Re: [R] Keep on getting message errors when trying to install and load packages 2

2017-09-20 Thread David Winsemius
> On Sep 20, 2017, at 7:26 AM, Paul Bernal wrote: > > Dear all, > > Is it normal for R to store installed packages in paths like the following? > > C:\Users\PaulBernal\AppData\Local\Temp\RtmpgXA5VS\downloaded_packages Yes. Packages are first built or unpacked in a temporary directory and then

Re: [R] Network meta-analysis help

2017-09-20 Thread Bert Gunter
No "clear guidelines" ??!! A google search on "network meta-analysis" produced a whole bunch of hits, including this: https://www.ncbi.nlm.nih.gov/pubmed/23674332 While "clear" is undefined (what is clear to you may be opaque to me), it is hard for me to believe that none of the search results s

[R] i keep getting a check data: there are more than 3 classes for f2 error and I am not sure how to fix it i am using onemap

2017-09-20 Thread Kulvinder Gill
SNP <- read.mapmaker(dir = "~/desktop", "1674_SNP.raw”) --please do not edit the information below-- R Version: platform = x86_64-apple-darwin15.6.0 arch = x86_64 os = darwin15.6.0 system = x86_64, darwin15.6.0 status = major = 3 minor = 4.1 year = 2017 month = 06 day = 30 svn rev = 72865 langua

Re: [R] Network meta-analysis help

2017-09-20 Thread Jim Lemon
Hi Sherief, First thing is your data set did not make it If it is not too large, perhaps you could send the output of "dput" in the body of the message or send a CSV file with the extension changed to ".txt". If the data set is very large, perhaps you could send a subset as described above. Jim

Re: [R] arguments imply differing number of rows

2017-09-20 Thread Shivi Bhatia
Thank you Bob, this is what i was looking for. Really appreciate. Regards, Shivi On Wed, Sep 20, 2017 at 8:41 PM, Bob O'Hara wrote: > 4000:6000 gives you 4000, 4001, ..., 6000. I suspect you want > population= c(seq(4000, 6000, length=5), seq(3500, 4300, length=5), > seq(3000, 3200, length=5))

[R] phylo.pca

2017-09-20 Thread Sergio Ferreira Cardoso
Dear all, I'm trying to use phylo.pca function from phytools for the first time. I'm using an ultrametric tree with 167 tips and all branch lengths transformed to 1. I lunched the pPCA like this: pPCA<-phyl.pca(tree,data,method = "lambda") For some reason it takes for ever and never reach

Re: [R] How to use depmix for HMM with intial parameters

2017-09-20 Thread Ismail SEZEN
> On 20 Sep 2017, at 11:14, niharika singhal > wrote: > > Hello, > > I have initial parameters for HMM model and I want to use depmixS4 package. > The parameters are in the form > > intial_prob_matrix=matrix(c(0.07614213, 0.45177665, 0.47208122), nrow=1, > ncol=3, byrow = TRUE) > > transitio

Re: [R] arguments imply differing number of rows

2017-09-20 Thread ruipbarradas
Hello, Just count: city is 3*5 == 15, population is length(4000:6000) + length(3500:4300) + length(3000:3200) == 2001 + 801 + 201 == 3003 Hope this helps, Rui Barradas Citando Shivi Bhatia : Hi Team, I using the syntax as: data.df<- data.frame( city= c(rep(c("Delhi",

Re: [R] arguments imply differing number of rows

2017-09-20 Thread Bert Gunter
What do you think 4000:6000 means? Perhaps you need to spend time with an R tutorial or two and stop searching google. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom C

Re: [R] arguments imply differing number of rows

2017-09-20 Thread Bob O'Hara
4000:6000 gives you 4000, 4001, ..., 6000. I suspect you want population= c(seq(4000, 6000, length=5), seq(3500, 4300, length=5), seq(3000, 3200, length=5)) Bob On 20 September 2017 at 17:07, Shivi Bhatia wrote: > Hi Team, > > I using the syntax as: > > data.df<- data.frame( > city= c(rep(c("D

[R] arguments imply differing number of rows

2017-09-20 Thread Shivi Bhatia
Hi Team, I using the syntax as: data.df<- data.frame( city= c(rep(c("Delhi", "Bangalore","Chandigarh"),each=5)), population= c(4000:6000,3500:4300,3000:3200) ) But i am getting the error as arguments imply differing number of rows: 15, 3003. Tried searching google but could not understand &

[R] Keep on getting message errors when trying to install and load packages 2

2017-09-20 Thread Paul Bernal
Dear all, Is it normal for R to store installed packages in paths like the following? C:\Users\PaulBernal\AppData\Local\Temp\RtmpgXA5VS\downloaded_packages Regards, Paul [[alternative HTML version deleted]] __ R-help@r-project.org mailing li

[R] Keep on getting message errors when trying to install and load packages

2017-09-20 Thread Paul Bernal
Dear R friends, I am currently using Windows 8, 64-bit operating system, x64-based processor. I have installed R version 3.4.1 "Single Candle". Also, I have several packages installed in this path: C:\Users\PaulBernal\Documents\R\win-library\3.4 Plus some other packages installed in this other

Re: [R] pheatmap: incomplete figure

2017-09-20 Thread Fix Ace via R-help
Thank you so much for the reply! I thought the file would automatically adjust accordingly. But I just checked and found pheatmap does has width as parameter! Ace On Monday, September 18, 2017 3:00 PM, David Winsemius wrote: > On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help wrote: >

Re: [R] Install the Package "ISwR"

2017-09-20 Thread AbouEl-Makarim Aboueissa
I simply answered Yes, Yes, Yes. It works now. thank you very much abou On Wed, Sep 20, 2017 at 6:09 AM, Eric Berger wrote: > What if you answer 'Yes' ? > > On Wed, Sep 20, 2017 at 1:03 PM, AbouEl-Makarim Aboueissa < > abouelmakarim1...@gmail.com> wrote: > >> Dear All: good morning >> >> I am

Re: [R] Install the Package "ISwR"

2017-09-20 Thread Eric Berger
What if you answer 'Yes' ? On Wed, Sep 20, 2017 at 1:03 PM, AbouEl-Makarim Aboueissa < abouelmakarim1...@gmail.com> wrote: > Dear All: good morning > > I am trying to install the "" package, but I am getting this error message. > > > *> utils:::menuInstallPkgs()* > *Warning in install.packages(NU

[R] Install the Package "ISwR"

2017-09-20 Thread AbouEl-Makarim Aboueissa
Dear All: good morning I am trying to install the "" package, but I am getting this error message. *> utils:::menuInstallPkgs()* *Warning in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :* * 'lib = "C:/Program Files/R/R-3.4.1/library"' is not writable* *Error in insta

Re: [R] Convert data into zoo object using Performance analytics package

2017-09-20 Thread PIKAL Petr
Hi Gabor's code works as expeceted without error. What is "u" in your case? Cheers Petr > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Upananda > Pani > Sent: Wednesday, September 20, 2017 11:06 AM > To: Gabor Grothendieck > Cc: r-help > Subject:

Re: [R] Convert data into zoo object using Performance analytics package

2017-09-20 Thread Upananda Pani
Dear Sir, Thanks for your mail and help. I got this error while trying to run your code. sbux1.z <- read.csv.zoo(u, FUN = as.yearmon, format = fmt) Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection Thanks and Regards,

[R] [R-pkgs] Update to R package envDocument

2017-09-20 Thread Jackson (Genomics), Donald
An updated version of my envDocument package is now available on CRAN at https://CRAN.R-project.org/package=envDocument with code at https://github.com/dgJacks0n/envDocument/tree/V_2.4.0 The main function from this package, env_doc(), provides a detailed, automated report on the environment in

[R] How to use depmix for HMM with intial parameters

2017-09-20 Thread niharika singhal
Hello, I have initial parameters for HMM model and I want to use depmixS4 package. The parameters are in the form intial_prob_matrix=matrix(c(0.07614213, 0.45177665, 0.47208122), nrow=1, ncol=3, byrow = TRUE) transition_matrix=matrix(c(0.4667,0.4667,0.0667, 0.067