[R] [R-pkgs] randomForestSRC 1.5.0 is on CRAN

DeaR useRs: Version 1.5.0 of the package randomForestSRC is now on CRAN. >From the NEWS file: - Changes to RELEASE 1.5.0 Significant improvements to CPU and RAM usage profiles in serial and OpenMP modes of execution.

[R] error in mixed logit model using mlogit function

Dear all, I am trying to estimate an mlm with 8 alternatives, but I received the following error message: Error in `colnames<-`(`*tmp*`, value = "disto.disto") : attempt to set colnames on object with less than two dimensions My data look like this: > head(dtb) votechoice disto.CVP disto.F

Re: [R] stop a function

Yes. Give us a minimal and reproducible example of your code and don't post in HTML. See fortunes::fortune(244) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekst

Re: [R] Put short string labels vertically near tick marks on bottom axis

Full error message is there in my neat May 13, 2014; 9:54pm post. For some reason your last post is a mess. Hurr -- View this message in context: http://r.789695.n4.nabble.com/Put-short-string-labels-vertically-near-tick-marks-on-bottom-axis-tp4690452p4690492.html Sent from the R help mailing

Re: [R] stop a function

Here is my code... I tried to remove many parts and keep the part which is related to evalWithTimeout. I have two similar while(1) loop in my original code. I only include one here. tnx a lot NO while (perm <= 1000) {   setTimeLimit(cpu = Inf, elapsed = Inf)   while (1)   {     data <- main_data

Re: [R] Put short string labels vertically near tick marks on bottom axis

I can't find a post from you with that timestamp. Anyway I did this in my R: ### Rcode verData=c(1,365,809,1252,1753,2191,2922,3409,3896,4383,4819,5255,5691,6128,6564,7000) horData=c(1,300,800,1200,1700,2100,2900,3400,3800,4300,4800,5200,5600,6100,6500,7000) horTicLocs=c(1,365,809,1252,1753,2191

Re: [R] gumbel distribution

On 14/05/14 18:01, Frede Aakmann Tøgersen wrote: Don't know if I understand your last comment but I surely don't think that the Weibull and Gumbel distributions are the same. See their density function on e.g. Wikipedia. Then *why* did you answer Ms. Botto's question about the Gumbel distribut

Re: [R] gumbel distribution

Oh, I see now. I'm blushing. Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance & Modeling Technology & Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.com http://www.vestas.com Company reg. name: Vestas Wind Systems A/S This e

[R] using animation with persp

I would like to generate animating 3D plot. I have a matrix with 416 columns and 128 rows. a piece of my matrix looks like this:[,1] [,2] [,3] [,4] [,5] [,6] [1,] NA 0.4118836 0.6411741 0.7286600 0.7622486 0.7523395 [2,] NA 0.3481329 0.6066273 0.693448

[R] S3 - how to implement "colnames<-"

Have a class for which I would like to provide a "colnames<-.myclass" function so that colnames(myintsance) <- c("a","b","c") can be called. Witold -- Witold Eryk Wolski [[alternative HTML version deleted]] __ R-help@r-project.org mailing l

[R] R equivalent functions of some EXCEL functions

Dear R forum, EXCEL has some standard functions e.g.  (1) PRICE function : Returns the price per $100 face value of a security that pays periodic interest. (2) COUPDAYBS : Returns the number of days from the beginning of the coupon period to the settlement date. (3) COUPDAYS : Returns the

[R] install sann package in R R version 3.0.3

Dear all, I try to install the package SANN but unfortunatly received this warning Warning in install.packages : package ‘sann’ is not available (for R version 3.0.3) > do yo know how can i solve this? or if you know another helping package with example to be used for simulated annealing a

Re: [R] gumbel distribution

Having acquired some evidence that I am not *totally* confused, let me suggest to Ms. Botto that she have a look at the FAdist package which appears to provide [dpqr]gumbel() with the usual sort of syntax. There is also an implementation of the Gumbel distribution in the VGAM package. RSite

[R] Cure and data type

Hi, I have a simple table of age and frequency What data type should I use to represent this kind of data in R, and kindly how can I plot it in a curve thanks in advance RAE [[alternative HTML version deleted]] ___

[R] Problem with R "density" function

Hello, My friend has the following issue with R. I will be glad to receive any response. Thanks, Dhiman Bhadra Hello everyone, I am trying to use the 'density' function available with the base package of R to estimate the density of a data set for subsequent use. I just noticed that with even 100

Re: [R] S3 - how to implement "colnames<-"

Hi Witold, you should first of all redefine colnames to use UseMethod. Then you have to write a colnames.default that uses base::colnames (so that it does not interfere with existing code and other functions) and the you can define the method for your class. I would suggest, though, to use attribu

Re: [R] S3 - how to implement "colnames<-"

DO *NOT* post to both R-help and R-devel !! That is considered *very* impolite. As this is a question for R-help only, i.e., not fit for R-devel anyway : > Witold E Wolski > on Wed, 14 May 2014 10:57:09 +0200 writes: > Have a class for which I would like to provide a "colnames

Re: [R] S3 - how to implement "colnames<-"

Please do *NOT* crosspost to R-devel@ ... Be careful to remove it from CC when you "reply to all" R-help is way enough! Martin Maechler, (in the function R-* mailing list manager) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listi

Re: [R] Problem with R "density" function

Hi, Have you tried using a different bandwidth rather than the number of points, the default bandwidth gives ... x <- rnorm(1) dd <- density(x,kernel="epanechnikov",n=101) sum(dd$y)*(dd$x[2]-dd$x[1]) [1] 1.001014 Martyn -Original Message- From: r-help-boun...@r-project.org [mailto:

Re: [R] Put short string labels vertically near tick marks on bottom axis

Ok, I want to try to avoid the miscommunications that you all seem to think I cause. The following code works now because I use the single apostrophe-type of quote. It gives the the horLabels at the bottom. horAxisLims=c(0,7200) verData=c(1,365,809,1252,1753,2191,2922,3409,3896,4383,4819,5255,56

Re: [R] Put short string labels vertically near tick marks on bottom axis

So the error you get when trying to install the plotrix package says: Error in install.packages(plotrix) : object 'plotrix' not found So install.packages thinks that you provided an R object as an argument. But the object cannot be founded. Did you then read ?install.packages to see what types

Re: [R] Put short string labels vertically near tick marks on bottom axis

Thank you so much Frede Aakmann Tøgersen-2. Yes, the following code works with the 'plotrix' quotes and gives: 1) labels are vertical 2) the bottom of the labels line up with the ticks install.packages('plotrix') horAxisLims=c(0,7200) verData=c(1,365,809,1252,1753,2191,2922,3409,3896,4383,4819,525

[R] nested design

Dear useRs, I would like to apply a nested ANOVA on my dataset, but I cannot find a satisfying answer on how to implement it in R. For example, fac2 is nested within fac1: df <- data.frame(resp=rnorm(12), fac1=rep(LETTERS[1:2],each=6), fac2=rep(letters[1:6],each=2)) I have found three differ

[R] nls() help please

Someone might be able to come up with a neat expression, but my own approach would be to write a residual function to create the vector res from the parameters, for which core line would be res<- D1/(p1*((E/(p2-E))^(1/p3)))+D2/(p6*((E/(p2-E))^(1/p4))) +(p5*D1*D2)/(p1*p6*((E/(p2-E))^(0.5/p3+0.5/p4

Re: [R] Problem with R "density" function

Try adding plots, e.g. set.seed(20140514) x <- rnorm(100) hist(x, prob=TRUE, ylim=c(0,10)) dd <- density(x, n=10001, bw=0.001) lines(dd, col=2, type="s") dd <- density(x, n=101, bw=0.001) lines(dd, col=3, type="s") The density function you produce with bw=0.001

Re: [R] gumbel distribution

Dear Arun, Rolf and Frede, Thankyou very much for youe help. I managed to draw gumbel plot by using following command. > guplot.default(dataset2, main = "Gumbel Plot", xlab = "Reduced data", ylab = > "Observed data", type = "p") But I want to draw gumbel probability plot instead of simple gumbe

Re: [R] how to make R plot under Linux

Vojtěch Zeisek opensuse.org> writes: > > On Linux You can use Rkward http://rkward.sourceforge.net/ - very nice and > good graphical user interface for R. > > Dne Pá 19. února 2010 19:39:53 xinwei stat.psu.edu napsal(a): > > Hi, I am using R in Linux environment. How can i make plot in Linux

Re: [R] gumbel distribution

Like in ?qqplot Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: eliza botto Dato:14/05/2014 15.19 (GMT+01:00) Til: smartpink...@yahoo.com,r-help@r-project.org Emne: Re: [R] gumbel distribution Dear Arun, Rolf and Frede, Thankyou very much for youe help. I mana

Re: [R] Issues with fa() function in "psych"

Hi Sagnik, sagnik chakravarty wrote >- Request you to add option for *"equamax" rotation* also if possible. As GPApackage doesn't provide an explicit function termed "Equamax" you may want to use Crawford-Ferguson rotation from the GPApackage ( "cfT"). With the additional argument kappa=m*/(

Re: [R] Put short string labels vertically near tick marks on bottom axis

Hi, Try: install.packages("plotrix") A.K. On Wednesday, May 14, 2014 7:39 AM, Hurr wrote: Ok, I want to try to avoid the miscommunications that you all seem to think I cause. The following code works now because I use the single apostrophe-type of quote. It gives the the horLabels at the bo

[R] Voronoi-Diagrams in R

Hello everyone! I have returned to R after a longish break and am currently working on a project where I need Delaunay-Triangulations and Voronoi-Diagrams. If I understood it correctly, the Geometry-Package only offers functions for the Delaunay-Triangulation at the moment. Is this correct and if s

Re: [R] Put short string labels vertically near tick marks on bottom axis

I want to split the long label strings by separating out the alphabetical unit part and put the number to the left (above) the unit. I will have the separation done by my other program if necessary. Then I would need to put some strings not at tick marks. Or is there a way to do that (semi) aut

Re: [R] Voronoi-Diagrams in R

Try: install.packages("deldir") library(deldir) ?deldir set.seed(16180) x <- runif(20); y <- runif(20); window <- c(0,1,0,1) tess <- deldir(x, y, rw = window) plot.deldir(tess, wpoints="real", wlines="tess") Cheers, Boris On 2014-05-14, at 8:18 AM, Raphael Päbst wrote: > Hello everyone! > I ha

Re: [R] How to create multi variables

Hi, I know all what you said, but it seems that you don't understand my problem. I am sorry about my poor english level. I know that we can use a list to store complicated objects. e.g. x<-cbind(rnorm(10),rnorm(10),rnorm(10)) y<-cbind(rnorm(10),rnorm(10),rnorm(10)) lm1<-summary(lm(y[,1]~x[,1])) lm2

Re: [R] gumbel distribution

Dear Frede, Totally Unhderstood! Thankyou very much 4 your help. Eliza From: fr...@vestas.com To: eliza_bo...@hotmail.com; smartpink...@yahoo.com; r-help@r-project.org Date: Wed, 14 May 2014 15:58:37 +0200 Subject: RE: [R] gumbel distribution Like in ?qqplot Br. Frede Sendt fra Samsung mo

[R] matrix column division by vector

Hi, What is the elegant script to divide the columns of a matrix by the respective position of a vector elements? m=rbind(c(6,4,2),c(3,2,1)) v= c(3,2,1) res= 6/3   4/2  2/1     3/3   2/2    1/1 this is correct  mat2 = NULL for (i in 1: ncol(m))     mat2 = cbind(mat2, m[,i]/ v[i]) but

Re: [R] matrix column division by vector

You don't need do.call: > t(t(m)/v) [,1] [,2] [,3] [1,]222 [2,]111 > t(apply(m, 1, function(x) x/v)) [,1] [,2] [,3] [1,]222 [2,]111 - David L Carlson Department of Anthropology Texas A&M University Coll

Re: [R] matrix column division by vector

Have a look at ?sweep Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: carol white Dato:14/05/2014 16.53 (GMT+01:00) Til: r-h...@stat.math.ethz.ch Emne: [R] matrix column division by vector Hi, What is the elegant script to divide the columns of a matrix by the res

Re: [R] matrix column division by vector

Oh my goodness David! Don't forget that matrices are just vectors in column major order. > m/rep(v,e=2) [,1] [,2] [,3] [1,]222 [2,]111 (the generalization is obvious) should be far more efficient and simpler than running apply loops. -- Cheers, Bert Bert Gunter G

Re: [R] matrix column division by vector

Please post in plain text... your email is getting distorted and hard to read by the HTML. I don't know how to use do.call for this, but when you understand how vectors recycle and matrices and arrays are laid out in memory (read the Introduction to R document if not) then the following comes t

Re: [R] S3 - how to implement "colnames<-"

Hi So how would I actually implement it - what is the signature? "dimnames<-.myclass" <- function(data,newnames){ colnames(data) = newnames return(data) } ? On 14 May 2014 11:53, Martin Maechler wrote: > DO *NOT* post to both R-help and R-devel !! > That is considered *very* impolite. > >

[R] roxygen2 question

How to document S3Methods with roxygen so that I have only 1 entry in the package documentation page per S3Method. In the package documentation page they show up than as follows read2msExperiment read 2 feature alginer long format and generate an msexperiment read2msExperiment.data.frame convert

Re: [R] matrix column division by vector

Bert wins the race: > system.time(replicate(1e5, m/rep(v,e=2))) user system elapsed 0.250.000.25 > system.time(replicate(1e5, m/matrix( v, ncol=ncol(m), nrow=nrow(m), > byrow=TRUE))) user system elapsed 0.420.000.42 > system.time(replicate(1e5, t(t(m)/v))) use

Re: [R] gumbel distribution

The Weibull and Gumbel distributions are NOT the same. Frede Aakmann Tøgersen Sent by: r-help-boun...@r-project.org 05/14/2014 02:01 AM To eliza botto , "r-help@r-project.org" , cc Subject Re: [R] gumbel distribution Don't know if I understand your last comment but I surely don't thi

Re: [R] matrix column division by vector

Yes, but Jeff and I advocated essentially the same approach and the difference between our versions is unimportant. All the other approaches are at least aesthetically less desirable. One "criticism" of our solution: it relies on the underlying implementation of matrices rather than the matrix()

Re: [R] How to create multi variables

I am really sorry, I misunderstand your meanings. Your suggestions are useful, and it works! ls<-vector("list",3) for(i in 1:3) { ls[[i]]<-summary(lm(y[,i]~x[,i])) } Thanks for your help very much and sorry for my mistake. -- View this message in context: http://r.789695.n4.nabble.com/How-

Re: [R] matrix column division by vector

I'm wrong. Jeff's approach DOES use the matrix API and so I would say is better than mine. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Wed, May

Re: [R] gumbel distribution

Eliza, See the gamlss package's Gumbel distribution[1], where you will find your solution. OTOH, why does GAMLSS duplicate what's built-in to R? -- H 1. http://artax.karlin.mff.cuni.cz/r-help/library/gamlss.dist/html/GU.html On 14 May 2014 09:16, wrote: > The Weibull and Gumbel distributions ar

[R] data presentation -curve

dear group, I had table of ages and their related frequancy. What data type can I use to reoresent ir? Can I plot it in curve ? thanks in advance ARE [[alternative HTML version deleted]] __ R-help@r-p

Re: [R] data presentation -curve

1. data.frame 2. yes Read the posting guide and work through a free tutorial or manual on R: http://cran.r-project.org/other-docs.html David C -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ragia Ibrahim Sent: Wednesday, May 14,

Re: [R] S3 - how to implement "colnames<-"

The last argument of a replacement function (one used on the left side of an assignment) must be called 'value'. Bill Dunlap TIBCO Software wdunlap tibco.com On Wed, May 14, 2014 at 8:38 AM, Witold E Wolski wrote: > Hi > > So how would I actually implement it - what is the signature? > > > "dimn

Re: [R] Put short string labels vertically near tick marks on bottom axis

Have a look at regular expression in R! Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance & Modeling Technology & Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.com http://www.vestas.com Company reg. name: Vestas Wind Systems

Re: [R] matrix column division by vector

Maybe I am missing the point -- but what is wrong with line 3 of: m=rbind(c(6,4,2),c(3,2,1)) v= c(3,2,1) m%*%diag(1/v) # [,1] [,2] [,3] # [1,]222 # [2,]111 Ted. On 14-May-2014 15:03:36 Frede Aakmann Tøgersen wrote: > Have a look at ?sweep > > Br. Frede >

[R] Interpreting results of rq() when tau = -1

I've read the quantreg vignette and ?rq and applied rq() to Brownlee's stack loss data set. The results when I specify the desired output quantile (tau) are easily understood. When I specify tau = -1 (as in the 4th example in ?rq) I do not know what I'm seeing as the results. The code is: data(

Re: [R] matrix column division by vector

Scores well on notational simplicity. Loses big on computational efficiency (lots of terms multiplied with zero, then added to the one nonzero term). --- Jeff NewmillerThe . . Go Liv

Re: [R] Correlelogram with partial correlation coefficients

Bill, For package-specific questions, you should email the package maintainer (for corrgram, that's me). Michael Friendly's paper on corrgrams includes an example of partial correlations. The code to reproduce his example is hiding in the "tests" directory of the corrgram sourcecode zip file.

Re: [R] R equivalent functions of some EXCEL functions

You could search all of CRAN using the RSiteSearch function for terms like bond or coupon. There are also Task Views for Finance and Econometrics that may point you towards useful packages. On Wed, May 14, 2014 at 3:07 AM, Katherine Gobin wrote: > Dear R forum, > > > EXCEL has some standard func

Re: [R] Convert to integers all entries of a table (for DESeq2)

Sorry, I am pretty new using R. Here is my code to read the table: library("DESeq2") setwd("~/Dropbox/TESIS/DGEA_2.0/Chapter_4_thesis/DE_analysis/DESeq2") matrix = read.table (file.choose(), header=TRUE, row.names=1) CeleDesign <- data.frame( row.names = colnames(matrix), condition = factor(c

[R] Creating multiple orthogonal designs

Hi, I am trying to create multiple orthogonal designs using the Conjoint package. I have 4 factors with 5 levels in each. library(conjoint) experiment<-expand.grid( price<-c("a1","a2","a3","a4","a5"), tag<-c("b1","b2","b3","b4","b5"), smell<-c("c1","c2","c3","c4","c5"), aroma<-c("f1","f2

[R] model selection for nested factorial design

Stats beginner here. I have a dataset composed of observations taken from 16 separate experimental panels, each nested into one of 4 conditions (Treatment A Level 1, Treatment A Level 2, Treatment B Level 1, Treatment B Level 2; see photo: http://imgur.com/ZbzFPNq). There are 100 observations of t

Re: [R] Interpreting results of rq() when tau = -1

Rich: When you use tau=-1 in rq() then under the $sol you are getting estimates for all possible quantiles for the given regression model, which includes the objective function value minimized, the quantile value, estimates for all the parameters, and I think the output still includes the estimate

Re: [R] Put short string labels vertically near tick marks on bottom axis

Hi, May be this helps: num <- gsub("[[:alpha:]]+","",horLabels)##from your previous post Chr <- gsub("[0-9.]+","",horLabels)  horLabelsNew <- parse(text=paste("{}","^", num,"*",Chr,sep="")) plot(horData, verData,xaxt='n',xlim= horAxisLims) axis(1,tick=TRUE,at= horTicLocs,labels=rep("",length(hor

Re: [R] How to create multi variables

Hi, I guess you can also use ?assign with ?get #For e.g. set.seed(39) mat1 <- matrix(sample(1:10, 10*5, replace=TRUE), ncol=10) vec1 <- paste0("t",1:ncol(mat1)) for(i in 1:ncol(mat1)){  assign(vec1[i], sum(mat1[,i]))  }  t1 #[1] 15  t2 #[1] 28 sapply(vec1,get) # t1  t2  t3  t4  t5  t6  t7  t8  t9

Re: [R] How to create multi variables

Hi, Try: ls <- vector("list",3) for (i in 1:3)  {    ls[[i]] <- summary(lm(y[,i]~x[,i]))  } names(ls) <- paste0("lm",1:3) A.K. On Wednesday, May 14, 2014 10:45 AM, yuanzhi wrote: Hi, I know all what you said, but it seems that you don't understand my problem. I am sorry about my poor englis

Re: [R] Interpreting results of rq() when tau = -1

On Wed, 14 May 2014, Cade, Brian wrote: When you use tau=-1 in rq() then under the $sol you are getting estimates for all possible quantiles for the given regression model, ... Brian, Thank you. And Roger pointed out that I overlooked ?rq.process.object. Mea culpa! (see Cade and Noon 2003

Re: [R] How to create multi variables

Yes, it works, thanks for your help. -- View this message in context: http://r.789695.n4.nabble.com/How-to-create-multi-variables-tp4690465p4690572.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list htt

Re: [R] Put short string labels vertically near tick marks on bottom axis

Thank you Frede Aakmann Tøgersen, but your suggestion is too difficult for me to understand. Two problems: 1)If I let the labels on the bottom horizontal scale be horizontal, then when I change the graph's size horizontally some labels disappear and reappear depending on the amount of stretch.

Re: [R] Cure and data type

On Wed, 14 May 2014 11:33:30 AM Ragia Ibrahim wrote: > Hi, > I have a simple table of age and frequency > What data type should I use to represent this kind of data in R, and kindly > how can I plot it in a curve thanks in advance > RAE > Hi RAE, Here is one way: agetable<-table(sample(0:100,100

Re: [R] model selection for nested factorial design

K C gmail.com> writes: > [snip] > I have a dataset composed of observations taken from 16 separate > experimental panels, each nested into one of 4 conditions (Treatment A > Level 1, Treatment A Level 2, Treatment B Level 1, Treatment > B Level 2; see > photo: http://imgur.com/ZbzFPNq). The

Re: [R] Put short string labels vertically near tick marks on bottom axis

Perhaps, but Arun answered you question using regular expressions. So didn't that not do the job? Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: Hurr Dato:14/05/2014 22.48 (GMT+01:00) Til: r-help@r-project.org Emne: Re: [R] Put short string labels vertically

[R] How to illustrate an interaction with plotLMER.fnc

Hello, I have built a linear mixed model (with lmer). To illustrate an interaction between two (originally) continuous variable, I would like to plot the effects of X1 versus Y for 1=low and 2=high X2. I am using plotLMER.fnc but have not been able to figure out the code. Could you help? Thank

[R] filename of current device

Hi all, how do I find out about the filename, the currently open (let's say pdf) device is writing to? If I find 'dev.cur()' returning 'pdf 3' when I expect 'nulldevice 1' I would like to know, which file that pdf device is actually targeting. Any help for my poor organization is highly apprecia

[R] Bubble map in R

Hi, I would like to create a nice looking bubble map in R. Here is what I have done so far (the data is found below): # library(ggplot2) if (dev.cur() == 1) x11(width=8,height=6) par(mfcol=c(1,1)) ggplot

Re: [R] using animation with persp

On May 14, 2014, at 1:50 AM, Babak Bastan wrote: > I would like to generate animating 3D plot. I have a matrix with 416 > columns and 128 rows. a piece of my matrix looks like this:[,1] > [,2] [,3] [,4] [,5] [,6] > [1,] NA 0.4118836 0.6411741 0.7286600 0.762

Re: [R] filename of current device

On May 14, 2014, at 3:04 PM, Andreas Leha wrote: > Hi all, > > how do I find out about the filename, the currently open (let's say pdf) > device is writing to? > > If I find 'dev.cur()' returning 'pdf 3' when I expect 'nulldevice 1' I > would like to know, which file that pdf device is actually

Re: [R] filename of current device

Hi David, Thank you for following up on that. David Winsemius writes: > On May 14, 2014, at 3:04 PM, Andreas Leha wrote: > >> Hi all, >> >> how do I find out about the filename, the currently open (let's say pdf) >> device is writing to? >> >> If I find 'dev.cur()' returning 'pdf 3' when I ex

Re: [R] filename of current device

On May 14, 2014, at 3:44 PM, Andreas Leha wrote: > Hi David, > > Thank you for following up on that. > > David Winsemius writes: > >> On May 14, 2014, at 3:04 PM, Andreas Leha wrote: >> >>> Hi all, >>> >>> how do I find out about the filename, the currently open (let's say pdf) >>> device i

Re: [R] filename of current device

Hi David, David Winsemius writes: > On May 14, 2014, at 3:44 PM, Andreas Leha wrote: > >> Hi David, >> >> Thank you for following up on that. >> >> David Winsemius writes: >> >>> On May 14, 2014, at 3:04 PM, Andreas Leha wrote: >>> Hi all, how do I find out about the filenam

Re: [R] filename of current device

On May 14, 2014, at 4:43 PM, Andreas Leha wrote: > Hi David, > > David Winsemius writes: > >> On May 14, 2014, at 3:44 PM, Andreas Leha wrote: >> >>> Hi David, >>> >>> Thank you for following up on that. >>> >>> David Winsemius writes: >>> On May 14, 2014, at 3:04 PM, Andreas Leha wr

Re: [R] How to create multi variables

On May 13, 2014, at 7:22 PM, yuanzhi wrote: > Thank you for your reply. > > Yes, there is a problem according to you suggestion. > What if the value are not numerical, e.g. I want to use the variable to > store the results of linear regression. > can I use > myvec <- vector( "numeric", 10 ) If

[R] lognormal frailty in frailtypack

Hi everyone I am attempting to estimate a model with a frailty effect distributed as a lognormal variable.I am using the following code: frailtyPenal(formula, data, ..., RandDist = "LogN") I get the following error message: Error in frailtyPenal(Surv(,) ~ + , : unused argument(s) (RandDist

Re: [R] how to make R plot under Linux

Yes, install R so that X11 is enabled, then do x11() hist( c(1:10) ) and you should see your histogram. -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 5/14/14 1:26 AM, "Owen" <815551...@qq.com> wrote: >Vojtěch Zeisek open

Re: [R] How to illustrate an interaction with plotLMER.fnc

Haverinen-Shaughnessy Ulla thl.fi> writes: > > Hello, I have built a linear mixed model (with lmer). > To illustrate an interaction between > two (originally) continuous variable, I would like to > plot the effects of X1 versus Y for 1=low and 2=high > X2. I am using plotLMER.fnc but have not

Re: [R] Issues with fa() function in "psych"

Sagnik, I did some more checking and in fact you can do equamax through GPA rotation. (Gunter Nickel pointed this out in a post to R-help). I will implement this in version 1.4.6 (1.4.5 is now working its way through the various CRAN mirrors). You might like 1.4.5 in that I have added various

Re: [R] Convert to integers all entries of a table (for DESeq2)

Hi, I remember I got the same error when I used:  setAs("numeric", "NumerictoInteger", function(from) as.integer(from)) ##Using the same dataset datx1 <- read.table(text=a, header=TRUE, stringsAsFactors=FALSE, colClasses=c("character",rep("NumerictoInteger",11))) #Error in methods::as(data[[i]

[R] Character type and size using spatstats

The spatstat package has hundreds of useful functions but I'm having trouble understanding the intricate ways it does things. I've read lots of Rspatialcourse_CMIS_PDF Standard.pdf from here: http://www.csiro.au/resources/pf16h but can't find what I need to know. I'm particularly interested i

Re: [R] Character type and size using spatstats

Dear Patrick, (a) Your attachment did not come through; only attachments with extensions belonging to a limited class are passed through by the list software. Perhaps you could email your data set to me privately, (b) I have only had a quick glance at your code. A few comments: * In yo

[R] for loop using index values

Hi all I have point data along a transect and I want to divide the transect into small blocks of 10m length each. I have named the blocks as a list i.e subset[[i]]. Now the issue is I want to process only those blocks that have at least 100 data points and keep the original index values of those s

Re: [R] how to make R plot under Linux

In our server, R is already installed. But the X11 is DISABLE. The operational system of server is Ubuntu. It is only a command line system without graph interface. Do you know how to Enable X11 in R on the Ubuntu server? I have a short chat with the administrator, he told me it is technical

[R] survival estimates for covariate values

Hi all, let's say we can fit a Cox model with a numeric variable "x" as the independent variable. The we can calculate, say 10-year survival, for any given value of "x" (0 to 10 in increment of 0.1 in the example below): > fit <- coxph(Surv(time, event)~x,dat) > surv10yr<- summary(survfit(fit,ne

[R] WGCNA on heterogeneous RNA-seq

Dear list, Apologies for posting this to both Bioconductor and here. I recently read a Bioconductor post where the developer of the WGCNA suggested the use of the package for RNA-seq data analysis after implementing a variance stabilization normalization to the raw counts. I have read the tuto

Re: [R] for loop using index values

On May 14, 2014, at 9:23 PM, David Gwenzi wrote: Hi all I have point data along a transect and I want to divide the transect into small blocks of 10m length each. I have named the blocks as a list i.e subset[[i]]. Now the issue is I want to process only those blocks that have at least 10

Re: [R] how to make R plot under Linux

This is not an Ubuntu tech support list. It is possible to install the X11 client support even on headless servers, which is one of the things R on the server needs to send graphics commands to your computer. However, if your sysadmin won't do it then it is not going to happen, and we are most

Re: [R] for loop using index values

As David says it will be good to see how the structure of the list subset is. Now I'm going to guess that the i'th element of subset is a dataframe since you are using nrow(subset[[i]]). Now you're doing select<-which(nrow(subset[[i]])>=100) ## added a missing closing ) so now select holds th

Re: [R] filename of current device

You know, there is a more conventional way to handle this (at least from an R users perspective): Don't do that. The normal method of analysis in R is to perform analysis computations in separate functions than the functions that display/print results. You can easily take this one step further

Re: [R] for loop using index values

Hi David Please keep the r-help list on when you reply, I’m not your personal consultant and David Winsemius would also like see how this progress since he is also trying to help you. I’m still guessing, so is this what you want For (i in c(1,5,8)){ } Please, if you hope to get some

Re: [R] how to make R plot under Linux

On 15/05/14 17:18, Jeff Newmiller wrote: This is not an Ubuntu tech support list. It is possible to install the X11 client support even on headless servers, which is one of the things R on the server needs to send graphics commands to your computer. However, if your sysadmin won't do it then it

Re: [R] WGCNA on heterogeneous RNA-seq

Hi Pan, On Wed, May 14, 2014 at 9:14 PM, Panos Bolan wrote: > Dear list, > > Apologies for posting this to both Bioconductor and here. I recently read a > Bioconductor post where the developer of the WGCNA suggested the use of the > package for RNA-seq data analysis after implementing a variance