[R] Elaborate OrgChart

Hi, I'm trying to draw a chart such as the one provided by gvisOrgChart in the GoogleVis demo, that would provide more options such as boxes with varying size or the ability to add basic statistics on each subgroup represented by a box. Any idea ? Thanks [[alternative HTML version delet

[R] Fwd: Error: memory exhausted (limit reached?)

tu 16.10's R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Forwarded Message Subject: Error: memory exhausted (limit reached?) Date: Mon, 13 Mar 2017 16:51:15 +0100 From: Guillaume MULLER To: r-help@r-project.org Hello everyone, I was working on a DeepNet pro

[R] Error: memory exhausted (limit reached?)

Hello everyone, I was working on a DeepNet project at home, with an old PC with 4Gb RAM, running Ubuntu 16.04. For efficiency reason, I stored my dataset as a csv file with write.csv and reloaded it at will with read.csv. I did it several time, everything was working fine. This morning, at wo

[R] Average of x normalizations

le, I would also like to get the standard deviation for each field, preferably in a seperate table. This would allow me to thoroughly analyze the normalization data. If anyone would be able to assist me with this, I would be very grateful! Sincerely, Guillaume Tahon Example OTU_

[R] 3D point cloud fitting

X Y Z LH 4.627 270.1359368 -346.0554962 LL 4.63 270.1264744 -358.0371904 RH 4.336 -270.2775009 -346.043514 RL 4.29 -270.2889739 -358.0252081 R 4.581 -270.251483 -274.4168414 L 4.531 270.1487988 -274.4168417 C 0 0 0 Thanks in advance, Guillaume [[alternative HTML versi

Re: [R] RODBC package not found (in English)

z vous! La patience des membres de la mailing list R est limitée surtout pour les questions qui ont été posées mille fois et dont les réponses sont dans le FAQ. A bon entendeur, Bonne journée Guillaume 2015-04-20 13:01 GMT+02:00 CHIRIBOGA Xavier : > Dear members, > > > &g

[R] Fitting Structural Equation Model with sem package and Summary issues

nt covariances cannot be computed I also tried to set one loading to 1 instead of setting equality among loadings, but the results were the same. Could it be possible that the low number of data (N=39 but no NA inside) may be the cause of the error? In the model, the df is 1, thus all the parameter

[R] how to combine apply and which or alternative ways to do so

vector 2 correspond. I tried to combine the "which" and "apply" but I dit not succeed and I have no idea about a possible vectorization. Can someone help me ? Thanks Guillaume __ R-help@r-project.org mailing list https://

Re: [R] R CMD in batch mode/trycatch() keeps hold on resources

Problem fixed. http://stackoverflow.com/questions/7103429/all-the-connections-are-in-use-execution-halted/7108799#7108799 It can happen when the error handling is not properlly done. trycatch enter in finally and get stuck. 2013/2/13 guillaume Le Ray > HI all, > > I am using R (versi

[R] R CMD in batch mode/trycatch() keeps hold on resources

when I try to delete the folder it cannot... do you have any idea of which function can be the origin of the problem? or how to kill the process? Regards, Guillaume Le Ray [[alternative HTML version deleted]] __ R-help@r-project.org mailing

[R] Getting the latex file from R CMD check

d to save it. Any idea how I can save this tex file? Thanks Guillaume __ 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 and provide commented, mi

Re: [R] Creating tiff with 1200 dpi

I also had a lot of trouble to create the figs exactly as I want then using R alone. Now, I generally create a postscript image in R and I use gimp after so I can easily modify the resolution. On 10/3/2012 11:56 AM, David Winsemius wrote: On Oct 3, 2012, at 11:52 AM, David Winsemius wrote:

Re: [R] RGL

hed packages: [1] rgl_0.92.892 fortunes_1.5-0 snowfall_1.84 snow_0.3-9 Le Jul 27, 2012 à 3:48 AM, David Winsemius a écrit : > > On Jul 26, 2012, at 4:46 AM, Guillaume Meurice wrote: > >> Dear all, >> >> I was willing to use the library "rgl" to plot

[R] RGL

n from binaries - installation from sources - sessionInfo() Bests, -- Guillaume Meurice - PhD Plateforme de Bioinformatique Here is the installation from binaries : === > install.packages("rgl") trying URL 'http://mirror.ibcp.fr/pub/CRAN/bin/macosx/

Re: [R] CSV format issues

Dear all thanks for support. I'll set up an heuristic so as to catch most of the case. For the handful of ambiguous case, I'll exclude them from analysis, with a feedback to the software editor so as he can correct the format of the csv file. Bests, -- Guillaume Le Jul 23, 2012

[R] CSV format issues

question which is not totally related to R (which I'm using). Do you know if there any facilities using R to get the data in the good format ? Bests, -- Guillaume Meurice - PhD __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/lis

Re: [R] Finding the column with the maximum value by row

Hi, You should be able to reach your goal using functions "which" and "apply" On 7/17/2012 3:03 PM, Christopher Desjardins wrote: Hi, Let's say I have the following data: a=matrix(c(1,2,4,4,2,1,1,2,4),nrow=3,byrow=T) a [,1] [,2] [,3] [1,]124 [2,]421 [3,]1

Re: [R] Smoothing a persp graph

small variations of the terrain. Guillaume [[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.htm

[R] Smoothing a persp graph

I have not been able to find one for a 3D graph. Thanks! Guillaume __ 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 and provide commented, minimal, self-contained, reproducible code.

[R] graphic problems with special characters

ssional version 2002 with service pack 3 best regards, Guillaume Le Ray [[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-proj

Re: [R] simulate an gradually increase of the number of subjects based on two variables

,mean(y),sd(y))) simu[[i]]$x<-x simu[[i]]$y<-y } return(simu) } test=simu(x,y,60) lapply(test, function(x) cor.test(x$x,x$y)) As you could see, the correlation is disappearing with increasing N. Perhaps, a bootstrap with lm or cor.test could solve my problem.

[R] simulate an gradually increase of the number of subjects based on two variables

Dear R list, I have a population with two groups. I want to simulate an gradually increase of the number of subjects for group 1 based on mean and sd of two variables (correlated). Bootstrap ? Sample ? Simulation ? ( I just search some clues. Thank you Guillaume [[alternative HTML

[R] Sweave

Dear all, I'm trying to use sweave, but running the demo example, I got problem. First, I'm realluy a beginner with LaTeX and sweave, so sorry if my question seems weird. First I've installed mactex distribution : http://www.tug.org/mactex/2011/ I've set up the "SWEAVE_STYLEPATH_DEFAULT" envi

Re: [R] Memory limit in Aggregate()

, FUN = FUN) tableOut <- merge( x = tableOut , y = tableBy , by = "byKey") tableOut$byKey <- NULL return(tableOut) } Thanks again, Guillaume -- View this message in

Re: [R] Memory limit in Aggregate()

the aggregated table?) Thanks a lot, Guillaume -- View this message in context: http://r.789695.n4.nabble.com/Memory-limit-in-Aggregate-tp3711819p3713042.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] Memory limit in Aggregate()

aste("nrow ", length((listX[[1]] [1];"ncol x 3" [1];"ncol By 4" [1];"nrow 9083" It seems the "large" (=4) number of columns in listBy creates the troubles... Thanks, Guillaume -- View this message in context: http://r.789695.n4.nabble.com

[R] Memory limit in Aggregate()

message "impossible d'allouer un vecteur de longueur 1224643220" ) Why would R create such a long vector (my original lists , and is there a way to avoid this error ? Thank you for your help, Guillaume -- View this message in context: http://r.789695.n4.nabble.com/Memory-limit-in-Agg

Re: [R] grImport/ghostscript problems

Hi Paul, I'm using the latest version 0.7-2 with the version 9.00 of ghostscript on a windows XP machine. The error is still there and there is no xml file genrerated but a .rds file... Guillaume 2011/4/5 Paul Murrell > Hi > > > On 5/04/2011 9:30 p.m., guillaume Le Ray

Re: [R] grImport/ghostscript problems

Hi Al, I'm facing exactly the same problem as you are, have you manage to fix it? If yes I eager to know the trick. Regards, Guillaume 2011/3/27 Al Roark > Paul Murrell auckland.ac.nz> writes: > > > > > Hi > > > > On 28/03/2011 8:13 a.m., Al Roar

[R] xYplot Hmisc with CI shifting between groups

l shifting between the the groups in order to avoid overlapping, the problem is I have to do it in lattice. I looked throught the options but I did not found my solution. Best Regards, Guillaume Le Ray [[alternative HTML version deleted]] __ R-

[R] factorial block design with missing data

Trt1 31069.5 31069.5 180.2905 6.227e-13 *** Clone 7 1206.2 172.3 0.0.4544 Trt:Clone 7 570.381.5 0.47280.8450 Residuals 25 4308.2 172.3 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Thank you very much

[R] What symbols are loaded when require()ing?

Hello. I would need to know of a programmatic way to get a list of all the new symbols you get when require(9)ing a package/library. I'd like to know how to do that from within R, or with the C API. Pointers to relevant documentation are also welcome. All the best, -- Guil

Re: [R] constraining functions for optim()

st made changes to see what happened, but forgot to bring it back. Thank you for your help, again. Guillaume > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Guillaume Théroux Rancourt > Sent: Monday, Februa

[R] constraining functions for optim()

-B method. I would like to also optimize where y.1 and y.2 are equal or near zero. So the three conditions here are: y.1 = 0 y.2 = 0 y = 0 In the data set below, we get: > res$value [1] 0.0004200628 but: > y.1 [1] 4.772095 > y.2 [1] -2.379089 Thank you for your help. guillaume

[R] Append multiple optim result with a loop (or apply?)

data correctly (is the data frame correct or should I convert the data into a matrix?). Any improvement is warmly welcome. Thank you for your help. Guillaume Guillaume Théroux Rancourt Ph.D. candidate --- Plant Biology Université Laval, Québec, QC, Canada guillaume.theroux-rancour...@ulaval.ca

Re: [R] Minimizing two non-linear functions with genoud - Trying to minimize or converge near zero

Vcmax and gi. Using optim, I see that it is very sensitive to the starting parameters. Using c(0.15, 100) give parameters close to what should be expected, but it is still not close enough to 7.478 for f.1 (for example). Thank you for your help, Guillaume > I do not understand completely w

[R] Minimizing two non-linear functions with genoud - Trying to minimize or converge near zero

max, gi){ (-(((Vcmax-0.89189)/gi)+164.6573+272.38*(1+21*10/165.82))+sqrtVcmax-0.89189)/gi)+164.6573+272.38*(1+21*10/165.82))^2-4*(-1/gi)*(0.89189*(164.6573+272.38*(1+21*10/165.82))-Vcmax*(164.6573-(5*21/2.605459)/(-2/gi) } test(res$par[1],res$par[2]) ## End Thank you for your help! Guilla

Re: [R] [Fwd: snowfall on Win7]

ars)){ if (names(IncludeVars)[i] %in% ExcludeVars) next cat('"',names(IncludeVars)[i],'", "',IncludeVars[i],'";\n',sep='') } cat(" ]\n\n") cat("end\n"

Re: [R] code for [[.data.frame

owing how to do this from the toploop. Thanks a lot. -- Guillaume Yziquel http://yziquel.homelinux.org/ __ 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/pos

[R] code for [[.data.frame

special syntacting handling. Could someone kindly show me how to display the code of [[.data.frame in the R toploop? All the best, -- Guillaume Yziquel http://yziquel.homelinux.org/ __ R-help@r-project.org mailing list https://stat.ethz.

[R] Listing what a package exports.

things before. All the best, -- Guillaume Yziquel http://yziquel.homelinux.org/ __ 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 and p

[R] Problem loading fAssets.

ont pas exportés par 'namespace:timeSeries' Erreur : le chargement du package / espace de noms a échoué pour 'fAssets' Two questions: -1- Being quite new to R, I'm wondering what this means exactly. -2- Does this seem to be an issue with fAssets itself, or with Debian

Re: [R] Silently loading an R package.

gards, Yihui Thank you so much... Guillaume Yziquel. -- Yihui Xie Phone: 515-294-6609 Web: http://yihui.name Department of Statistics, Iowa State University 3211 Snedecor Hall, Ames, IA On Fri, Nov 13, 2009 at 6:02 PM, Guillaume Yziquel wrote: Hello. I've been working an a binding

[R] Silently loading an R package.

ossible to squeeze off this output on stdout? All the best, Guillaume Yziquel. yziq...@seldon:~$ ocaml-batteries Objective Caml version 3.11.1 _ | | | | [| + | | Batterie

Re: [R] as.POSIXct month problem

I am on Ubuntu Karmic. 2009/10/26 Peter Dalgaard > guillaume chaumet wrote: > >> Thank you for your quick response >> >> >> sessionInfo() >>> >> R version 2.9.2 (2009-08-24) >> x86_64-pc-linux-gnu >> >> locale: >> >> L

Re: [R] as.POSIXct month problem

That's work with Sys.setlocale("LC_TIME","en_US.UTF-8") Thank you 2009/10/26 Jorge Ivan Velez > Hi Guillaume, > > What is your sessionInfo() ? It works me: > > > x <- c("1jan1960", "2jan1960", "31mar1960", &quo

Re: [R] as.POSIXct month problem

E=C;LC_MEASUREMENT=fr_FR.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base I need to change fr by en? 2009/10/26 Jorge Ivan Velez > Hi Guillaume, > > What is your sessionInfo() ? It works me: > > > x <-

[R] as.POSIXct month problem

Hi everybody When I try example of strptime x <- c("1jan1960", "2jan1960", "31mar1960", "30jul1960") z <- strptime(x, "%d%b%Y") The result is; > z [1] NA NA NA NA I have got the same result with complete form of month but not with numeric form. Any idea? [[alternative HTML version dele

[R] problem with pdf in batch mode

't know how to disable this option. Thanks Guillaume Le Ray Delta, SenseLab [[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-pro

[R] save wmf with a batch file

encounter problem with win.metafile. Thanks Guillaume [[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-

[R] Usage of OCaml/R binding.

gs as first argument, then a unit ( think of it a C void value containing nothing), and I get back an integer. The '?argv:' stuff is concerned with optional arguments, so no real big deal. Documentation and examples of how the API works to embed R in an application would be highly a

[R] exportation of xml file from R

for data I basically used the function xmlNode,addChildren,xmlchildren. I don't know if it's sufficient to recognise a xml file So thanks for your help! Regards, Guillaume [[alternative HTML version deleted]] __ R-help@r-projec

[R] Manipulate single line in textfile

Hello all, Is it possible to modify a single line in a textfile? I know it is possible to load the whole text file, do the change, and save this as a new file. However, this is not practical in my case, because the document is huge and cannot be fully loaded in R. Any idea? Best, Guillaume

Re: [R] How to separate huge dataset into chunks

Hello Thomas, Thanks for your help! Sadly your code does not work for the last chunk, because its length is shorter than nrows. I tried try(chunk<-read.table(conn, nrows=1,col.names=nms), silent=TRUE) but it gives me an error (go figure!) Best, Guillaume Quoting Thomas Lum

[R] How to separate huge dataset into chunks

crashing (with no error message) at about the 680 line. This is extremely frustrating. To try to fix this, I used connections with read.table. However, I now get a cryptic error telling me “no lines available in input”. Is there any way to make this work? Best, Guillaume

[R] How do I add a variable to a text file?

Hello all, I have a 2.0 GB dataset that I can't load into R, due to memory issues. The dataset itself is in a tab-delimited .txt file with 25 variables. I have a variable I'd like to add to the dataset. How do I do this? Best, Guillaume _

[R] Mersenne-Twister RNG

They are still available through the alternative generators gsl_rng_mt19937_1999 and gsl_rng_mt19937_1998. What is the exact version of Mersenne-Twister in R? Is it the 2002 revision, or the original 1998 one? Thank you! Guillaume __ R-help@r-p

[R] Lattice: how to have multiple wireframe nice intersection?

FALSE)) However, the intersection between the wireframes is not properly drawn. Is there a way to fix this with lattice, or should I use another package more suitable for this? Thanks! Guillaume __ R-help@r-project.org mailing list https://stat.ethz

Re: [R] Linked count between matrix columns

Because we want the values in table(x[,2]) where the **names** are as.character(x[,1][x[,1] > 0])], not the positions x[,1][x[,1] > 0])]. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the p

Re: [R] Linked count between matrix columns

table(x2)[as.character(x[,1][x[,1] > 0])] Why do I need as.character() here? I checked it does not work without, but I don't see why. The help says "as.character attempts to coerce its argument to character type". Thanks ver

Re: [R] Linked count between matrix columns

Thank you! This is exactly what I wanted. Could you please explain the logic behind your code? x[,2][x[,1][x[,1] > 0]] <- table(x[,2])[as.character(x[,1][x[,1] > 0])] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-he

[R] Linked count between matrix columns

4,]05 So for example, x[3,2] = 6, because length(x[x[,1]==0 & x[,2]==3,2]) = 6 I have tried this: x[x[,1]!=0,2] <- length(x[x[,1]==0 & x[,2] %in% which(x[,1]!=0),2]) but it does not work correctly as it put the same value in the changed rows. Thanks for yo

Re: [R] Randomly remove condition-selected rows from a matrix

I believe this does what you want: m[-sample(which(m[,1]<8 & m[,2]>12),2),] Analysis: Get a boolean vector of rows fitting criteria: m[,1]<8 & m[,2]>12 What are their indexes? which(...) Choose two among those indexes: sample(...,2) Thanks, but this does not seem to always work.

[R] Randomly remove condition-selected rows from a matrix

ating new objects. Any idea? Thanks! Cheers Guillaume __ 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 and provide commented, minimal, self-

[R] Symbols to use in text

Hello all, I'm trying to use text symbols in R, such are greek letters and mathematical operators. Do you know where I can find a list telling me how to use all those symbols? I'd like to have them displayed in my graphs. Best, Guillaume __

[R] Matrix starting at [0,0] instead of [1,1]?

Hello all, When I create a matrix, is there a way to make it start at [0,0], instead of [1,1]? That way, a 2x2 matrix would go from [0,0] to [1,1], instead of [1,1] to [2,2]. Best, Guillaume __ R-help@r-project.org mailing list https

[R] building experimental paradigm with R as "Brainard/Pelli Psych Toolbox"

Hi R users, I would known if any attempt of building psychological experimental paradigm with R as "Brainard/Pelli Psych Toolbox" on Matlab or e-prime was done. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://st

[R] Ubuntu vs Mac OS X

s far better than this Desk computer. I know Macs are good but that difference of performance is surprising me, did I do something wrong considering the large difference in processor? Thanks in advance Guillaume Blanchet __ R-help@r-project.org mailin

[R] Logistic regression

Here is the original dataset I am working on: > myTime Time Series: Start = 0 End = 1066 Frequency = 0.0769230769230769 [1]0 13 26 39 52 65 78 91 104 117 130 143 156 169 182 [16] 195 208 221 234 247 260 273 286 299 312 325 338 351 364 377 [31] 390 403

Re: [R] Logistic regression

> > >/ I am trying to fit a non linear regression model to time series data. > />/ > />/ If I do this: > />/ reg.logis = nls(myVar~SSlogis(myTime,Asym,xmid,scal)) > />/ I get this error message (translated to English from French): > />/ Erreur in nls(y ~ 1/(1 + exp((xmid - x)/scal)), data = xy, st

[R] Logistic regression

r gradient matrix at initial parameter estimates Could someone tell me what I am doing wrong? Many thanks Guillaume. __ 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/po

Re: [R] assistance with RDAtest beta version application

ab11.3<-read.table("Table_11-3.txt",header=TRUE,row.names=1) ### Extract the species (Y) and the environmental variables (X) from tab11.3 Y<-tab11.3[,1:6] X<-tab11.3[,7:10] ### Calculate the RDA coco<-rdaTest(Y,X,testF=TRUE,nperm=999) coco ### Draw the triplot gr

Re: [R] assistance with RDAtest beta version application

Hi ! I am familiar with the rdaTest package. It works perfectly find for me. Can you give me more details on the problems you have so I can be of greater help ! Have a nice day ! Guillaume Blanchet PhD student Stanfield, Les (MNR) a écrit : > Pierre Legendre has developed a beta version o

[R] lme equivalent of formula aov

value with anova(). Thanks in advance Guillaume [[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

[R] aov within subject and contrasts

Dear R list, again a newbie question here, so I wish I do not exasperated reader. This is example of my data.frame subject length consistency context acc frt 1 1200high scene_c 0.8181818 396.6642 2 2200high scene_c 1.000 595.7778 3

Re: [R] main title x title and y title with ggplot2

Thierry and Ingo, Thanks for these smart responses. It works fine. Guillaume 2008/3/5, Ingo Michaelis <[EMAIL PROTECTED]>: > > > > ONKELINX, Thierry inbo.be> writes: > > > > > Guillaume, > > > > You'll have to add the appropriate sca

Re: [R] main title x title and y title with ggplot2

Thierry First thank you for the celerity of your response. Second I use ggplot2 like this : >ggplot(data, aes(x,y,fill)) + geom_point() + etc. Where did you your xlab and ylab when using ggplot2 like that? Guillaume 2008/3/5, ONKELINX, Thierry <[EMAIL PROTECTED]>: > > Guillaume,

[R] main title x title and y title with ggplot2

Hi R people, I'm a R newbie and I'm trying to put main title, x title and y title in my graph with no success. Any idea? I'm sorry for this newbie question.. Guillaume [[alternative HTML version deleted]] __ R-help@r-project.o

[R] anova repeated measure

iduals25 And so what could I do with my epsilon? Previous aov() revealed me that there no effects of my groups but is my 6 times measures factor and my test factor were always significant? Guillaume [[alternative HTML version deleted]] __ R-

[R] anova (repeated measure)

do with my epsilon? Previous aov() revealed me that there no effects of my groups but is my 6 times measures factor and my test factor were always significant? Guillaume [[alternative HTML version deleted]] __ R-help@r-project.org mailing li