2009/7/15 <r-help-request@r-project.org>
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> Today's Topics:
>
> 1. Error installing package sna (Greenerpole)
> 2. How does logLik(lm(...)) find the maximum log likelihoods
> (Lars Bergemann)
> 3. Re: .RData signature (Duncan Murdoch)
> 4. hi friends, is there any wait function in R (deepak m r)
> 5. Re: How does logLik(lm(...)) find the maximum log likelihoods
> (Achim Zeileis)
> 6. Help needed in identifying type of plot (Girish A.R.)
> 7. Re: graph: axis label font (S Ellison)
> 8. Re: hi friends, is there any wait function in R
> (ONKELINX, Thierry)
> 9. Re: read.delim skips first column (why?) (Gabor Grothendieck)
> 10. Odp: hi friends, is there any wait function in R (Petr PIKAL)
> 11. Re: Nested for loops (David Winsemius)
> 12. Re: Help needed in identifying type of plot (Christopher Jones)
> 13. Re: Help needed in identifying type of plot (ONKELINX, Thierry)
> 14. How to provide list as an argument for the data.frame()
> (Gaurav Kumar)
> 15. Re: Help needed in identifying type of plot (Girish A.R.)
> 16. Re: Nested for loops (Gabor Grothendieck)
> 17. Re: How to provide list as an argument for the data.frame()
> (David Winsemius)
> 18. Re: hi friends, is there any wait function in R (deepak m r)
> 19. Re: hi friends, is there any wait function in R (deepak m r)
> 20. Re: How to provide list as an argument for the data.frame()
> (Marc Schwartz)
> 21. 2 x 2 x 10 x 2 binomial setup (Suresh Krishna)
> 22. Re: nls - find good starting values (Antje)
> 23. Re: Nested for loops (Michael Knudsen)
> 24. Re: Nested for loops (Michael Knudsen)
> 25. Re: 2 x 2 x 10 x 2 binomial setup (Marc Schwartz)
> 26. Re: hi friends, is there any wait function in R (Duncan Murdoch)
> 27. Attributes lost after 'merge' (Frank Bloos)
> 28. LondonR meeting - 21st of July (Francisco Gochez)
> 29. Re: hi friends, is there any wait function in R (deepak m r)
> 30. Re: hi friends, is there any wait function in R (deepak m r)
> 31. Tinn-R 2.3.0.0 released (Jose Claudio Faria)
> 32. Re: Help needed in identifying type of plot (John Kane)
> 33. Re: LAPACK package (Steve Lianoglou)
> 34. Re: Fortran function for quantiles (roger koenker)
> 35. Re: hi friends, is there any wait function in R (Duncan Murdoch)
> 36. Re: hi friends, is there any wait function in R (deepak m r)
> 37. exporting list of installed packages for import on another
> system? (Jan Theodore Galkowski)
> 38. Error when sampling from SpatialLines (Elke MOONS)
> 39. Problem with GroupedData (FMH)
> 40. Linear Regression Problem (Alex Roy)
> 41. paste (" " x " ") (Paulo E. Cardoso)
> 42. Re: Linear Regression Problem (Vito Muggeo (UniPa))
> 43. Runtime Error with multinom (Andreas Wittmann)
> 44. hi, how can we avoid maskiing error in R (deepak m r)
> 45. Re: Linear Regression Problem (Alex Roy)
> 46. plotting confidence intervals (Erin Hodgess)
> 47. Re: Linear Regression Problem (Liaw, Andy)
> 48. Re: Linear Regression Problem (Ravi Varadhan)
> 49. Re: exporting list of installed packages for import on
> another system? (Marc Schwartz)
> 50. Re: exporting list of installed packages for import on
> another system? (Jan Theodore Galkowski)
> 51. Re: exporting list of installed packages for import on
> another system? (Marc Schwartz)
> 52. From list to variable name (Michelle Greve)
> 53. Re: Linear Regression Problem (Alex Roy)
> 54. Re: From list to variable name (Gabor Grothendieck)
> 55. Re: plotting confidence intervals (Marc Schwartz)
> 56. Re: hi, how can we avoid maskiing error in R (Charles C. Berry)
> 57. Trig functions strange results (Nair, Murlidharan T)
> 58. Re: plotting confidence intervals (Daniel Malter)
> 59. Re: plotting confidence intervals (Daniel Malter)
> 60. Proper Paste for Data Member (Idgarad)
> 61. Re: Proper Paste for Data Member (David Winsemius)
> 62. Re: Trig functions strange results (Ben Bolker)
> 63. Re: Problem with GroupedData (Kingsford Jones)
> 64. Re: Proper Paste for Data Member (David Winsemius)
> 65. Re: Trig functions strange results (jim holtman)
> 66. Re: paste (" " x " ") (Thomas Roth (geb. Kaliwe))
> 67. Re: paste (" " x " ") (Thomas Roth (geb. Kaliwe))
> 68. Comprehensive power analysis/sample size package in R?
> (ukoenig@med.uni-marburg.de)
> 69. How to import BIG csv files with separate "map"? (giusto)
> 70. Re: hi, how can we avoid maskiing error in R (deepak m r)
> 71. Re: Trig functions strange results (Nair, Murlidharan T)
> 72. Re: How to import BIG csv files with separate "map"?
> (Gabor Grothendieck)
> 73. Re: How to import BIG csv files with separate "map"?
> (Steve Lianoglou)
> 74. Re: hi, how can we avoid maskiing error in R (Steve Lianoglou)
> 75. Re: Trig functions strange results (Stavros Macrakis)
> 76. Re: problems with contrast matrix (Greg Snow)
> 77. Re: Nonlinear Least Squares nls() programming help (spencerg)
> 78. SweaveListingUtils question (Karsten Weinert)
> 79. (simple) xml into data.frame and reverse (stefan.duke@gmail.com)
> 80. nnet function - help! (Lars Bishop)
> 81. SOS! error in GLM logistic regression... (Michael)
> 82. Re: nls, reach limit bounds (UyenThao Nguyen)
> 83. Re: How to order an data.table by values of an column?
> (Matthew Dowle)
> 84. How do I know where is R? - VB Programming (Haoda Fu)
> 85. Re: How do I know where is R? - VB Programming (Duncan Murdoch)
> 86. Re: nls, reach limit bounds (Ravi Varadhan)
> 87. Re: How do I know where is R? - VB Programming
> (Gabor Grothendieck)
> 88. Re: SOS! error in GLM logistic regression... (Ben Bolker)
> 89. Re: getting a timeseries element into a string (spencerg)
> 90. How to combine two data frames by ID (Christopher Desjardins)
> 91. Re: How to combine two data frames by ID (jim holtman)
> 92. Matrix multiplication precision (Nair, Murlidharan T)
> 93. Read PNG file and display with more than 256 colors RGDAL
> (Paul.Rustomji@csiro.au)
> 94. ifultools on ppc debian (stephen sefick)
> 95. Correlation question (from a newbie) (Santosh)
> 96. Re: Correlation question (from a newbie) (David Winsemius)
> 97. Averaging dataframes that are stored in a list (Mark Na)
> 98. Standalone program from R script (Tanmoy Talukdar)
> 99. Re: ifultools on ppc debian (Moshe Olshansky)
> 100. Re: Standalone program from R script (Gabor Grothendieck)
> 101. POSIX, timezones and R-ODBC (Cedrick Johnson)
> 102. Re: Standalone program from R script (Tanmoy Talukdar)
> 103. Grouping data in dataframe (Timo Schneider)
> 104. Re: Grouping data in dataframe (Peter Alspach)
> 105. Re: Grouping data in dataframe (Moshe Olshansky)
> 106. Snow/openmpi (bfoubert)
> 107. Simulation functions for underdispered Poisson and binomial
> distributions (Shinichi Nakagawa)
> 108. Re: Standalone program from R script (Cedrick Johnson)
> 109. Re: Correlation question (from a newbie) (Santosh)
> 110. Re: dse model setup help (spencerg)
> 111. Re: Standalone program from R script (Gabor Grothendieck)
> 112. Re: (simple) xml into data.frame and reverse (Duncan Temple Lang)
> 113. Re: How do I know where is R? - VB Programming (Peter Dalgaard)
> 114. Re: Correlation question (from a newbie) (Santosh)
> 115. Re: (simple) xml into data.frame and reverse (Dieter Menne)
> 116. Re: Grouping data in dataframe (Dieter Menne)
> 117. Re: SOS! error in GLM logistic regression... (Gavin Simpson)
> 118. The greatest common divisor between more than two integers
> (Atte Tenkanen)
> 119. Re: The greatest common divisor between more than two
> integers (Michael Knudsen)
> 120. Re: How to deploy statistical models built in R in
> real-time? (Allan Engelhardt)
> 121. Starting RCmdr from the Commandline (and a shortcut) in
> Windows (Scott Hyde)
> 122. Re: How do I know where is R? - VB Programming
> (Gabor Grothendieck)
> 123. loading multiple .Rdata and preserving variable names (?rout?k)
> 124. Re: Averaging dataframes that are stored in a list
> (baptiste auguie)
> 125. Re: loading multiple .Rdata and preserving variable names
> (Duncan Murdoch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 14 Jul 2009 03:10:00 -0700 (PDT)
> From: Greenerpole <greenerpole@gmail.com>
> Subject: [R] Error installing package sna
> To: r-help@r-project.org
> Message-ID: <24476784.post@talk.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Dear R-users,
>
> These days, I have been struggling to install the package sna on my Ubuntu
> 8.04 laptop. My R version is currently R 2.7.2. And I had no trouble
> installing any other packages (including network).
>
> However when I run 'install.packages("sna")', compilation
of C codes is ok,
> but a syntax error is reported when building help pages and sna does not
> want to install.
>
> I copied the log (just the part about help pages) at the end of this post.
>
> Many thanks !
>
>
> ---
>
> ** help
> >>> Building/Updating help pages for package 'sna'
> Formats: text html latex example
> add.isolates text html latex example
> bbnam text html latex example
> bbnam.bf text html latex example
> betweenness text html latex example
> bicomponent.dist text html latex example
> blockmodel text html latex example
> blockmodel.expand text html latex example
> bn text html latex example
> bonpow text html latex example
>
>
> ******* Syntax error: \item in
> /-----
> Gould and Fernandez (following Marsden and others) describe
> <EM>brokerage</EM> as the role played by a social actor who
mediates
> contact
> between two alters. More formally, vertex v is a broker for distinct
> vertices a and b iff a -> v -> b and a -!> b. Where
actors belong
> to a priori distinct groups, group membership may be used to segment
> brokerage roles into particular types. Let A -> B -> C
denote the
> two-path associated with a brokerage structure, such that some vertex from
> group B brokers the connection from some vertex from group A to a vertex in
> group C. The types of brokerage roles defined by Gould and Fernandez (and
> their accompanying two-path structures) are then defined in terms of group
> membership as follows:
> </p>
> <p>
> <dl>
> \item{eqn{Coordinator role; the broker mediates contact between two
> individuals from his or her own group. Two-path structure: A -> A
->
> A}
>
>
\itemnormal-bracket32bracket-normaleqnnormal-bracket35bracket-normalItinerant
> broker role; the broker mediates contact between two individuals from a
> single group to which he or she does not belong. Two-path structure: A
> -> B -> Anormal-bracket35bracket-normal
>
>
\itemnormal-bracket38bracket-normaleqnnormal-bracket41bracket-normalGatekeeper
> role; the broker mediates an incoming contact from an out-group member to
> an
> in-group member. Two-path structure: A -> B ->
> Bnormal-bracket41bracket-normal
>
>
\itemnormal-bracket44bracket-normaleqnnormal-bracket47bracket-normalRepresentative
> role; the broker mediates an outgoing contact from an in-group member to an
> out-group member. Two-path structure: A -> A ->
> Bnormal-bracket47bracket-normal
> \itemnormal-bracket49bracket-normaleqnnormal-bracket52bracket-normalLiaison
> role; the broker mediates contact between two individuals from different
> groups, neither of which is the group to which he or she belongs. Two-path
> structure: A -> B -> Cnormal-bracket52bracket-normal
> \itemnormal-bracket54bracket-normaleqnnormal-bracket55bracket-normalTotal
> (cumulative) brokerage role occupancy. (Any of the above
> two-paths.)normal-bracket55bracket-normal
> </dl>
> </p>
> <p>
> The <EM>brokerage score</EM> for a given vertex with respect to
a given
> role
> is the number of ordered pairs having the appropriate group membership(s)
> brokered by said vertex. brokerage computes the brokerage scores for each
> vertex, given an input graph and vector of class memberships. Aggregate
> scores are also computed at the graph level, which correspond to the total
> frequency of each role type within the network structure. Expectations and
> variances of the brokerage scores conditional on size and density are
> computed, along with approximate z-tests for incidence of brokerage. (Note
> that the accuracy of the normality assumption is not known in the general
> case; see Gould and Fernandez (1989) for details. Simulation-based tests
> may be desirable as an alternative.)\-----
> ERROR: building help failed for package 'sna'
> ** Removing '/usr/local/lib/R/site-library/sna'
>
> The downloaded packages are in
> /tmp/Rtmp1hqr3H/downloaded_packages
> Warning message:
> In install.packages("sna") :
> installation of package 'sna' had non-zero exit status
>
> --
> View this message in context:
> http://www.nabble.com/Error-installing-package-sna-tp24476784p24476784.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 14 Jul 2009 11:57:20 +0200
> From: Lars Bergemann <lars.bergemann@hotmail.com>
> Subject: [R] How does logLik(lm(...)) find the maximum log likelihoods
> To: <r-help@r-project.org>
> Message-ID: <BLU129-W8B7F355C48BBE8C1EEF2C96230@phx.gbl>
> Content-Type: text/plain
>
>
> Hi. Thanks for your help with my previous question (comparing two lm()
> models with a maximum likelihood ratio test)
>
>
>
> I had a look at lrtest from the package lmtest as it has been suggested to
> me, but I am not 100% sure if that is the right thing to do ...
>
>
>
> lrtest uses the same log likelihoods as you can extract by hand from lm()
> with logLik - are this the maximum log likelihoods? How does R calculate
> them? I tried google to find information about that, but I could not find
> anything of interest.
>
>
>
> Many thanks,
>
> Lars
>
> _________________________________________________________________
>
> s. It's easy!
>
> aspx&mkt=en-us
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 14 Jul 2009 06:51:53 -0400
> From: Duncan Murdoch <murdoch@stats.uwo.ca>
> Subject: Re: [R] .RData signature
> To: stephenb <stenka1@go.com>
> Cc: r-help@r-project.org
> Message-ID: <4A5C6349.7080809@stats.uwo.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> stephenb wrote:
> > any ideas? has anybody tried to recover RData files before?
> >
>
> I have seen messages about that problem here before (see
> RSiteSearch(".RData corrupted") for a sampling), but I don't
think I've
> seen any really satisfactory solutions. It would be nice to have an
> error tolerant .RData dumper: it would load and display objects until
> it hit an error, then report on the error, and perhaps partial
> information on the object it was loading. With something like that
> you'd know if you had successfully recovered the .RData file, and if
> not, would have some hints about what was missing.
>
> The source for the regular loader is in
> https://svn.r-project.org/R/trunk/src/main/serialize.c, and this could
> be a start for the dumper.
>
> Duncan Murdoch
> >
> >
> >
> > Duncan Murdoch-2 wrote:
> >
> >> On 7/13/2009 3:38 PM, stenka1@go.com wrote:
> >>
> >>> Is there a way to identify the beginning and end of an
.RData file?
> >>> I am trying to restore lost files on opensolaris where the
table of
> >>> contents
> >>> is overwritten and will be reading the raw disk byte by
byte.
> >>> I looked at several files in hex and the end seems
different, while
> >>> most of
> >>> them, but not all begin with RDX2.X
> >>>
> >> No, there is nothing special written at the end of a file. Many
.RData
> >> files are compressed (by internal gzip), so the RDX2 header is
hidden,
> >> and you'll see bytes 1F 8B instead. (I don't think we
write the trailer
> >> bytes on the gzip stream, but I'm not sure about that.)
> >>
> >> Duncan Murdoch
> >>
> >> ______________________________________________
> >> R-help@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.
> >>
> >>
> >>
> >
> >
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 14 Jul 2009 07:17:01 -0400
> From: deepak m r <deepaknbr@gmail.com>
> Subject: [R] hi friends, is there any wait function in R
> To: r-help@r-project.org
> Message-ID:
<5024f7590907140417p3cc67x5a8b4a7704c90a19@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> hi,
> is there any wait function in R. I am running one R script to plot
> many graphs it is in the for loop. its showing no error but its not
> plotting well I think i can solve this problem with a wait function.
> Please help me in this regards. If u need any clarification about
> programme. u can find the script below.
>
> best regards,
> Deepak.M.R
> Biocomputing Group
> University of Bologana.
>
>
> #!/usr/bin/R
>
>
s<-c("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
>
,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> for(t in 1:length(s))
> {
>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> attach (a)
> names(a)
>
al<-1:length(paste("alp",s[t],"_mean",sep=""))
>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> attach(b)
> names(b)
>
bl<-1:length(paste("bet",s[t],"_mean",sep=""))
>
>
p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s[t],"mean.sat",sep=""),header=T)
> attach(p)
> names(p)
>
pl<-1:length(paste("apb",s[t],"_mean",sep=""))
>
>
o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s[t],"mean.sat",sep=""),header=T)
> attach(o)
> names(o)
>
ol<-1:length(paste("aob",s[t],"_mean",sep=""))
>
postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean Distance
Plot for
> ",s[t]," Rsidue pair",sep=""),ylab="Mean
Distance in
> Angstrom",xlab="Residue Seperation Number")
>
lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
>
lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
>
lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
>
lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> legend("topleft",c("Alpha Proteins","Beta
Proteins","Alpha +
> Beta","Alpha or Beta"),lty >
c(2,2,2,2),col=c("blue","yellow","red","green"))
> dev.off()
> }
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 14 Jul 2009 13:22:20 +0200 (CEST)
> From: Achim Zeileis <Achim.Zeileis@wu-wien.ac.at>
> Subject: Re: [R] How does logLik(lm(...)) find the maximum log
> likelihoods
> To: Lars Bergemann <lars.bergemann@hotmail.com>
> Cc: r-help@r-project.org
> Message-ID:
>
<Pine.LNX.4.64.0907141227090.17931@paninaro.stat-math.wu-wien.ac.at
> >
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> On Tue, 14 Jul 2009, Lars Bergemann wrote:
>
> > Hi. Thanks for your help with my previous question (comparing two lm()
> > models with a maximum likelihood ratio test)
> >
> > I had a look at lrtest from the package lmtest as it has been
suggested
> > to me, but I am not 100% sure if that is the right thing to do ...
>
> That clearly depends on what you consider to be "right".
>
> In any case, lrtest() computes (in an object-oriented way) -2 times the
> loglikelihood difference and compares that with a chi-squared distribution
> with the corresponding degrees of freedom (difference in df of the
> models).
>
> > lrtest uses the same log likelihoods as you can extract by hand from
> > lm() with logLik - are this the maximum log likelihoods?
>
> It's the maximized log-likelihood. Thus, it's the sum of (normal)
> log-densities, evaluated at the observations and the estimated parameters.
>
> > How does R
> > calculate them? I tried google to find information about that, but I
> > could not find anything of interest.
>
> I assume that you read help("logLik.lm")? If all else fails,
looking at
> the code of stats:::logLik.lm should also help. In essence, it is
> 0.5 * (sum(log(w)) - N * (log(2 * pi) + 1 - log(N) +
> log(sum(w * res^2))))
> where all variables have the obvious meaning.
> Z
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 14 Jul 2009 04:30:37 -0700 (PDT)
> From: "Girish A.R." <garamach@gmail.com>
> Subject: [R] Help needed in identifying type of plot
> To: r-help@r-project.org
> Message-ID: <24477714.post@talk.nabble.com>
> Content-Type: text/plain
>
>
> Hi folks,
>
> Can someone please help me in identifying the type of plot shown here?
> Sample R code or specific package name would be of help as well.
>
> Thanks,
> -Girish
>
> http://www.nabble.com/file/p24477714/example_plot.jpg
>
>
> --
> View this message in context:
>
http://www.nabble.com/Help-needed-in-identifying-type-of-plot-tp24477714p24477714.html
> Sent from the R help mailing list archive at Nabble.com.
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 14 Jul 2009 12:34:02 +0100
> From: "S Ellison" <S.Ellison@lgc.co.uk>
> Subject: Re: [R] graph: axis label font
> To: "serbring" <bracardi82@email.it>, "Michael
Knudsen"
> <micknudsen@gmail.com>
> Cc: r-help@r-project.org
> Message-ID: <sa5c7b4b.086@tedmail.lgc.co.uk>
> Content-Type: text/plain; charset=US-ASCII
>
> R on windows includes some useful functions for windows font handling.
> Start with
> ?windowsFonts
>
> windowsFonts()
> should show Arial mapped to "sans". (Arial is the default in
Windows,
> at least in my locale; ?windows tells you that too)
>
> Then try
> par(family="sans", font=2) #specifies Arial bold as default
>
> However, this just affects text (as in text() ). You need to be more
> specific to specify fonts for particular named plot elements. For
> example
> plot(1:10, main="Title in Arial Bold", font.main=2, font.axis=3,
> font.lab=4) #specifies bold main title, italic axis tick labels and
> italic bold axis labels
>
> compare this with
>
> par(family="serif") #specifies Times
> plot(1:10, main="Title in Times Bold", font.main=2, font.axis=3)
> #specifies bold main title and italic axis labels
> #note that _all_ the text is in Times.
>
> #If you know your windows font names, you can change the mappings or
> add a family:
>
> windowsFonts(comic="TT Comic Sans MS") #sets up your own
'comic'
> mapping
> par(family="comic") #specifies that this mapping is the default
> plot(1:10, main="Comic", font.main=2, font.axis=3) #specifies
bold main
> title and italic axis labels - in Comic sans 'cos that's what we
set up
>
> Hope that helps,
>
> Steve E
>
> >>> Michael Knudsen <micknudsen@gmail.com> 13/07/2009
18:45:48 >>>
> On Mon, Jul 13, 2009 at 5:31 PM, serbring<bracardi82@email.it> wrote:
>
> > excuse me for my english, i am using R on windows and i have to do
> several
> > graphs with axis labels and the axis text thicks has a specified font
> type,
> > (Arial) and a specified font size. How can i do these? Thank you in
> advance
>
> Interesting question, I didn't know the answer to, so I tried to look
> it up. There might be some help towards the bottom of this page:
>
> http://www.statmethods.net/advgraphs/parameters.html
>
> It seems to be specific for Windows, so I can't test it myself.
>
> --
> Michael Knudsen
> micknudsen@gmail.com
> http://lifeofknudsen.blogspot.com/
>
> ______________________________________________
> R-help@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.
>
> *******************************************************************
> This email and any attachments are confidential. Any use...{{dropped:8}}
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 14 Jul 2009 13:34:24 +0200
> From: "ONKELINX, Thierry" <Thierry.ONKELINX@inbo.be>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: "deepak m r" <deepaknbr@gmail.com>,
<r-help@r-project.org>
> Message-ID:
> <2E9C414912813E4EB981326983E0A104069D93FF@inboexch.inbo.be>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Deepak,
>
> You'll need to clarify what EXACTLY is happening? If empty plots are
> created then try to wrap the plot() in print() statements.
> print(plot(...)).
>
> Furthermore I would recommend to avoid attach.
>
> HTH,
>
> Thierry
>
>
>
> ------------------------------------------------------------------------
> ----
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest
> Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
> methodology and quality assurance
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
> tel. + 32 54/436 185
> Thierry.Onkelinx@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> Namens deepak m r
> Verzonden: dinsdag 14 juli 2009 13:17
> Aan: r-help@r-project.org
> Onderwerp: [R] hi friends, is there any wait function in R
>
> hi,
> is there any wait function in R. I am running one R script to plot
> many graphs it is in the for loop. its showing no error but its not
> plotting well I think i can solve this problem with a wait function.
> Please help me in this regards. If u need any clarification about
> programme. u can find the script below.
>
> best regards,
> Deepak.M.R
> Biocomputing Group
> University of Bologana.
>
>
> #!/usr/bin/R
>
s<-c("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","G
>
N","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP"
>
,"AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","
>
VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH
>
","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE",
>
"LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","I
>
D","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ"
>
,"MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","
>
FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE
>
","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR",
>
"PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","T
>
Y","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK"
>
,"CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","
>
NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
>
,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> for(t in 1:length(s))
> {
>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),
> header=T)
> attach (a)
> names(a)
>
al<-1:length(paste("alp",s[t],"_mean",sep=""))
>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),h
> eader=T)
> attach(b)
> names(b)
>
bl<-1:length(paste("bet",s[t],"_mean",sep=""))
>
>
p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s[t],"mean.sat"
> ,sep=""),header=T)
> attach(p)
> names(p)
>
pl<-1:length(paste("apb",s[t],"_mean",sep=""))
>
>
o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s[t],"mean.sat
> ",sep=""),header=T)
> attach(o)
> names(o)
>
ol<-1:length(paste("aob",s[t],"_mean",sep=""))
>
postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean Distance
Plot
> for ",s[t]," Rsidue pair",sep=""),ylab="Mean
Distance in
> Angstrom",xlab="Residue Seperation Number")
>
lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
>
lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
>
lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
>
lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> legend("topleft",c("Alpha Proteins","Beta
Proteins","Alpha +
> Beta","Alpha or Beta"),lty >
c(2,2,2,2),col=c("blue","yellow","red","green"))
> dev.off()
> }
>
> ______________________________________________
> R-help@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.
>
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver
> weer
> en binden het INBO onder geen enkel beding, zolang dit bericht niet
> bevestigd is
> door een geldig ondertekend document. The views expressed in this message
> and any annex are purely those of the writer and may not be regarded as
> stating
> an official position of INBO, as long as the message is not confirmed by a
> duly
> signed document.
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 14 Jul 2009 07:37:19 -0400
> From: Gabor Grothendieck <ggrothendieck@gmail.com>
> Subject: Re: [R] read.delim skips first column (why?)
> To: dalloliogm@gmail.com
> Cc: r-help@r-project.org
> Message-ID:
> <971536df0907140437v28774ddbgb0f756200d195f2@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Try
>
> count.fields("myfile.txt", sep = "\t")
>
> read.delim uses sep = "\t" but there are trailing tabs
> on some lines.
>
> The first line, i.e. with the headers, has three trailing tabs
> so it thinks that there are 15 columns rather than 12.
>
> The 5th line of the file (4th line of data) has 4 trailing
> tabs so it thinks that there are up to 16 fields in each
> data line.
>
> Since it now believes that there are 16 fields of data and
> 15 fields of headers it assumes the extra field, i.e. the
> first one, is the row names.
>
>
> On Tue, Jul 14, 2009 at 5:11 AM, Giovanni Marco
> Dall'Olio<dalloliogm@gmail.com> wrote:
> > Hi,
> > I have uploaded a copy of the file here:
> > - http://pastebin.com/fd0edfab
> >
> > the file has also been passed throught the unix command tool unexpand,
> but
> > it doesn't solve the problem.
> >
> > using head=TRUE instead of head=T has also the same effect.
> >
> > the output of print(names) is:
> >> print(names(ngly), quote=TRUE)
> > ?[1] "snp" ? ? ? ? ? ? ? ? ? ? ? "gene"
> > ?[3] "chromosome" ? ? ? ? ? ? ?
?"distance_from_gene_center"
> > ?[5] "position" ? ? ? ? ? ? ? ? ?"ame"
> > ?[7] "csasia" ? ? ? ? ? ? ? ? ? ?"easia"
> > ?[9] "eur" ? ? ? ? ? ? ? ? ? ? ? "mena"
> > [11] "oce" ? ? ? ? ? ? ? ? ? ? ? "ssafr"
> > [13] "X" ? ? ? ? ? ? ? ? ? ? ? ? "X.1"
> > [15] "X.2"
> >
> > Thank you to all the people who answered me to my mail address, but I
> > couldn't solve the problem yet.
> >
> >
> > On Tue, Jul 14, 2009 at 12:36 AM, jim holtman
<jholtman@gmail.com>
> wrote:
> >
> >> Can you send your file as an attachment since it is impossible to
see
> >> where the separator characters are.
> >>
> >> On Mon, Jul 13, 2009 at 1:27 PM, Giovanni Marco
> >> Dall'Olio<dalloliogm@gmail.com> wrote:
> >> > Hi people,
> >> > I have a text file like this one posted:
> >> >
> >> > snp_id ?gene ? ?chromosome ? ? ?distance_from_gene_center
> >> > position ? ? ? ?pop1 ? ?pop2 ? ?pop3 ? ?pop4 ? ?pop5 ? ?pop6
? ?pop7
> >> > rs2129081 ? ? ? RAPT2 ? 3 ? ? ? -129993 "upstream"
? ? ?0.439009
> >> > 1.169210 ? ? ? ?NA ? ? ?0.233020 ? ? ? ?0.093042 ? ? ? ?NA
> >> > -0.902596
> >> > rs1202698 ? ? ? RAPT2 ? 3 ? ? ? -128695 "upstream"
? ? ?NA
> >> > 1.815000 ? ? ? ?NA ? ? ?0.399079 ? ? ? ?1.814270 ? ? ?
?1.382950
> >> > NA
> >> > rs1163207 ? ? ? RAPT2 ? 3 ? ? ? -128224 "upstream"
? ? ?NA ? ? ?NA
> >> > NA ? ? ?NA ? ? ?NA ? ? ?NA ? ? ?NA
> >> > rs1834127 ? ? ? RAPT2 ? 3 ? ? ? -128106 "upstream"
? ? ?NA ? ? ?NA
> >> > NA ? ? ?NA ? ? ?NA ? ? ?NA ? ? ?2.180670
> >> > rs2114211 ? ? ? RAPT2 ? 3 ? ? ? -126738 "upstream"
? ? ?-0.468279
> >> > -1.447620 ? ? ? NA ? ? ?0.010616 ? ? ? ?-0.414581 ? ? ? NA
> >> > 0.550447
> >> > rs2113151 ? ? ? RAPT2 ? 3 ? ? ? -124620 "upstream"
? ? ?-0.897660
> >> > -1.971020 ? ? ? NA ? ? ?-0.920327 ? ? ? -0.764658 ? ? ? NA
> >> > 0.337127
> >> > rs2524130 ? ? ? RAPT2 ? 3 ? ? ? -123029 "upstream"
? ? ?-0.109795
> >> > -0.004646 ? ? ? -0.412059 ? ? ? 1.116740 ? ? ? ?0.667567
> >> > -0.924529 ? ? ? 0.962841
> >> > rs1381318 ? ? ? RAPT2 ? 3 ? ? ? -12818 ?"upstream"
? ? ?-0.911662
> >> > -1.791580 ? ? ? NA ? ? ?-0.945716 ? ? ? -1.239640 ? ? ? NA
> >> > 0.004876
> >> > rs2113319 ? ? ? RAPT2 ? 3 ? ? ? -122028 "upstream"
? ? ?-0.911662
> >> > -1.738610 ? ? ? NA ? ? ?-0.945716 ? ? ? -1.240950 ? ? ? NA ?
?
> ?-0.005318
> >> >
> >> > When I use read.delim (or any read function) on it, R skips
the first
> >> > column, and I don' understand why.
> >> >
> >> > For example:
> >> > $: R
> >> >> data = read.delim('snp_file.txt', head=T,
sep='\t')
> >> >
> >> > Now, I would expect data$snp_id to contain snp ids, and
data$gene to
> >> contain
> >> > gene names; but it is not like this:
> >> >
> >> >> data$snp_id
> >> > [1] RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2 RAPT2
> >> > Levels: RAPT2
> >> >> data$gene
> >> > [1] 3 3 3 3 3 3 3 3 3
> >> >
> >> >> summary(data)
> >> > ?snp_id ? ? ? gene ? ? chromosome ? ?
?distance_from_gene_center
> >> > ?RAPT2:9 ? Min. ? :3 ? Min. ? :-129993 ? upstream:9
> >> > ? ? ? ? ? 1st Qu.:3 ? 1st Qu.:-128224
> >> > ? ? ? ? ? Median :3 ? Median :-126738
> >> > ? ? ? ? ? Mean ? :3 ? Mean ? :-113806
> >> > ? ? ? ? ? 3rd Qu.:3 ? 3rd Qu.:-123029
> >> > ? ? ? ? ? Max. ? :3 ? Max. ? : -12818
> >> > ....
> >> >
> >> >> data$pop7
> >> > [1] NA NA NA NA NA NA NA NA NA
> >> >
> >> >
> >> > Notice that it did use snp_id as the header for the first
column, but
> it
> >> > skips completely al the data from that column, and all the
fields are
> >> > shifted, so the last column is filled with NA values.
> >> >
> >> > What I am doing wrong? Can it be a problem of my data files?
I have
> tried
> >> to
> >> > modify them a bit (add new columns, etc..) but it didn't
work.
> >> >
> >> > I am running R from an Ubuntu system:
> >> >> sessionInfo()
> >> > R version 2.9.1 (2009-06-26)
> >> > i486-pc-linux-gnu
> >> >
> >> > locale:
> >> >
> >>
>
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C
> >> >
> >> > attached base packages:
> >> > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods
? base
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > Giovanni Dall'Olio, phd student
> >> > Department of Biologia Evolutiva at CEXS-UPF (Barcelona,
Spain)
> >> >
> >> > My blog on bioinformatics: http://bioinfoblog.it
> >> >
> >> > ? ? ? ?[[alternative HTML version deleted]]
> >> >
> >> > ______________________________________________
> >> > R-help@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
> >> Cincinnati, OH
> >> +1 513 646 9390
> >>
> >> What is the problem that you are trying to solve?
> >>
> >
> >
> >
> > --
> > Giovanni Dall'Olio, phd student
> > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
> >
> > My blog on bioinformatics: http://bioinfoblog.it
> >
> > ? ? ? ?[[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@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.
> >
>
>
>
> ------------------------------
>
> Message: 10
> Date: Tue, 14 Jul 2009 13:48:25 +0200
> From: Petr PIKAL <petr.pikal@precheza.cz>
> Subject: [R] Odp: hi friends, is there any wait function in R
> To: deepak m r <deepaknbr@gmail.com>
> Cc: r-help@r-project.org
> Message-ID:
> <
> OF90EDB7D3.FBE47550-ONC12575F3.003FD3DA-C12575F3.0040D0AB@precheza.cz>
>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi
>
> For this type of problems I do multipage pdf.
>
> pdf("file", ....)
> for (i in ...) {
> do all stuff including plot
> }
> dev.off()
>
> and then check the plots afterwards. Recently there was some post about
> how to wait but you do not want only wait you want also to interactively
> change plotting parameters, won't you.
>
> cat("\n","Enter x","\n") # prompt
> x=scan(n=1) # read 1 line from console
>
> this construction print something on console and reads one line from
> console. There are also some packages which leave you choose from several
> options. I think in car and randomForest are such routines so you could
> check how it is done.
>
> Regards
> Petr
>
> r-help-bounces@r-project.org napsal dne 14.07.2009 13:17:01:
>
> > hi,
> > is there any wait function in R. I am running one R script to plot
> > many graphs it is in the for loop. its showing no error but its not
> > plotting well I think i can solve this problem with a wait function.
> > Please help me in this regards. If u need any clarification about
> > programme. u can find the script below.
> >
> > best regards,
> > Deepak.M.R
> > Biocomputing Group
> > University of Bologana.
> >
> >
> > #!/usr/bin/R
> > s<-c
> >
>
>
("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
> >
,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> > for(t in 1:length(s))
> > {
> >
>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> > attach (a)
> > names(a)
> >
al<-1:length(paste("alp",s[t],"_mean",sep=""))
> >
>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> > attach(b)
> > names(b)
> >
bl<-1:length(paste("bet",s[t],"_mean",sep=""))
> >
p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s
> > [t],"mean.sat",sep=""),header=T)
> > attach(p)
> > names(p)
> >
pl<-1:length(paste("apb",s[t],"_mean",sep=""))
> >
o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s
> > [t],"mean.sat",sep=""),header=T)
> > attach(o)
> > names(o)
> >
ol<-1:length(paste("aob",s[t],"_mean",sep=""))
> >
postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> > plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean Distance
Plot for
> > ",s[t]," Rsidue pair",sep=""),ylab="Mean
Distance in
> > Angstrom",xlab="Residue Seperation Number")
> >
lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
> >
lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
> >
lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
> >
lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> > legend("topleft",c("Alpha Proteins","Beta
Proteins","Alpha +
> > Beta","Alpha or Beta"),lty > >
c(2,2,2,2),col=c("blue","yellow","red","green"))
> > dev.off()
> > }
> >
> > ______________________________________________
> > R-help@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.
>
>
>
> ------------------------------
>
> Message: 11
> Date: Tue, 14 Jul 2009 07:56:38 -0400
> From: David Winsemius <dwinsemius@comcast.net>
> Subject: Re: [R] Nested for loops
> To: Michael Knudsen <micknudsen@gmail.com>
> Cc: r-help@r-project.org
> Message-ID: <AF28E2C7-083D-4FAA-95AD-A33DD51016D5@comcast.net>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On Jul 14, 2009, at 2:25 AM, Michael Knudsen wrote:
>
> > On Tue, Jul 14, 2009 at 8:20 AM, Michael
> > Knudsen<micknudsen@gmail.com> wrote:
> >
> >> What do you mean? It looks a like a very general solution to me.
> >
> > Just got an email suggesting using the functions col and row. For
> > example
> >
> > temp = matrix(c(1:36),nrow=6)
> > which(col(temp)>row(temp))
>
> >
> > This gives the indices (in the matrix viewed as a vector) of the
> > above-diagonal entries.
> >
>
> If you want the entries it would then be:
> temp[ col(temp) > row(temp) ]
>
> But more simply:
>
> > temp[ upper.tri(temp) ]
> [1] 7 13 14 19 20 21 25 26 27 28 31 32 33 34 35
> >
>
> If you want the row and column numbers then:
> > row(temp)[ col(temp) > row(temp)]
> [1] 1 1 2 1 2 3 1 2 3 4 1 2 3 4 5
> > col(temp)[ col(temp) > row(temp) ]
> [1] 2 3 3 4 4 4 5 5 5 5 6 6 6 6 6
>
> Any solution that uses col and row will create two additional matrices
> of the same size as the original at least for the duration of the
> operation.
>
> For the sub-and super-diagonals:
>
> http://finzi.psych.upenn.edu/Rhelp08/2009-March/191379.html
> --
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>
>
> ------------------------------
>
> Message: 12
> Date: Tue, 14 Jul 2009 13:03:43 +0100
> From: Christopher Jones <c.jones@ucl.ac.uk>
> Subject: Re: [R] Help needed in identifying type of plot
> To: r-help@R-project.org
> Message-ID: <A12B491F-2A88-4BD8-8628-8126CD6B1B0C@ucl.ac.uk>
> Content-Type: text/plain
>
>
> On 14 Jul 2009, at 12:30, Girish A.R. wrote:
>
> > Can someone please help me in identifying the type of plot shown here?
>
> Its a Forest Plot
>
>
> Chris.
>
>
> -----------------------
> Gynaecological Cancer Research Laboratories,
> UCL EGA Institute for Women's Health,
> University College London,
> Paul O'Gorman Building,
> 72 Huntley Street,
> London
> WC1E 6DD
> United Kingdom
>
> Telephone; 020 3108 2007
> Fax; 020 3108 2010
>
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 13
> Date: Tue, 14 Jul 2009 14:11:50 +0200
> From: "ONKELINX, Thierry" <Thierry.ONKELINX@inbo.be>
> Subject: Re: [R] Help needed in identifying type of plot
> To: "Girish A.R." <garamach@gmail.com>,
<r-help@r-project.org>
> Message-ID:
> <2E9C414912813E4EB981326983E0A104069D940E@inboexch.inbo.be>
> Content-Type: text/plain; charset="us-ascii"
>
> It is a plot with pointranges. Here is an example with the ggplot2
> package
>
>
> library(ggplot2)
> #use the diamond data set from ggplot2
> diamonds$A <- diamonds$depth < 60
> dmod <- lm(price ~ cut * A, data=diamonds)
> cuts <- unique(diamonds[, c("cut", "A")])
> cuts <- cbind(cuts, predict(dmod, cuts,
se=T)[c("fit","se.fit")])
>
> #the actual plot
> ggplot(cuts, aes(x = cut, y = fit, ymin = fit - se.fit, ymax=fit +
> se.fit, colour = factor(A))) + geom_pointrange(position >
position_dodge(width = 0.2)) + coord_flip()
>
> More details on the ggplot2 website: http://had.co.nz/ggplot2/
>
> HTH,
>
> Thierry
>
>
> ------------------------------------------------------------------------
> ----
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest
> Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
> methodology and quality assurance
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
> tel. + 32 54/436 185
> Thierry.Onkelinx@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> Namens Girish A.R.
> Verzonden: dinsdag 14 juli 2009 13:31
> Aan: r-help@r-project.org
> Onderwerp: [R] Help needed in identifying type of plot
>
>
> Hi folks,
>
> Can someone please help me in identifying the type of plot shown here?
> Sample R code or specific package name would be of help as well.
>
> Thanks,
> -Girish
>
> http://www.nabble.com/file/p24477714/example_plot.jpg
>
>
> --
> View this message in context:
> http://www.nabble.com/Help-needed-in-identifying-type-of-plot-tp24477714
> p24477714.html
> Sent from the R help mailing list archive at Nabble.com.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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.
>
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver
> weer
> en binden het INBO onder geen enkel beding, zolang dit bericht niet
> bevestigd is
> door een geldig ondertekend document. The views expressed in this message
> and any annex are purely those of the writer and may not be regarded as
> stating
> an official position of INBO, as long as the message is not confirmed by a
> duly
> signed document.
>
>
>
> ------------------------------
>
> Message: 14
> Date: Tue, 14 Jul 2009 17:44:07 +0530 (IST)
> From: Gaurav Kumar <gaurav@gauravkumar.org>
> Subject: [R] How to provide list as an argument for the data.frame()
> To: r-help@r-project.org
> Message-ID: <602764.61295.qm@web94603.mail.in2.yahoo.com>
> Content-Type: text/plain
>
> Hi R -users,
>
> i've a table as describe below. I'm reading the numeric value
presented in
> this table to populate a list.
>
> #table
> #===========> #X A B C
> #x1 2 3 4
> #x2 5 7 10
> #x4 2 3 5
> #===========>
> rawData <- read.table("raw_data.txt",header=T,
sep="\t")
> myList=list()
> counter=0
> for (i in c(1:length(rawData$X)))
> {
> print (i)
> myList[counter <- counter +1]=as.numeric(rawData$A[i]);
> myList[counter <- counter +1]=as.numeric(rawData$B[i]);
> myList[counter <- counter +1]=as.numeric(rawData$C[i]);
> }
> print(myList)
>
> comp <-
factor(rep(c("A","B","C"),c(3,3,3)))
> cell <- factor(rep(c("x1","x2","x3"),3))
>
> t <- data.frame(comp,cell)
> print(t)
>
> i'm looking for the output show below
> # comp cell value
> #1 A x1 2
> #2 A x2 5
> #3 A x3 2
> #4 B x1 3
> #5 B x2 7
> #6 B x3 3
> #7 C x1 4
> #8 C x2 10
> #9 C x3 5
>
> Help needed as how i should provide list as a third argument to
> data.frame().
>
> Thanks in advance.
>
>
> Gaurav Kumar
> www.gauravkumar.org
>
> PhD Student, Chemistry and Biomolecular Sciences, Macquarie , Sydney,
> Australia.
> MS (Computational Biology), NCBS-TIFR, Bangalore, India.
>
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 15
> Date: Tue, 14 Jul 2009 05:20:19 -0700 (PDT)
> From: "Girish A.R." <garamach@gmail.com>
> Subject: Re: [R] Help needed in identifying type of plot
> To: r-help@r-project.org
> Message-ID: <24478359.post@talk.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
>
> Thanks, Chris and Thierry! I think I can explore both your solutions.
>
> best,
> -Girish
>
>
> It is a plot with pointranges. Here is an example with the ggplot2
> package
>
>
> library(ggplot2)
> #use the diamond data set from ggplot2
> diamonds$A <- diamonds$depth < 60
> dmod <- lm(price ~ cut * A, data=diamonds)
> cuts <- unique(diamonds[, c("cut", "A")])
> cuts <- cbind(cuts, predict(dmod, cuts,
se=T)[c("fit","se.fit")])
>
> #the actual plot
> ggplot(cuts, aes(x = cut, y = fit, ymin = fit - se.fit, ymax=fit +
> se.fit, colour = factor(A))) + geom_pointrange(position >
position_dodge(width = 0.2)) + coord_flip()
>
> More details on the ggplot2 website: http://had.co.nz/ggplot2/
>
> HTH,
>
> Thierry
>
>
> ------------------------------------------------------------------------
> ----
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest
> Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
> methodology and quality assurance
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
> tel. + 32 54/436 185
> Thierry.Onkelinx@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
>
>
> --
> View this message in context:
>
http://www.nabble.com/Help-needed-in-identifying-type-of-plot-tp24477714p24478359.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 16
> Date: Tue, 14 Jul 2009 08:29:58 -0400
> From: Gabor Grothendieck <ggrothendieck@gmail.com>
> Subject: Re: [R] Nested for loops
> To: Michael Knudsen <micknudsen@gmail.com>
> Cc: r-help@r-project.org
> Message-ID:
> <971536df0907140529j59caca27lc2e420ef94d25af8@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Try this:
>
> seq. <- function(from, to) seq(from = from, length = max(0, to - from +
1))
>
> seq.(11, 10)
>
>
>
> On Tue, Jul 14, 2009 at 1:38 AM, Michael
Knudsen<micknudsen@gmail.com>
> wrote:
> > Hi,
> >
> > I have spent some time locating a quite subtle (at least in my
> > opinion) bug in my code. I want two nested for loops traversing the
> > above-diagonal part of a square matrix. In pseudo code it would
> > something like
> >
> > for i = 1 to 10
> > {
> > ? for j = i+1 to 10
> > ? {
> > ? ? ?// do something
> > ? }
> > }
> >
> > However, trying to do the same in R, my first try was
> >
> > for (i in 1:10)
> > {
> > ? for (j in (i+1):10)
> > ? {
> > ? ? ? // do something
> > ? }
> > }
> >
> > but there's a problem here. For i=10, the last for loop is over
11:10.
> > Usually programming laguages would regard what corresponds to 11:10 as
> > empty, but A:B with A bigger than B is in R interpreted as the numbers
> > from B to A in reverse order.
> >
> > Is there a clever way to make nested loops like the one above in R?
> >
> > --
> > Michael Knudsen
> > micknudsen@gmail.com
> > http://lifeofknudsen.blogspot.com/
> >
> > ______________________________________________
> > R-help@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.
> >
>
>
>
> ------------------------------
>
> Message: 17
> Date: Tue, 14 Jul 2009 08:30:48 -0400
> From: David Winsemius <dwinsemius@comcast.net>
> Subject: Re: [R] How to provide list as an argument for the
> data.frame()
> To: gaurav@gauravkumar.org
> Cc: r-help@r-project.org
> Message-ID: <0265F45F-1770-4D3C-BDBF-CA35AD5E3E7D@comcast.net>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On Jul 14, 2009, at 8:14 AM, Gaurav Kumar wrote:
>
> > Hi R -users,
> >
> > i've a table as describe below. I'm reading the numeric value
> > presented in this table to populate a list.
> >
> > #table
> > #===========> > #X A B C
> > #x1 2 3 4
> > #x2 5 7 10
> > #x4 2 3 5
> > #===========> >
> > rawData <- read.table("raw_data.txt",header=T,
sep="\t")
> > myList=list()
> > counter=0
> > for (i in c(1:length(rawData$X)))
> > {
> > print (i)
> > myList[counter <- counter +1]=as.numeric(rawData$A[i]);
> > myList[counter <- counter +1]=as.numeric(rawData$B[i]);
> > myList[counter <- counter +1]=as.numeric(rawData$C[i]);
> > }
> > print(myList)
> >
> > comp <-
factor(rep(c("A","B","C"),c(3,3,3)))
> > cell <-
factor(rep(c("x1","x2","x3"),3))
> >
> > t <- data.frame(comp,cell)
> > print(t)
> >
> > i'm looking for the output show below
> > # comp cell value
> > #1 A x1 2
> > #2 A x2 5
> > #3 A x3 2
> > #4 B x1 3
> > #5 B x2 7
> > #6 B x3 3
> > #7 C x1 4
> > #8 C x2 10
> > #9 C x3 5
> >
> > Help needed as how i should provide list as a third argument to
> > data.frame().
>
>
> To answer your narrow question:
>
> ?unlist
>
>
> But wouldn't it have been a lot easier to to this, and skip all that C
> style looping?
>
> cbind(cell=factor(rep(c("x1","x2","x3"),3)),
stack(rawData) )
> ###
> cell values ind
> 1 x1 2 A
> 2 x2 5 A
> 3 x3 2 A
> 4 x1 3 B
> 5 x2 7 B
> 6 x3 3 B
> 7 x1 4 C
> 8 x2 10 C
> 9 x3 5 C
> >
> > Thanks in advance.
> >
> >
> > Gaurav Kumar
> > www.gauravkumar.org
> >
> > PhD Student, Chemistry and Biomolecular Sciences, Macquarie ,
> > Sydney, Australia.
> > MS (Computational Biology), NCBS-TIFR, Bangalore, India.
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@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.
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>
>
> ------------------------------
>
> Message: 18
> Date: Tue, 14 Jul 2009 08:56:49 -0400
> From: deepak m r <deepaknbr@gmail.com>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: Petr PIKAL <petr.pikal@precheza.cz>
> Cc: r-help@r-project.org
> Message-ID:
> <5024f7590907140556p551fc717x8e70710a0edc6624@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> Empty plot is getting i dont know why. can u please clarify how
> can i use Print function instead of plot function.
> best regards
> deepak
>
> On Tue, Jul 14, 2009 at 7:48 AM, Petr PIKAL<petr.pikal@precheza.cz>
wrote:
> > Hi
> >
> > For this type of problems I do multipage pdf.
> >
> > pdf("file", ....)
> > for (i in ...) {
> > do all stuff including plot
> > }
> > dev.off()
> >
> > and then check the plots afterwards. Recently there was some post
about
> > how to wait but you do not want only wait you want also to
interactively
> > change plotting parameters, won't you.
> >
> > cat("\n","Enter x","\n") # prompt
> > x=scan(n=1) # read 1 line from console
> >
> > this construction print something on console and reads one line from
> > console. There are also some packages which leave you choose from
several
> > options. I think in car and randomForest are such routines so you
could
> > check how it is done.
> >
> > Regards
> > Petr
> >
> > r-help-bounces@r-project.org napsal dne 14.07.2009 13:17:01:
> >
> >> hi,
> >> ? ?is there any wait function in R. I am running one R script to
plot
> >> many graphs it is in the for loop. its showing no error but its
not
> >> plotting well I think i can solve this problem with a wait
function.
> >> Please help me in this regards. If u need any clarification about
> >> programme. u can find the script below.
> >>
> >> best regards,
> >> Deepak.M.R
> >> Biocomputing Group
> >> University of Bologana.
> >>
> >>
> >> #!/usr/bin/R
> >> s<-c
> >>
> >
>
("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
> >>
?,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> >> for(t in 1:length(s))
> >> ? ?{
> >>
> >
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> >> ? ?attach (a)
> >> ? ?names(a)
> >> ?
?al<-1:length(paste("alp",s[t],"_mean",sep=""))
> >>
> >
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> >> ? ?attach(b)
> >> ? ?names(b)
> >> ?
?bl<-1:length(paste("bet",s[t],"_mean",sep=""))
> >> ?
?p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s
> >> [t],"mean.sat",sep=""),header=T)
> >> ? ?attach(p)
> >> ? ?names(p)
> >> ?
?pl<-1:length(paste("apb",s[t],"_mean",sep=""))
> >> ?
?o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s
> >> [t],"mean.sat",sep=""),header=T)
> >> ? ?attach(o)
> >> ? ?names(o)
> >> ?
?ol<-1:length(paste("aob",s[t],"_mean",sep=""))
> >> ?
?postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> >> ? ?plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean
Distance Plot for
> >> ",s[t]," Rsidue
pair",sep=""),ylab="Mean Distance in
> >> Angstrom",xlab="Residue Seperation Number")
> >> ?
?lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
> >> ?
?lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
> >> ?
?lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
> >> ?
?lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> >> ? ?legend("topleft",c("Alpha
Proteins","Beta Proteins","Alpha +
> >> Beta","Alpha or Beta"),lty > >>
c(2,2,2,2),col=c("blue","yellow","red","green"))
> >> ? ?dev.off()
> >> ? ?}
> >>
> >> ______________________________________________
> >> R-help@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.
> >
> >
>
>
>
> ------------------------------
>
> Message: 19
> Date: Tue, 14 Jul 2009 08:58:48 -0400
> From: deepak m r <deepaknbr@gmail.com>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: Petr PIKAL <petr.pikal@precheza.cz>
> Cc: r-help@r-project.org
> Message-ID:
> <5024f7590907140558nd58bdc0p1858f6bcf7c0cd2a@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> where can i use this par(ask=TRUE) function i tried before dev.off()
> code but it is again the same.
> best regards,
> Deepak
>
> On Tue, Jul 14, 2009 at 8:56 AM, deepak m r<deepaknbr@gmail.com>
wrote:
> > Hi,
> > ? ?Empty plot is getting i dont know why. can u please clarify how
> > can i use Print function instead of plot function.
> > best regards
> > deepak
> >
> > On Tue, Jul 14, 2009 at 7:48 AM, Petr
PIKAL<petr.pikal@precheza.cz>
> wrote:
> >> Hi
> >>
> >> For this type of problems I do multipage pdf.
> >>
> >> pdf("file", ....)
> >> for (i in ...) {
> >> do all stuff including plot
> >> }
> >> dev.off()
> >>
> >> and then check the plots afterwards. Recently there was some post
about
> >> how to wait but you do not want only wait you want also to
interactively
> >> change plotting parameters, won't you.
> >>
> >> cat("\n","Enter x","\n") # prompt
> >> x=scan(n=1) # read 1 line from console
> >>
> >> this construction print something on console and reads one line
from
> >> console. There are also some packages which leave you choose from
> several
> >> options. I think in car and randomForest are such routines so you
could
> >> check how it is done.
> >>
> >> Regards
> >> Petr
> >>
> >> r-help-bounces@r-project.org napsal dne 14.07.2009 13:17:01:
> >>
> >>> hi,
> >>> ? ?is there any wait function in R. I am running one R script
to plot
> >>> many graphs it is in the for loop. its showing no error but
its not
> >>> plotting well I think i can solve this problem with a wait
function.
> >>> Please help me in this regards. If u need any clarification
about
> >>> programme. u can find the script below.
> >>>
> >>> best regards,
> >>> Deepak.M.R
> >>> Biocomputing Group
> >>> University of Bologana.
> >>>
> >>>
> >>> #!/usr/bin/R
> >>> s<-c
> >>>
> >>
>
("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
> >>>
?,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> >>> for(t in 1:length(s))
> >>> ? ?{
> >>>
> >>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> >>> ? ?attach (a)
> >>> ? ?names(a)
> >>> ?
?al<-1:length(paste("alp",s[t],"_mean",sep=""))
> >>>
> >>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> >>> ? ?attach(b)
> >>> ? ?names(b)
> >>> ?
?bl<-1:length(paste("bet",s[t],"_mean",sep=""))
> >>> ?
?p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s
> >>> [t],"mean.sat",sep=""),header=T)
> >>> ? ?attach(p)
> >>> ? ?names(p)
> >>> ?
?pl<-1:length(paste("apb",s[t],"_mean",sep=""))
> >>> ?
?o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s
> >>> [t],"mean.sat",sep=""),header=T)
> >>> ? ?attach(o)
> >>> ? ?names(o)
> >>> ?
?ol<-1:length(paste("aob",s[t],"_mean",sep=""))
> >>> ?
?postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> >>> ? ?plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean
Distance Plot for
> >>> ",s[t]," Rsidue
pair",sep=""),ylab="Mean Distance in
> >>> Angstrom",xlab="Residue Seperation Number")
> >>> ?
?lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
> >>> ?
?lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
> >>> ?
?lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
> >>> ?
?lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> >>> ? ?legend("topleft",c("Alpha
Proteins","Beta Proteins","Alpha +
> >>> Beta","Alpha or Beta"),lty > >>>
c(2,2,2,2),col=c("blue","yellow","red","green"))
> >>> ? ?dev.off()
> >>> ? ?}
> >>>
> >>> ______________________________________________
> >>> R-help@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.
> >>
> >>
> >
>
>
>
> ------------------------------
>
> Message: 20
> Date: Tue, 14 Jul 2009 08:04:09 -0500
> From: Marc Schwartz <marc_schwartz@me.com>
> Subject: Re: [R] How to provide list as an argument for the
> data.frame()
> To: gaurav@gauravkumar.org
> Cc: r-help@r-project.org
> Message-ID: <69866E57-F5BE-42AD-9687-763E0619300D@me.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Jul 14, 2009, at 7:14 AM, Gaurav Kumar wrote:
>
> > Hi R -users,
> >
> > i've a table as describe below. I'm reading the numeric value
> > presented in this table to populate a list.
> >
> > #table
> > #===========> > #X A B C
> > #x1 2 3 4
> > #x2 5 7 10
> > #x4 2 3 5
> > #===========> >
> > rawData <- read.table("raw_data.txt",header=T,
sep="\t")
> > myList=list()
> > counter=0
> > for (i in c(1:length(rawData$X)))
> > {
> > print (i)
> > myList[counter <- counter +1]=as.numeric(rawData$A[i]);
> > myList[counter <- counter +1]=as.numeric(rawData$B[i]);
> > myList[counter <- counter +1]=as.numeric(rawData$C[i]);
> > }
> > print(myList)
> >
> > comp <-
factor(rep(c("A","B","C"),c(3,3,3)))
> > cell <-
factor(rep(c("x1","x2","x3"),3))
> >
> > t <- data.frame(comp,cell)
> > print(t)
> >
> > i'm looking for the output show below
> > # comp cell value
> > #1 A x1 2
> > #2 A x2 5
> > #3 A x3 2
> > #4 B x1 3
> > #5 B x2 7
> > #6 B x3 3
> > #7 C x1 4
> > #8 C x2 10
> > #9 C x3 5
> >
> > Help needed as how i should provide list as a third argument to
> > data.frame().
> >
> > Thanks in advance.
>
> Read your data in as follows:
>
> # Set the rownames to the values in 'X' and coerce to a matrix
> rawData <- as.matrix(read.table("raw_data.txt", header = TRUE,
> sep = "\t", row.names =
"X"))
>
>
> # Note that you have 'x3' in your results, but 'x4' was in
the
> # initial data table, so I kept 'x4'
> > rawData
> A B C
> x1 2 3 4
> x2 5 7 10
> x4 2 3 5
>
>
> # Set the row and column names
> names(dimnames(rawData)) <- list("cell", "comp")
>
> > rawData
> comp
> cell A B C
> x1 2 3 4
> x2 5 7 10
> x4 2 3 5
>
>
> # See ?as.data.frame.table
> > as.data.frame.table(rawData, responseName = "value")
> cell comp value
> 1 x1 A 2
> 2 x2 A 5
> 3 x4 A 2
> 4 x1 B 3
> 5 x2 B 7
> 6 x4 B 3
> 7 x1 C 4
> 8 x2 C 10
> 9 x4 C 5
>
>
> HTH,
>
> Marc Schwartz
>
>
>
> ------------------------------
>
> Message: 21
> Date: Tue, 14 Jul 2009 15:09:15 +0200
> From: "Suresh Krishna" <madzientist@gmail.com>
> Subject: [R] 2 x 2 x 10 x 2 binomial setup
> To: r-help@r-project.org
> Message-ID: <op.uw16tpfphgmlxk@osiris.gwdg.de>
> Content-Type: text/plain; format=flowed; delsp=yes;
> charset=iso-8859-15
>
>
> Hello,
>
> I have a hierarchical dataset of this form and am trying to analyze it in
> R.
>
> 1 subject
> Tested under 2 conditions: A and B
> 10 sesssions in each condition
> In each session, 2 kinds of tests: Test 1 and Test 2
> 200 independent repetitions of each test-type, with 200 Yes/No answers
>
> So I think this is a 2 x 2 x 10 x 2 setup
>
> What I want to know is whether the difference in percentage of yes answers
> between Test1 and Test2 is different for the 2 conditions A and B. I guess
> I could also state this as looking for an effect at the highest stratum,
> after correctly pooling over all the lower strata... i.e. Is there an
> "interaction" between the Effect of Condition and the Effect of
Test.
>
> I looked through Agresti and Pinheiro/Bates and couldn't find an
example
> covering this situation. I would be really grateful if you could suggest a
> way to go about this analysis in R, or a place where I could read about
> this.
>
> I considered:
>
> Pool data from all the sessions for a given condition and test together,
> thus getting 2000 repetitions of Test1 and Test 2 in each condition. Now I
> have a 2x2x2 setup, which maps on to something in Agresti, but then I am
> ignoring within-session correlation information.
>
> I could simply get a difference between Test1 and Test2 percentages for
> each session, and then compare the distribution of these differences in
> conditions A and B (with something like a t-test), but then I only have 10
> points (one for each session) and so I guess I am throwing away a lot of
> information.
>
> Very best,
>
> Suresh
>
>
>
> ------------------------------
>
> Message: 22
> Date: Tue, 14 Jul 2009 15:14:00 +0200
> From: Antje <niederlein-rstat@yahoo.de>
> Subject: Re: [R] nls - find good starting values
> To: Bill.Venables@csiro.au
> Cc: r-help@stat.math.ethz.ch
> Message-ID: <4A5C8498.3010103@yahoo.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Bill,
>
> thanks for your answer.
>
> I don't see what you mean with "fitting a gaussian
distribution"...
>
> I'm pretty sure, that I'd like to fit a gaussian probability
density
> function :-) (not normalized, for example with a mean around -4 and a
> standard deviation of 0.5)
> I'm not sure if I understand your solution with the quadratic regession
> model...
> Maybe my approach is completely wrong but I didn't know any other
solution.
> Anyhow, I've solved the issue so far with the while-construct.
>
> Antje
>
>
> Bill.Venables@csiro.au wrote:
> > It is not at all clear what you are trying to do.
> >
> > Fitting a gaussian distribution is the simplest problem in all of
> statistics: the sample mean and sample variance (divisor n) are the
mle's of
> the two parameters involved. No non-linear regresson is required.
> >
> > If what you are really trying to do is fit a (normalized?) gaussian
> probability density function as a form of non-linear regression, i.e. by
> least squares, that is an entirely different problem. I'm a bit
stumped as
> to how this form of non-linear regresion should arise, particularly with
> equal variance both for values near the mode as well as in the tails, but
> stranger things have happened, I suppose. What I would do is, if you
> response values are non-negative, take logs and regress using a quadratic
> regression model, and then identify the approximate mean and variance
> parameters, which should then be reasonable starting values for the
> non-linear regression. Negative responses will pose a problem, of course.
> >
> > Bill Venables.
> > ________________________________________
> > From: r-help-bounces@r-project.org [r-help-bounces@r-project.org] On
> Behalf Of Antje [niederlein-rstat@yahoo.de]
> > Sent: 14 July 2009 17:21
> > To: r-help@stat.math.ethz.ch
> > Subject: [R] nls - find good starting values
> >
> > Hi there,
> >
> > it might be a very simple question and I'd be glad to even get a
link to
> > some useful documentation...
> > I have several data sets, I'd like to fit to a gaussian
distribution.
> > I've tried to give an estimate of the mean and the sd of this
> > distribution but still, I run into problems if these estimates are not
> > close enough.
> >
> > For example, nls() breaks with this message:
> > singular gradient matrix at initial parameter estimates
> >
> > I don't know how to avoid these bad start values because their
estimate
> > is automated. Better start values are often quite close.
> >
> > I was wondering whether there is any way to test several start-values
as
> > long as nls does not succeed.
> > I would do it with a while construct but maybe there is another
approach?
> >
> > Any hint is very welcome!
> >
> > Ciao,
> > Antje
> >
> > ______________________________________________
> > R-help@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.
> >
> >
>
>
>
> ------------------------------
>
> Message: 23
> Date: Tue, 14 Jul 2009 15:25:35 +0200
> From: Michael Knudsen <micknudsen@gmail.com>
> Subject: Re: [R] Nested for loops
> To: David Winsemius <dwinsemius@comcast.net>
> Cc: r-help@r-project.org
> Message-ID:
> <d039e9f40907140625w74465473q3207ac555704eb12@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Jul 14, 2009 at 1:56 PM, David
Winsemius<dwinsemius@comcast.net>
> wrote:
>
> >> temp[ upper.tri(temp) ]
> > ?[1] ?7 13 14 19 20 21 25 26 27 28 31 32 33 34 35
>
> Thanks! I didn't know about that function; it certainly makes things a
> lot easier. For example, until now I have used the following, homemade
> expression
>
> (1:N^2)[which((1:N^2)!=seq(0,(N-1)*N,by=N)+(1:N))]
>
> to get the indices of the non-diagonal entries of a matrix :-)
>
> --
> Michael Knudsen
> micknudsen@gmail.com
> http://lifeofknudsen.blogspot.com/
>
>
>
> ------------------------------
>
> Message: 24
> Date: Tue, 14 Jul 2009 15:26:14 +0200
> From: Michael Knudsen <micknudsen@gmail.com>
> Subject: Re: [R] Nested for loops
> To: Gabor Grothendieck <ggrothendieck@gmail.com>
> Cc: r-help@r-project.org
> Message-ID:
> <d039e9f40907140626wf1b9ac6r5f17aaa3f8db46e4@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Jul 14, 2009 at 2:29 PM, Gabor
> Grothendieck<ggrothendieck@gmail.com> wrote:
>
> > seq. <- function(from, to) seq(from = from, length = max(0, to -
from +
> 1))
>
> Really nice! Thank you!
>
> --
> Michael Knudsen
> micknudsen@gmail.com
> http://lifeofknudsen.blogspot.com/
>
>
>
> ------------------------------
>
> Message: 25
> Date: Tue, 14 Jul 2009 08:37:46 -0500
> From: Marc Schwartz <marc_schwartz@me.com>
> Subject: Re: [R] 2 x 2 x 10 x 2 binomial setup
> To: Suresh Krishna <madzientist@gmail.com>
> Cc: r-help@r-project.org
> Message-ID: <185F8F28-017E-4544-B88F-F360A223A179@me.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On Jul 14, 2009, at 8:09 AM, Suresh Krishna wrote:
>
> >
> > Hello,
> >
> > I have a hierarchical dataset of this form and am trying to analyze
> > it in R.
> >
> > 1 subject
> > Tested under 2 conditions: A and B
> > 10 sesssions in each condition
> > In each session, 2 kinds of tests: Test 1 and Test 2
> > 200 independent repetitions of each test-type, with 200 Yes/No answers
> >
> > So I think this is a 2 x 2 x 10 x 2 setup
> >
> > What I want to know is whether the difference in percentage of yes
> > answers between Test1 and Test2 is different for the 2 conditions A
> > and B. I guess I could also state this as looking for an effect at
> > the highest stratum, after correctly pooling over all the lower
> > strata... i.e. Is there an "interaction" between the Effect
of
> > Condition and the Effect of Test.
> >
> > I looked through Agresti and Pinheiro/Bates and couldn't find an
> > example covering this situation. I would be really grateful if you
> > could suggest a way to go about this analysis in R, or a place where
> > I could read about this.
> >
> > I considered:
> >
> > Pool data from all the sessions for a given condition and test
> > together, thus getting 2000 repetitions of Test1 and Test 2 in each
> > condition. Now I have a 2x2x2 setup, which maps on to something in
> > Agresti, but then I am ignoring within-session correlation
> > information.
> >
> > I could simply get a difference between Test1 and Test2 percentages
> > for each session, and then compare the distribution of these
> > differences in conditions A and B (with something like a t-test),
> > but then I only have 10 points (one for each session) and so I guess
> > I am throwing away a lot of information.
> >
> > Very best,
> >
> > Suresh
>
>
> You are likely going to want to look at using glmer() in the 'lme4'
> CRAN package by Doug and Martin. This functionality post-dates P&B.
>
> There is a R-sig-mixed models list where you are likely better off
> pursuing your query further, as there you will avail yourself of
> experts in the field, including the package authors.
>
> More information on that list is here:
>
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
> HTH,
>
> Marc Schwartz
>
>
>
> ------------------------------
>
> Message: 26
> Date: Tue, 14 Jul 2009 09:38:56 -0400
> From: Duncan Murdoch <murdoch@stats.uwo.ca>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: deepak m r <deepaknbr@gmail.com>
> Cc: r-help@r-project.org, Petr PIKAL <petr.pikal@precheza.cz>
> Message-ID: <4A5C8A70.6030503@stats.uwo.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 7/14/2009 8:56 AM, deepak m r wrote:
> > Hi,
> > Empty plot is getting i dont know why. can u please clarify how
> > can i use Print function instead of plot function.
>
> You need print() if you are using grid-based graphics (lattice,
> ggplot2,...) in a script. You are using classic graphics so it should
> not be necessary.
>
> If you are getting blank plots when you shouldn't, that's a bug.
If you
> can put together a reproducible example that shows its a bug in R,
> rather than a bug in your script, it will likely be fixed fairly quickly.
>
> Duncan Murdoch
>
>
> > best regards
> > deepak
> >
> > On Tue, Jul 14, 2009 at 7:48 AM, Petr
PIKAL<petr.pikal@precheza.cz>
> wrote:
> >> Hi
> >>
> >> For this type of problems I do multipage pdf.
> >>
> >> pdf("file", ....)
> >> for (i in ...) {
> >> do all stuff including plot
> >> }
> >> dev.off()
> >>
> >> and then check the plots afterwards. Recently there was some post
about
> >> how to wait but you do not want only wait you want also to
interactively
> >> change plotting parameters, won't you.
> >>
> >> cat("\n","Enter x","\n") # prompt
> >> x=scan(n=1) # read 1 line from console
> >>
> >> this construction print something on console and reads one line
from
> >> console. There are also some packages which leave you choose from
> several
> >> options. I think in car and randomForest are such routines so you
could
> >> check how it is done.
> >>
> >> Regards
> >> Petr
> >>
> >> r-help-bounces@r-project.org napsal dne 14.07.2009 13:17:01:
> >>
> >>> hi,
> >>> is there any wait function in R. I am running one R script
to plot
> >>> many graphs it is in the for loop. its showing no error but
its not
> >>> plotting well I think i can solve this problem with a wait
function.
> >>> Please help me in this regards. If u need any clarification
about
> >>> programme. u can find the script below.
> >>>
> >>> best regards,
> >>> Deepak.M.R
> >>> Biocomputing Group
> >>> University of Bologana.
> >>>
> >>>
> >>> #!/usr/bin/R
> >>> s<-c
> >>>
> >>
>
("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
>
> >>>
,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> >>> for(t in 1:length(s))
> >>> {
> >>>
> >>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> >>> attach (a)
> >>> names(a)
> >>>
al<-1:length(paste("alp",s[t],"_mean",sep=""))
> >>>
> >>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> >>> attach(b)
> >>> names(b)
> >>>
bl<-1:length(paste("bet",s[t],"_mean",sep=""))
> >>>
p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s
> >>> [t],"mean.sat",sep=""),header=T)
> >>> attach(p)
> >>> names(p)
> >>>
pl<-1:length(paste("apb",s[t],"_mean",sep=""))
> >>>
o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s
> >>> [t],"mean.sat",sep=""),header=T)
> >>> attach(o)
> >>> names(o)
> >>>
ol<-1:length(paste("aob",s[t],"_mean",sep=""))
> >>>
postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> >>> plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean
Distance Plot for
> >>> ",s[t]," Rsidue
pair",sep=""),ylab="Mean Distance in
> >>> Angstrom",xlab="Residue Seperation Number")
> >>>
lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
> >>>
lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
> >>>
lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
> >>>
lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> >>> legend("topleft",c("Alpha
Proteins","Beta Proteins","Alpha +
> >>> Beta","Alpha or Beta"),lty > >>>
c(2,2,2,2),col=c("blue","yellow","red","green"))
> >>> dev.off()
> >>> }
> >>>
> >>> ______________________________________________
> >>> R-help@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.
> >>
> >>
> >
> > ______________________________________________
> > R-help@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.
>
>
>
> ------------------------------
>
> Message: 27
> Date: Tue, 14 Jul 2009 15:44:09 +0200
> From: "Frank Bloos" <Frank.Bloos@med.uni-jena.de>
> Subject: [R] Attributes lost after 'merge'
> To: <r-help@r-project.org>
> Message-ID: <4A5CA7CC.B177.00F6.0@med.uni-jena.de>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> In my dataframes, I am using attributes such as 'units' and
'labels'
> from the Hmisc-package. However, when I join two dataframes with the
> merge-command, all these attributes are gone. Is there a way to preserve
> them?
>
> Thanks, Frank
>
> ____________________
> Universit?tsklinikum Jena
> K?rperschaft des ?ffentlichen Rechts und Teilk?rperschaft der
> Friedrich-Schiller-Universit?t Jena
> Bachstra?e 18, 07743 Jena
> Verwaltungsratsvorsitzender: Prof. Dr. Walter Bauer-Wabnegg;
> Medizinischer Vorstand: Prof. Dr. Klaus H?ffken;
> Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufm?nnischer
> Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse
> Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221;
> Gerichtsstand Jena
> Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777
>
>
>
> ------------------------------
>
> Message: 28
> Date: Tue, 14 Jul 2009 15:05:24 +0100
> From: "Francisco Gochez" <fgochez@mango-solutions.com>
> Subject: [R] LondonR meeting - 21st of July
> To: <r-help@r-project.org>
> Message-ID:
>
<3CBFCFB1FEFFA841BA83ADF2F2A9C6FA487D8B@mango-data1.Mango.local>
> Content-Type: text/plain
>
>
>
> Thank you to everyone for showing such an interest in the next LondonR
> meeting.
>
>
>
> Below is the agenda for the meeting:
>
>
>
>
>
> LondonR meeting - 21st July 2009
>
>
>
> Time: 4pm - 7pm
>
>
>
> Venue: The Wall
>
> 45 Old Broad Street
>
> London
>
> ECN 1HU
>
> Tel: 020 7588 4845
>
>
>
> Agenda:
>
>
>
> * 4pm - Richard Pugh
>
> Introduction
>
>
>
> * 4.15pm - Matthew Dowle
>
> Data.table: Higher speed time series queries
>
>
>
> * 4.45pm - Francisco Gochez (To be confirmed)
>
> An overview of RMetrics 2009
>
>
>
> * 5.15pm - Brandon Whitcher
>
> Developing S4 Classes for Medical Imaging Data: Initial Experience(s)
>
>
>
> * 5.45pm - Richard Weeks
>
> Thoughts from useR 2009 - Rennes
>
>
>
> * 6.15pm - General discussion
>
>
>
> * Networking and feedback
>
>
>
> The evening is a free event. Please e-mail Sarah Lewis at
> slewis@mango-solutions.com if you would like to attend.
>
>
>
> We hope the evening will be as successful as the last one. We look
> forward to meeting all of the attendees.
>
>
>
> Best Regards,
>
>
>
> Francisco Gochez
>
>
>
> mangosolutions
>
> data analysis that delivers
>
>
>
> T: +44 (0)1249 767700
>
> F: +44 (0)1249 767707
>
>
>
> Unit 2 Greenways Business Park
>
> Bellinger Close
>
> Chippenham
>
> Wilts
>
> SN15 1BN
>
> UK
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 29
> Date: Tue, 14 Jul 2009 10:06:15 -0400
> From: deepak m r <deepaknbr@gmail.com>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: Duncan Murdoch <murdoch@stats.uwo.ca>
> Cc: r-help@r-project.org, Petr PIKAL <petr.pikal@precheza.cz>
> Message-ID:
> <5024f7590907140706r4f13114t1a904f17c859d0bd@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
>
> On Tue, Jul 14, 2009 at 9:38 AM, Duncan Murdoch<murdoch@stats.uwo.ca>
> wrote:
> > On 7/14/2009 8:56 AM, deepak m r wrote:
> >>
> >> Hi,
> >> ? ?Empty plot is getting i dont know why. can u please clarify how
> >> can i use Print function instead of plot function.
> >
> > You need print() if you are using grid-based graphics (lattice,
> ggplot2,...)
> > in a script. ?You are using classic graphics so it should not be
> necessary.
> >
> > If you are getting blank plots when you shouldn't, that's a
bug. ?If you
> can
> > put together a reproducible example that shows its a bug in R, rather
> than a
> > bug in your script, it will likely be fixed fairly quickly.
> >
> > Duncan Murdoch
> >
> >
> >> best regards
> >> deepak
> >>
> >> On Tue, Jul 14, 2009 at 7:48 AM, Petr
PIKAL<petr.pikal@precheza.cz>
> wrote:
> >>>
> >>> Hi
> >>>
> >>> For this type of problems I do multipage pdf.
> >>>
> >>> pdf("file", ....)
> >>> for (i in ...) {
> >>> do all stuff including plot
> >>> }
> >>> dev.off()
> >>>
> >>> and then check the plots afterwards. Recently there was some
post about
> >>> how to wait but you do not want only wait you want also to
> interactively
> >>> change plotting parameters, won't you.
> >>>
> >>> cat("\n","Enter x","\n") #
prompt
> >>> x=scan(n=1) # read 1 line from console
> >>>
> >>> this construction print something on console and reads one
line from
> >>> console. There are also some packages which leave you choose
from
> several
> >>> options. I think in car and randomForest are such routines so
you could
> >>> check how it is done.
> >>>
> >>> Regards
> >>> Petr
> >>>
> >>> r-help-bounces@r-project.org napsal dne 14.07.2009 13:17:01:
> >>>
> >>>> hi,
> >>>> ? is there any wait function in R. I am running one R
script to plot
> >>>> many graphs it is in the for loop. its showing no error
but its not
> >>>> plotting well I think i can solve this problem with a wait
function.
> >>>> Please help me in this regards. If u need any
clarification about
> >>>> programme. u can find the script below.
> >>>>
> >>>> best regards,
> >>>> Deepak.M.R
> >>>> Biocomputing Group
> >>>> University of Bologana.
> >>>>
> >>>>
> >>>> #!/usr/bin/R
> >>>> s<-c
> >>>>
> >>>
> >>>
>
("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE"!
> >
> >>>>
?,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> >>>> for(t in 1:length(s))
> >>>> ? {
> >>>>
> >>>
> >>>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> >>>>
> >>>> ? attach (a)
> >>>> ? names(a)
> >>>> ?
al<-1:length(paste("alp",s[t],"_mean",sep=""))
> >>>>
> >>>
> >>>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> >>>>
> >>>> ? attach(b)
> >>>> ? names(b)
> >>>> ?
bl<-1:length(paste("bet",s[t],"_mean",sep=""))
> >>>> ?
p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s
> >>>> [t],"mean.sat",sep=""),header=T)
> >>>> ? attach(p)
> >>>> ? names(p)
> >>>> ?
pl<-1:length(paste("apb",s[t],"_mean",sep=""))
> >>>> ?
o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s
> >>>> [t],"mean.sat",sep=""),header=T)
> >>>> ? attach(o)
> >>>> ? names(o)
> >>>> ?
ol<-1:length(paste("aob",s[t],"_mean",sep=""))
> >>>> ?
postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> >>>> ? plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean
Distance Plot for
> >>>> ",s[t]," Rsidue
pair",sep=""),ylab="Mean Distance in
> >>>> Angstrom",xlab="Residue Seperation Number")
> >>>> ?
lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
> >>>> ?
lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
> >>>> ?
lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
> >>>> ?
lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> >>>> ? legend("topleft",c("Alpha
Proteins","Beta Proteins","Alpha +
> >>>> Beta","Alpha or Beta"),lty >
>>>>
c(2,2,2,2),col=c("blue","yellow","red","green"))
> >>>> ? dev.off()
> >>>> ? }
> >>>>
> >>>> ______________________________________________
> >>>> R-help@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.
> >>>
> >>>
> >>
> >> ______________________________________________
> >> R-help@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.
> >
> >
>
>
>
> ------------------------------
>
> Message: 30
> Date: Tue, 14 Jul 2009 10:07:16 -0400
> From: deepak m r <deepaknbr@gmail.com>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: Duncan Murdoch <murdoch@stats.uwo.ca>
> Cc: r-help@r-project.org, Petr PIKAL <petr.pikal@precheza.cz>
> Message-ID:
> <5024f7590907140707j3326ea55wd133b853ea35d344@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> I am not an expert to debug the R can u please help.
> best regards
> deepak
>
> On Tue, Jul 14, 2009 at 10:06 AM, deepak m r<deepaknbr@gmail.com>
wrote:
> > Hi,
> >
> >
> > On Tue, Jul 14, 2009 at 9:38 AM, Duncan
Murdoch<murdoch@stats.uwo.ca>
> wrote:
> >> On 7/14/2009 8:56 AM, deepak m r wrote:
> >>>
> >>> Hi,
> >>> ? ?Empty plot is getting i dont know why. can u please clarify
how
> >>> can i use Print function instead of plot function.
> >>
> >> You need print() if you are using grid-based graphics (lattice,
> ggplot2,...)
> >> in a script. ?You are using classic graphics so it should not be
> necessary.
> >>
> >> If you are getting blank plots when you shouldn't, that's
a bug. ?If you
> can
> >> put together a reproducible example that shows its a bug in R,
rather
> than a
> >> bug in your script, it will likely be fixed fairly quickly.
> >>
> >> Duncan Murdoch
> >>
> >>
> >>> best regards
> >>> deepak
> >>>
> >>> On Tue, Jul 14, 2009 at 7:48 AM, Petr
PIKAL<petr.pikal@precheza.cz>
> wrote:
> >>>>
> >>>> Hi
> >>>>
> >>>> For this type of problems I do multipage pdf.
> >>>>
> >>>> pdf("file", ....)
> >>>> for (i in ...) {
> >>>> do all stuff including plot
> >>>> }
> >>>> dev.off()
> >>>>
> >>>> and then check the plots afterwards. Recently there was
some post
> about
> >>>> how to wait but you do not want only wait you want also to
> interactively
> >>>> change plotting parameters, won't you.
> >>>>
> >>>> cat("\n","Enter x","\n") #
prompt
> >>>> x=scan(n=1) # read 1 line from console
> >>>>
> >>>> this construction print something on console and reads one
line from
> >>>> console. There are also some packages which leave you
choose from
> several
> >>>> options. I think in car and randomForest are such routines
so you
> could
> >>>> check how it is done.
> >>>>
> >>>> Regards
> >>>> Petr
> >>>>
> >>>> r-help-bounces@r-project.org napsal dne 14.07.2009
13:17:01:
> >>>>
> >>>>> hi,
> >>>>> ? is there any wait function in R. I am running one R
script to plot
> >>>>> many graphs it is in the for loop. its showing no
error but its not
> >>>>> plotting well I think i can solve this problem with a
wait function.
> >>>>> Please help me in this regards. If u need any
clarification about
> >>>>> programme. u can find the script below.
> >>>>>
> >>>>> best regards,
> >>>>> Deepak.M.R
> >>>>> Biocomputing Group
> >>>>> University of Bologana.
> >>>>>
> >>>>>
> >>>>> #!/usr/bin/R
> >>>>> s<-c
> >>>>>
> >>>>
> >>>>
>
("GG","GA","GV","GL","GI","GM","GF","GW","GP","GS","GT","GC","GY","GN","GQ","GD","GE","GK","GR","GH","AA","AV","AL","AI","AM","AF","AW","AP","AS","AT","AC","AY","AN","AQ","AD","AE","AK","AR","AH","VV","VL","VI","VM","VF","VW","VP","VS","VT","VC","VY","VN","VQ","VD","VE","VK","VR","VH","LL","LI","LM","LF","LW","LP","LS","LT","LC","LY","LN","LQ","LD","LE","LK","LR","LH","II","IM","IF","IW","IP","IS","IT","IC","IY","IN","IQ","ID","IE","IK","IR","IH","MM","MF","MW","MP","MS","MT","MC","MY","MN","MQ","MD","ME","MK","MR","MH","FF","FW","FP","FS","FT","FC","FY","FN","FQ","FD","FE","FK","FR","FH","WW","WP","WS","WT","WC","WY","WN","WQ","WD","WE","WK","WR","WH","PP","PS","PT","PC","PY","PN","PQ","PD","PE","PK","PR","PH","SS","ST","SC","SY","SN","SQ","SD","SE","SK","SR","SH","TT","TC","TY","TN","TQ","TD","TE","TK","TR","TH","CC","CY","CN","CQ","CD","CE","CK","CR","CH","YY","YN","YQ","YD","YE","YK","YR","YH","NN","NQ","ND","NE","NK","NR","NH","QQ","QD","QE","QK","QR","QH","DD","DE!
> "!
> >>
> >>>>>
?,"DK","DR","DH","EE","EK","ER","EH","KK","KR","KH","RR","RH","HH")
> >>>>> for(t in 1:length(s))
> >>>>> ? {
> >>>>>
> >>>>
> >>>>
>
a<-read.table(paste("../All_alpha_proteins/alp",s[t],"mean.sat",sep=""),header=T)
> >>>>>
> >>>>> ? attach (a)
> >>>>> ? names(a)
> >>>>> ?
al<-1:length(paste("alp",s[t],"_mean",sep=""))
> >>>>>
> >>>>
> >>>>
>
b<-read.table(paste("../All_beta_proteins/bet",s[t],"mean.sat",sep=""),header=T)
> >>>>>
> >>>>> ? attach(b)
> >>>>> ? names(b)
> >>>>> ?
bl<-1:length(paste("bet",s[t],"_mean",sep=""))
> >>>>> ?
p<-read.table(paste("../Alpha_and_beta_proteins_a+b/apb",s
> >>>>> [t],"mean.sat",sep=""),header=T)
> >>>>> ? attach(p)
> >>>>> ? names(p)
> >>>>> ?
pl<-1:length(paste("apb",s[t],"_mean",sep=""))
> >>>>> ?
o<-read.table(paste("../Alpha_and_beta_proteins_aorb/aob",s
> >>>>> [t],"mean.sat",sep=""),header=T)
> >>>>> ? attach(o)
> >>>>> ? names(o)
> >>>>> ?
ol<-1:length(paste("aob",s[t],"_mean",sep=""))
> >>>>> ?
postscript(file=paste("Mean_",s[t],"_Plot.ps",sep=""))
> >>>>> ?
plot(0,xlim=c(0,160),ylim=c(0,70),main=paste("Mean Distance Plot
> for
> >>>>> ",s[t]," Rsidue
pair",sep=""),ylab="Mean Distance in
> >>>>> Angstrom",xlab="Residue Seperation
Number")
> >>>>> ?
lines(al,paste("alp",s[t],"_mean",sep=""),col="blue",lty
= 2)
> >>>>> ?
lines(bl,paste("bet",s[t],"_mean",sep=""),col="yellow",lty
= 2)
> >>>>> ?
lines(pl,paste("apb",s[t],"_mean",sep=""),col="red",lty
= 2)
> >>>>> ?
lines(ol,paste("aob",s[t],"_mean",sep=""),col="green",lty
= 2)
> >>>>> ? legend("topleft",c("Alpha
Proteins","Beta Proteins","Alpha +
> >>>>> Beta","Alpha or Beta"),lty >
>>>>>
c(2,2,2,2),col=c("blue","yellow","red","green"))
> >>>>> ? dev.off()
> >>>>> ? }
> >>>>>
> >>>>> ______________________________________________
> >>>>> R-help@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.
> >>>>
> >>>>
> >>>
> >>> ______________________________________________
> >>> R-help@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.
> >>
> >>
> >
>
>
>
> ------------------------------
>
> Message: 31
> Date: Tue, 14 Jul 2009 11:08:33 -0300
> From: Jose Claudio Faria <joseclaudio.faria@gmail.com>
> Subject: [R] Tinn-R 2.3.0.0 released
> To: r-help <r-help@stat.math.ethz.ch>
> Message-ID:
> <c86bda880907140708t465ce249h9f4673225813b3dc@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> We would like to announce that a new version of the Tinn-R for Windows
> (2.3.0.0) was released and is available on SourceForge server:
> http://sourceforge.net/projects/tinn-r
>
> Tinn-R is a R script editor under the OS Windows.
>
> Changes:
> 2.3.0.0 (jul/10/2009)
> * Bugs fixed:
> - The error message when typing CTRL+TAB inside the Rterm
> interface whenever it was not split.
> - It now remembers the position of the Tabs files (top or
> botton) when starting.
> - It now properly organizes the Tabs files in relation to
> other toolbars whenever the user uses the show/hide option in the
> toolbars.
> - The intermittency of completion resources.
> - The Auto completion and Data completion now recognizes
> split by a dot as a complete word: for example my.function( and
> my.data$.
> - Under Windows Vista the option R/Configure/Permanent
> (Rprofile.site now checks if the user has administrative privileges to
> change the content of the file Rprofile.site, before to insert the
> necessary script. If the user receive a message error, it necessary to
> change manually the security properties enabling Full control of the
> folder etc where the R is installed.
> * The Completion resource migrated to XML, it is more flexible and
> easy to use. Now it is located in the the menu Tools/Database.
> * R card and R tip are now located in a more conveniente place:
> Tool/Database.
> * The R tip resource was updated.
> * Menu Format/Block was removed and all associated resources were
> relocated to a more logic place: Format/selection.
> * The User guide was expanded/enhanced in various topics.
> * The Application options interface was enhanced.
> * A new option in the Application options allows more specific
> recognition of Rgui. Now it is possible to avoid any windows caption
> with the word Console to be recognized as a R instance.
> * The interface Tinn-R hotkeys was fully reworked and it is now
> more simple and efficient.
> * Parts of the source code were optimized.
> * A new resource was added to the R send: Clipboard. It enables
> the user to send the content of the clipboard easily to Rterm.
> * Sorry, due to bugs the highlighters Deplate and Txt2tags were
> removed from the project. We will make new ones in the future.
>
> We think it is a very good and stable version of this program, btw, if
> you to notice any bug, please, tell us.
>
> Tinn-R team.
>
>
>
> ------------------------------
>
> Message: 32
> Date: Tue, 14 Jul 2009 07:12:49 -0700 (PDT)
> From: John Kane <jrkrideau@yahoo.ca>
> Subject: Re: [R] Help needed in identifying type of plot
> To: r-help@r-project.org, "Girish A.R."
<garamach@gmail.com>
> Message-ID: <461781.69940.qm@web38404.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> It looks like a forest plot normally used in meta-analysis work. See
> http://www.bmj.com/cgi/content/full/322/7300/1479 . See
> http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=114 for an
> example from rmeta package with accompanying code.
>
> I think that package metafor also gives forest plots.
>
> --- On Tue, 7/14/09, Girish A.R. <garamach@gmail.com> wrote:
>
> > From: Girish A.R. <garamach@gmail.com>
> > Subject: [R] Help needed in identifying type of plot
> > To: r-help@r-project.org
> > Received: Tuesday, July 14, 2009, 7:30 AM
> >
> > Hi folks,
> >
> > Can someone please help me in identifying the type of plot
> > shown here?
> > Sample R code or specific package name would be of help as
> > well.
> >
> > Thanks,
> > -Girish
> >
> > http://www.nabble.com/file/p24477714/example_plot.jpg
> >
> >
> > --
> > View this message in context:
>
http://www.nabble.com/Help-needed-in-identifying-type-of-plot-tp24477714p24477714.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > ??? [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@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.
> >
>
>
> __________________________________________________________________
> Looking for the perfect gift? Give the gift of Flickr!
>
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>
>
>
> ------------------------------
>
> Message: 33
> Date: Tue, 14 Jul 2009 10:23:55 -0400
> From: Steve Lianoglou <mailinglist.honeypot@gmail.com>
> Subject: Re: [R] LAPACK package
> To: Moumita Das <das.moumita.online@gmail.com>
> Cc: r-help@r-project.org
> Message-ID: <6B6A7E3C-4B78-44F9-95D5-E242937213F0@gmail.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi,
>
> On Jul 14, 2009, at 5:45 AM, Moumita Das wrote:
>
> > Hi All,
> > Can someone tell me if solve function shown below for my version of
> > R is
> > proper or not?
> >
> > I am using R 2.7.2 .Wherever i have used this function ,i got
> > results which
> > were different from the expected results as computed using SPSS.
>
> Can you give us a bit more info about your problem? What are the
> differences between R and SPSS? A reproducible example, even?
>
> Pasting the content from R's help file, and the source of the
> solve.default function as implemented in R isn't really helpful, since
> we all have access to that.
>
> Also, as an aside, upgrading to the latest R wouldn't hurt, if
> feasible :-)
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics and Systems Biology
> Weill Medical College of Cornell University
>
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>
>
> ------------------------------
>
> Message: 34
> Date: Tue, 14 Jul 2009 09:31:35 -0500
> From: roger koenker <rkoenker@uiuc.edu>
> Subject: Re: [R] Fortran function for quantiles
> To: DHIMAN BHADRA <dhimanbhadra@gmail.com>
> Cc: r-help@r-project.org
> Message-ID: <919CC257-03BF-415C-A5D2-F1BB3FE75287@uiuc.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> You could look at the function kuantile() in the package quantreg
> and the associated fortran code dsel05.f which implements a version
> of the Floyd and Rivest (CACM, 1975) algorithm.
>
>
> url: www.econ.uiuc.edu/~roger Roger Koenker
> email rkoenker@uiuc.edu Department of Economics
> vox: 217-333-4558 University of Illinois
> fax: 217-244-6678 Urbana, IL 61801
>
>
>
> On Jul 13, 2009, at 6:24 PM, DHIMAN BHADRA wrote:
>
> > Hi,
> > I was wondering whether there is any Fortran function or associated
> > library
> > for evaluating the quantiles of a set of values (something which the
> > R-function quantile() does). Any help will be much appreciated.
> > Thanks and regards,
> > Dhiman Bhadra
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@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.
>
>
>
> ------------------------------
>
> Message: 35
> Date: Tue, 14 Jul 2009 10:32:40 -0400
> From: Duncan Murdoch <murdoch@stats.uwo.ca>
> Subject: Re: [R] hi friends, is there any wait function in R
> To: deepak m r <deepaknbr@gmail.com>
> Cc: r-help@r-project.org, Petr PIKAL <petr.pikal@precheza.cz>
> Message-ID: <4A5C9708.7070301@stats.uwo.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 7/14/2009 10:07 AM, deepak m r wrote:
> > Hi,
> > I am not an expert to debug the R can u please help.
>
> No, because you haven't given us anything to work with. Simplify your
> example to something we can run, explain what you see and what you think
> you should see, and then maybe one of us could help.
>
> Duncan Murdoch
>
> > best regards
> > deepak
> >
> > On Tue, Jul 14, 2009 at 10:06 AM, deepak m
r<deepaknbr@gmail.com> wrote:
> >> Hi,
> >>
> >>
> >> On Tue, Jul 14, 2009 at 9:38 AM, Duncan
Murdoch<murdoch@stats.uwo.ca>
> wrote:
> >>> On 7/14/2009 8:56 AM, deepak m r wrote:
> >>>>
> >>>> Hi,
> >>>> E...
>
> [Mensaje recortado]
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