes
Message-ID: <29D67E79-2FA8-4827-BBA2-E1C668C22E5F at comcast.net>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
On Dec 10, 2010, at 5:02 PM, David Winsemius wrote:
>
> On Dec 10, 2010, at 4:39 PM, Patrick McKann wrote:
>
>> Hello all,
>> I don't understand why this won't work. I have entered:
>>
>> WriteXLS(alldata,'test.xls')
>
> I have gotten tripped up by the argument syntax in WriteXLS myself,
> many times. Please check the help page for argument names and use
> them, especially paying attention to the fact that the first
> argument needs to be a character _vector_ (and I suspect that
> passing it a list may not qualify) and I always use the name for the
> Excel file argument. I suspect that this may work:
>
> WriteXLS('alldata','test.xls')
OOOPs. I wrote that before I noted that you said you were using a
list, and I forgot to go back and fix it, so that would NOT
work.>
> --
> David.
>
>>
>> and I get this error message:
>>
>> Error in get(x, envir = envir) : variable names are limited to 256
>> bytes.
>>
>> My variable names are not very long, and are accepted by write.csv.
>>
>> alldata is a list containing 4 dataframes, with each dataframe
>> having the
>> the same variable names, which are:
>>
>>> names(avg8302)
>> [1] "ID" "cluster"
"rec.unit" "int.hib"
>> "yr.hib" "yr0309.hib"
"int.hib.se" "yr.hib.se" "
>> yr0309.hib.se" "int.cl"
>> [11] "yr.cl" "yr0309.cl"
"int.cl.se"
>> "yr.cl.se" "
>> yr0309.cl.se" "int.ru" "yr.ru"
"yr0309.ru"
>> "int.ru.se"
>> "yr.ru.se"
>> [21] "yr0309.ru.se" "int.sp"
"yr.sp"
>> "yr0309.sp" "
>> int.sp.se" "yr.sp.se" "yr0309.sp.se"
>>>
>>
>> Does anybody know how I can fix this? Or another way to write a
>> multi-sheet
>> xls?
>>
>> Thank you.
>>
>> [[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
>
> ______________________________________________
> 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: 73
Date: Fri, 10 Dec 2010 23:06:27 +0000 (UTC)
From: Ben Bolker <bbolker at gmail.com>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] Stricter read.table?
Message-ID: <loom.20101211T000025-611 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii
Stavros Macrakis <macrakis <at> alum.mit.edu> writes:
>
> read.table gives idiosyncratic results when the input is formatted
> strangely, for example:
>
> read.table(textConnection(
"a'b\nc'd\n"),header=FALSE,
fill=TRUE,sep="",quote="'")> => "c'd" "a'b" "c'd"
>
>
> read.table(textConnection(
"a'b\nc'd\nf'\n'\n"),
header=FALSE,fill=TRUE
sep="",quote="'")> => "f'" "\na" "b"
"c'd" "f'" "\n"
>
> Though read.table doesn't specify the syntax of its input precisely,
these
> results don't seem particularly useful or consistent.
>
> Is there a stricter version of read.table (perhaps in a package) that gives
> errors or warnings if it finds quotation marks in the middle of fields or
> encounters other such peculiar situations?
I dissected this behavior a bit more here
<https://stat.ethz.ch/pipermail/r-devel/2010-November/059016.html>
(it is due to an inconsistency between the way that scan() and
readLines() handle lines with unterminated quotes, IIRC)
and Martin Maechler said
<https://stat.ethz.ch/pipermail/r-devel/2010-November/059107.html>
"I think it can be defended to file as a bug, but it is tricky to pinpoint
exactly what the issue is."
I don't know of a stricter version of read.table(), but if you had
the time and inclination to pick through the code and (i) provide a
careful definition of desired behavior and (ii) supply patches, you could
do your little bit to make R better. (If I posted a bug report would you
annotate it with a discussion of desired behavior?)
------------------------------
Message: 74
Date: Fri, 10 Dec 2010 18:10:42 -0500
From: Stavros Macrakis <macrakis at alum.mit.edu>
To: r-help <r-help at r-project.org>
Subject: [R] Quantile with discrete types
Message-ID:
<AANLkTi=YXVGnd4NcrurJ3TXBsH74WMEgwWeMM3DaP6T_ at mail.gmail.com>
Content-Type: text/plain
I don't understand why 'quantile' works in this case:
> tt <- rep(c('a','b'),c(10,3))
> sapply(0:6/6,function(q) quantile(tt,probs=q,type=1))
0% 16.66667% 33.33333% 50% 66.66667% 83.33333% 100%
"a" "a" "a" "a"
"a" "b" "b"
and also
> quantile(tt,0:5/5,type=1)
0% 20% 40% 60% 80% 100%
"a" "a" "a" "a" "b"
"b"
but gives an error in this, which I would have thought equivalent to the
first case above:
> quantile(tt,0:6/6,type=1)
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
argument is not a numeric vector
I could of course write something like
sort(tt)[seq(1,length(tt),length.out=7)] -- but I'm wondering why quantile
fails in this case.
Thanks,
-s
[[alternative HTML version deleted]]
------------------------------
Message: 75
Date: Fri, 10 Dec 2010 23:10:18 +0000 (UTC)
From: Ben Bolker <bbolker at gmail.com>
To: r-help at stat.math.ethz.ch
Subject: Re: [R] [r] overlap different line in a xyplot (lattice)
Message-ID: <loom.20101211T000730-842 at post.gmane.org>
Content-Type: text/plain; charset=us-ascii
Peter Ehlers <ehlers <at> ucalgary.ca> writes:
>
> On 2010-12-10 07:04, Francesco Nutini wrote:
> >
> > dear [R] users,
> > is there a way to plot different data (but with the same x-variables)
> in the same xyplot window?
> > There are already a similar question, but the answer is
> not enought explanatory...
>
> Something like this?
>
[snip]
Also possibly the layer() command in the latticeExtra package.
If there is an answer that doesn't make sense to you it might
be most efficient to post an edited version of that question/answer,
attempting to clarify which parts of the answer you do and don't
understand ...
A reproducible example would be nice too.
Ben Bolker
------------------------------
Message: 76
Date: Fri, 10 Dec 2010 15:51:49 -0500
From: Layla Parast <lparast at fas.harvard.edu>
To: r-help at r-project.org
Subject: [R] locfit weights not working as expected
Message-ID:
<AANLkTikzs66VrZbO13iq=WhSWxc-GSLmyOtCRNgxsNV2 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello! I am having a problem understanding what the weights option in
the locfit command of the locfit package is doing. I
have written a sample program which illustrates the issue (below). The
example involves using bootstrap however, that is not my main
goal but it illustrates where my problem lies.
As you know, to compute a bootstrap estimate of a particular quantity
using a sample size of size N, I would sample a multinomial vector
which should be of size N with possible values 1:N. I should get the
exact same answer whether I a) estimate the quantity using this
multinomial vector as the indices i.e. literally make a new sample by
choosing each element according to the number of time in the
corresponding index or b) estimate the quantity using the original
data and specify this multinomial vector as the "weights". In all
commands that I have tried, the weights functions works such that this
is always true. This is not true for the locfit command. The models
are different, the coefficients are different, the predictions are
different. I have tried several combinations of things including
specifying different options for the evaluation points, different
kernels, different datasets to predict and I cannot find any way to
make these equal. For my particular simulation, I need to understand
exactly what the weights option is doing since it is clearly not doing
what I expected it to. I would gratefully appreciate any advice or
help that anyone can give on this issue and I appreciate your time very much.
library(MASS)
library(splines)
library(sm)
library(quantreg)
library(locfit)
set.seed(20)
Zi = rnorm(5000,0, 2)
ei = mvrnorm(5000, c(.6,2), matrix(c(.7,0,0,.9),2,2))
X1i = exp(-.5*Zi + ei[,1])
X2i = exp(-.5*(Zi*log(T1i) -log(T1i) + Zi) + ei[,2])
X1i = log(X1i)
boot.weight = rmultinom(1,5000, prob=rep(1/5000, 5000))
boot.subset = rep(1:5000, boot.weight)
loc.model.1 = locfit(1*(X2i[boot.subset]< 10) ~ lp(X1i[boot.subset],
Zi[boot.subset], style = c ? ? ?("n","cpar"), h=0.4, deg =
1, nn=0), family
= "binomial", link = "logit")
loc.model.2 = locfit(1*(X2i< 10) ~ lp(X1i, Zi, style =
c("n","cpar"),
h=0.4, deg = 1,nn=0), family = "binomial", link = "logit",
weights=boot.weight)
print(loc.model.1)
print(loc.model.2)
t.vector = log(seq(0.5,10, length=300))
p.0.1 = predict(loc.model.1, newdata=cbind(t.vector, rep(0,length(t.vector))))
p.0.2 = predict(loc.model.2, newdata=cbind(t.vector, rep(0,length(t.vector))))
#quantity below should be vector of zeros but it is not.
p.0.1-p.0.2
------------------------------
Message: 77
Date: Fri, 10 Dec 2010 17:05:10 -0600
From: simon lu <simonlmg at gmail.com>
To: r-help at r-project.org
Subject: [R] R question: memory usage
Message-ID:
<AANLkTimMP1NibCS4xpK_zSwhhuSG=nis5EegLrZGHmbv at mail.gmail.com>
Content-Type: text/plain
Hi
I have a large R progress that that is constently running into memory
issues, I am trying to rewrite some of the code to make more efficeint
However, one thing I have found is that the memory usage shown by gc() is
very different from what i see from unix termilnal
Garbage collection 2047 = 1398+243+406 (level 2) ...
12.4 Mbytes of cons cells used (3%)
998.6 Mbytes of vectors used (23%)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 231884 12.4 8140556 434.8 12719620 679.4
Vcells 130881306 998.6 572307468 4366.4 713657158 5444.8
vs
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
26291 s_edge 25 0 2883m 8.2g 4276 R 99.7 48.0 10:35.31 R
Am i missing something here?
Thanks a lot for the help
Simon
[[alternative HTML version deleted]]
------------------------------
Message: 78
Date: Fri, 10 Dec 2010 23:59:10 -0500
From: Dennis Duro <dennis.duro at gmail.com>
To: r-help at r-project.org
Subject: [R] randomForest: help with combine() function
Message-ID:
<AANLkTind5kV=Ku5GXX=YGvk5fx5DY-cRE_gbHCGB=QYz at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I've built two RF objects (RF1 and RF2) and have tried to combine
them, but I get the following error:
Error in rf$votes + ifelse(is.na(rflist[[i]]$votes), 0, rflist[[i]]$votes) :
non-conformable arrays
In addition: Warning message:
In rf$oob.times + rflist[[i]]$oob.times :
longer object length is not a multiple of shorter object length
Both RF models use the same variables, although the NAs in both models
likely differ (using na.roughfix in both models). I assume this is
part of the reason that my arrays are "non-conformable". If so, does
anyone have any suggestions on how to combine in such a situation? How
similar do RFs have to be in order to combine?
Cheers
------------------------------
Message: 79
Date: Fri, 10 Dec 2010 23:15:22 -0600
From: Yihui Xie <xie at yihui.name>
To: casperyc <casperyc at hotmail.co.uk>
Cc: r-help at r-project.org
Subject: Re: [R] How to print colorful R output??
Message-ID:
<AANLkTimPn=WhvAyrMOH6U+kMrWDVM7Pyjgf=fvGWzT2e at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Yes (depending on what you mean by "output"), but maybe there is a
long way to go. The vignette of the Rd2roxygen package is an example:
http://cran.r-project.org/web/packages/Rd2roxygen/vignettes/Rd2roxygen.pdf
It makes use of the highlight package and Sweave to output colored
code. If the style of the above vignette is what you want, more
details are here:
http://yihui.name/en/2010/10/how-to-start-using-pgfsweave-in-lyx-in-one-minute/
Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Fri, Dec 10, 2010 at 3:53 PM, casperyc <casperyc at hotmail.co.uk>
wrote:>
> Hi All,
>
> I wonder if there is a way to print the R output with COLOR?
> Not the color plots, but the outputs in the console.
>
> Thank.
>
> casper
> --
> View this message in context:
http://r.789695.n4.nabble.com/How-to-print-colorful-R-output-tp3082750p3082750.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: 80
Date: Fri, 10 Dec 2010 23:57:14 -0600
From: Marc Schwartz <marc_schwartz at me.com>
To: David Winsemius <dwinsemius at comcast.net>
Cc: r-help at r-project.org, Patrick McKann <pcmckann at gmail.com>
Subject: Re: [R] WriteXLS error:Error in get(x, envir = envir) :
variable names are limited to 256 bytes
Message-ID: <0DF6AE39-8D86-424C-9E1B-765D372DC376 at me.com>
Content-Type: text/plain; charset=us-ascii
On Dec 10, 2010, at 4:14 PM, David Winsemius wrote:
>
> On Dec 10, 2010, at 5:02 PM, David Winsemius wrote:
>
>>
>> On Dec 10, 2010, at 4:39 PM, Patrick McKann wrote:
>>
>>> Hello all,
>>> I don't understand why this won't work. I have entered:
>>>
>>> WriteXLS(alldata,'test.xls')
>>
>> I have gotten tripped up by the argument syntax in WriteXLS myself,
many times. Please check the help page for argument names and use them,
especially paying attention to the fact that the first argument needs to be a
character _vector_ (and I suspect that passing it a list may not qualify) and I
always use the name for the Excel file argument. I suspect that this may work:
>>
>> WriteXLS('alldata','test.xls')
>
> OOOPs. I wrote that before I noted that you said you were using a list, and
I forgot to go back and fix it, so that would NOT work.
>>
>> --
>> David.
>>
>>>
>>> and I get this error message:
>>>
>>> Error in get(x, envir = envir) : variable names are limited to 256
bytes.
>>>
>>> My variable names are not very long, and are accepted by write.csv.
>>>
>>> alldata is a list containing 4 dataframes, with each dataframe
having the
>>> the same variable names, which are:
>>>
>>>> names(avg8302)
>>> [1] "ID" "cluster"
"rec.unit" "int.hib"
>>> "yr.hib" "yr0309.hib"
"int.hib.se" "yr.hib.se" "
>>> yr0309.hib.se" "int.cl"
>>> [11] "yr.cl" "yr0309.cl"
"int.cl.se" "yr.cl.se" "
>>> yr0309.cl.se" "int.ru" "yr.ru"
"yr0309.ru" "int.ru.se"
>>> "yr.ru.se"
>>> [21] "yr0309.ru.se" "int.sp"
"yr.sp" "yr0309.sp" "
>>> int.sp.se" "yr.sp.se"
"yr0309.sp.se"
>>>>
>>>
>>> Does anybody know how I can fix this? Or another way to write a
multi-sheet
>>> xls?
>>>
>>> Thank you.
Hi David and Patrick,
Apologies for the delay in my reply as I am away on vacation at the moment.
As David surmised initially, the name of the object(s) to be exported, needs to
be passed as a character vector. The vector can either contain the names of one
or more data frames, or can be the single name of a list of data frames. The
latter option was added in a September update. See the help page for an example
of use.
Thus:
WriteXLS("alldata", "test.xls")
should work.
HTH,
Marc Schwartz
------------------------------
Message: 81
Date: Sat, 11 Dec 2010 10:12:32 +0100
From: Liviu Andronic <landronimirc at gmail.com>
To: casperyc <casperyc at hotmail.co.uk>
Cc: r-help at r-project.org
Subject: Re: [R] How to print colorful R output??
Message-ID:
<AANLkTikLBC2-VA0k7r8Wj5xfCGa1PmOd-9o37MdXZy+- at mail.gmail.com>
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Hello
On Fri, Dec 10, 2010 at 10:53 PM, casperyc <casperyc at hotmail.co.uk>
wrote:> I wonder if there is a way to print the R output with COLOR?
> Not the color plots, but the outputs in the console.
>
I once asked for this on the list [1], and the are two points:
- although technically feasible, say using ncurses, there are
currently no facilities for automated formatting of input/output
- go for editors that do this automatically, say Emacs or JGR
Regards
Liviu
[1] http://www.mail-archive.com/r-help at r-project.org/msg86512.html
------------------------------
Message: 82
Date: Sat, 11 Dec 2010 20:17:00 +1100
From: Michael Bedward <michael.bedward at gmail.com>
To: Michael D <mike409 at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] help with RSQLite adding a new column
Message-ID:
<AANLkTikMWCtY7wkLDcknnXunHRsQhHYfnUgxUVV0dKtk at mail.gmail.com>
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Hi Michael,
Sorry if I'm being slow, but I've read your post three times and still
can't quite work out what you're trying to do (the changing variables
names are a bit confusing).
I use RSQLite a lot and might be able to help if you could explain
your inputs and desired output in simple terms.
(another) Michael
On 11 December 2010 05:18, Michael D <mike409 at gmail.com>
wrote:> I'm new to using sql so I'm having difficulties (and worries) in
adding a
> new column of data to a table I have. Its a very large file (around 5 Gb)
> which is why I'm having to use SQL
>
> I have a table with variables ID, IDrec and IDdes and the variables IDrec
> and IDdes give a mapping of some other values but the other values are
> associated with the ID variable (think of IDrec and IDdes being character
> strings and ID being numeric)
>
> (Imagine the transposed)
> Table1:
> ID: 1,2,3,4,...
> IDrec: A,B,C,D...
> IDdes: B,C,A,E...
>
> So I've created a table with the final form I need it to be in
>
> dbGetQuery(db, "CREATE TABLE Map
> ? ? ? ? ? ? ? ?(ID int, IDrec int, IDrec1 int,
> ? ? ? ? ? ? ? ?IDdes int, IDdes1 int)")
>
> And the finished table would look something like:
> Map:
> ID: 1, 2, 3, 4,...
> IDrec: 1, 2, 3, 4,...
> IDrec1: A, B, C, D,...
> IDdes: 2, 3, 1, 5,....
> IDdes1: B, C, A, E,...
>
> So I copy in the first set of values easily:
> dbGetQuery(db, "INSERT INTO Map(ID, IDrec, IDrec1, IDdes1)
> ? ? ? ? ? ? ? ?SELECT ID, ID, IDrec, IDdes FROM Ntemp")
>
> Giving me a table that looks like:
> Map:
> ID: 1, 2, 3, 4,...
> IDrec: 1, 2, 3, 4,...
> IDrec1: A, B, C, D,...
> IDdes: NA,NA,NA,NA,...
> IDdes1: B, C, A, E,...
>
> Then I create a new table with just the IDdes values I need:
> dbGetQuery(db, "Create table temp2 as
> ? ? ? ? ? ? ? ?SELECT temp.ID
> ? ? ? ? ? ? ? ?FROM Ntemp, temp
> ? ? ? ? ? ? ? ?WHERE Ntemp.IDdes1 = temp.IDrec1")
>
> Giving me temp2 (not sure what the variable name is)
> V1: 2, 3, 1, 5,...
>
> But when I try to copy in the new data:
> dbGetQuery(db, "INSERT INTO Map(IDdes)
> ? ? ? ? ? ? ? ?SELECT * FROM temp2")
>
> My map table isn't updated:
> Map:
> ID: 1, 2, 3, 4,...
> IDrec: 1, 2, 3, 4,...
> IDrec1: A, B, C, D,...
> IDdes: NA,NA,NA,NA,...
> IDdes1: B, C, A, E,...
>
> Is there something I'm missing? Or am I just going about inserting the
IDdes
> variables the wrong way?
>
> Thanks for the help.
> Michael
>
> ? ? ? ?[[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: 83
Date: Sat, 11 Dec 2010 20:51:02 +1100
From: Jim Lemon <jim at bitwrit.com.au>
To: Simon Kiss <simonjkiss at yahoo.ca>
Cc: r-help at r-project.org
Subject: Re: [R] 45 Degree labels on barplot? Help understanding code
previously posted.
Message-ID: <4D034986.9070001 at bitwrit.com.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 12/11/2010 02:25 AM, Simon Kiss wrote:> Dear colleagues,
> i found a line or two of code in the help archives from Uwe Ligges about
creating slanted x-labels for a barplot and it works well for my purposes (code
below). However, I was hoping someone could explain to me precisely what the
code is doing.
> I'm aware it's invoking the text command, and I know the first ttwo
arguments to text are x and y co-ordinates. I'm also aware that
par("usr")[3] is grabbing the third element of the vector of plotting
co-ordinates. But I tried replacing par("usr")[3] with just
"0" and that didn't work; all the labels got bunched up on the
left. Is it necessary to create a new object via "barplot" and then
quote that in the x,y coordinates of text?
> Like I said, the code works great, but I'm trying to actually
understand the rationale behind the elements so I can apply it in future.
Hi Simon,
The staxlab function will add an axis to an existing plot with either
staggered or rotated labels. It is somewhat similar to Uwe's function.
Looking at both the code and the examples on the help page might give
you some idea why the function was written. It is principally to allow
the user to add more labels than would be displayed on the default axes,
and to decide whether staggering or rotating those labels will produce a
better looking plot. The problem most often mentioned in adding custom
labels to a plot produced by barplot is that the bars are centered on
non-integer values, and so the user must get the return value of barplot
and use that for the axis label positions.
Jim
------------------------------
Message: 84
Date: Sat, 11 Dec 2010 11:36:30 +0100
From: Petr PIKAL <petr.pikal at precheza.cz>
To: Amelia Vettori <amelia_vettori at yahoo.co.nz>
Cc: r-help at r-project.org
Subject: Re: [R] Adding numbers in Outputs
Message-ID:
<OFB14F81D0.633C61D4-ONC12577F6.0039EC79-C12577F6.003A5B1A at
precheza.cz>
Content-Type: text/plain; charset="US-ASCII"
Hi
r-help-bounces at r-project.org napsal dne 10.12.2010 15:00:12:
> Dear Mr Holtman Sir,
>
> Thanks a lot for your great solution. This certainly is helping me
achieve > what I need to get. However, I shall be hugely thankful to you if you
can > guide me in one respect.
>
> Sir, you have used following commands to assign values to x and y.
>
> > x <- list(40, c(80,160), c(160,80,400))
> > y <- list(10, c(10,30), c(5,18,20))
> > z <- c(1,2,3)
>
> But Sir, the problem is these values are basically outputs of some other
> process which I am running and chances are these will vary. Sir, it will
be a > great help if you can guide me to convert the output (which I am
getting)>
> X
> [[1]]
> [1] 40
>
> [[2]]
> [1] 80 160
>
> [[3]]
> [1] 160 80 400
>
I believe this object is probably list too so Jim's answer shall work on
it. See what str(X) gives you as an output.
Regards
Petr
> to what you have suggested
>
> x <- list(40, c(80,160), c(160,80,400))
>
> So, in that case once I get output in my format, I will convert that
output as> provided by you.
>
> I apologize for taking the liberty of writing to you, but I shall be
really > grateful to you, as I have just started getting the feel of 'R' and
I
know I > need to take lots of efforts to begin with.
>
> Thanks and eagerly waiting for your guidance.
>
> Amelia Vettori
>
> --- On Fri, 10/12/10, jim holtman <jholtman at gmail.com> wrote:
>
> From: jim holtman <jholtman at gmail.com>
> Subject: Re: [R] Adding numbers in Outputs
> To: "Amelia Vettori" <amelia_vettori at yahoo.co.nz>
> Cc: r-help at r-project.org
> Received: Friday, 10 December, 2010, 1:43 PM
>
> try this:
>
> > x <- list(40, c(80,160), c(160,80,400))
> > y <- list(10, c(10,30), c(5,18,20))
> > z <- c(1,2,3)
> > mapply(function(a1,a2,a3){
> + a3 * sum(a1 * a2)
> + }
> + , x
> + , y
> + , z
> + )
> [1] 400 11200 30720
>
>
> On Fri, Dec 10, 2010 at 5:41 AM, Amelia Vettori
> <amelia_vettori at yahoo.co.nz> wrote:
[[elided Yahoo spam]]> >
> > I am Amelia from Auckland and work for a bank. I am new to R and I
have > started my venture with R just a couple of weeks back and this is my
first > mail to R-forum. I need following assistance
> >
> > Suppose my R code generates following outputs as
> >
> >
> >> X
> > [[1]]
> > [1] 40
> >
> > [[2]]
> > [1] 80 160
> >
> > [[3]]
> > [1] 160 80 400
> >
> >
> >> Y
> >
> > [[1]]
> >
> > [1] 10
> >
> >
> >
> > [[2]]
> >
> > [1] 10 30
> >
> >
> >
> > [[3]]
> >
> > [1] 5 18 20
> >
> > and suppose
> >
> > Z = c(1, 2, 3)
> >
> > I need to perform the calculation where I will be multiplying
corresponding > terms of X and Y individually and multiplying their sum by Z and store
these > results in a dataframe.
> >
> > I.e. I need to calculate
> >
> > (40*10) * 1 # (first element of X +
First > element of Y) * Z[1] = 400
> >
> > ((80*10)+(160*30)) * 2 # 2 row of X and 2nd row of Y =
11200> >
> > ((160*5)+(80*18)+(400*20)) * 3 # 3rd row of X and 3 row of Y and
Z[3] = 30720> >
> >
> >
> > So the final output should be
> >
> > 400
> > 11200
> > 30720
> >
> >
> > One way of doing it is write R code for individual rows and
> > arrive at the result e.g.
> >
> > ([[X]][1]*[[Y]][1])*1 will result in 400. However, I was just trying
to know> some smart way of doing it as there could be number of rows and writing
code > for each row will be a cumbersome job. So is there any better way to do
it?> >
> > Please guide me.
> >
> > I thank you in advance.
> >
> > Thanking
> > all
> >
> > Amelia
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > [[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.
> >
> >
>
>
>
> --
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
>
>
>
>
> [[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.
------------------------------
_______________________________________________
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.
End of R-help Digest, Vol 94, Issue 11
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