similar to: R advice

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

If I have 100 objekts in a folder and I prefer not to load them manually I wonder how I do this in R if using a for-loop. I was thinking initially to do something like this: infiles <- dir(pattern=".RData") for(i in length(infiles)) { load(infiles[i]) paste("kalle", i, sep="") <- saveLoadReference } But the line

Hi R users, Is there a simple function that can add a folder into current R search path? For example, suppose my current work directory is "D:\work", but my input files are stored in folder "C:\inFiles\", I know I can change work directory or add "C:\inFiles\" before files name when I scan them, but I don't want to do that. I want to find a function that can

I have a data set like this in one .txt file (cols separated by !): APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! it contains over 14 000 000 records. Now

Hello, I'm in need of running a PVA and want to load {popbio}. However, I can't find it. I can't see where or how to load it. I have added repositories and changed the CRAN mirror site. I see {polynom} and {popgen} but no {popbio} between. What am I doing wrong? Thanks, Michelle [[alternative HTML version deleted]]

Dear all, It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'. Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj'

I thought I would post this in case it might be of any use to anyone. Not anything special but it does work. Keep in mind you need sox and wmix. Here is some relevant exerpts of my extensions.conf using John Todds macro. [globals] CALLFILENAME=foo FOO=foo CALLERIDNUM=foo [default] exten => 287,1,Macro(dial,SIP/agent20002|20) exten => 287,2,Voicemail(u287) exten =>

Hello, I've just downloaded and installed the RAqua onto my Mac and I have R up and running fine. Now I'm trying to get 'ape' downloaded and installed and having quite the difficulty. I am following the directions specified under 'Installing packages' where packages can be downloaded and installed from within R. I get the following error messages: 1: argument

Dear Sir or Madam, I am very new to R, and I am trying to install seqinr-package. In the manual I read that I need to install ape-package first, and I failed to do it. I had the following error messges: /usr/bin/ld: cannot find -lgfortran collect2: ld returned 1 exit status make: *** [ape.so] ?????? 1 ERROR: compilation failed for package 'ape' ** Removing

Dear all, I don't understand the following behaviour: Running compar.gee (in library ape ) with and without the option 'data', it give me different results Example: .... Start R .... > load("eiber.RData") > ls() [1] "gee.na" "mydata" "mytree" > library(ape) > # runnig with the option data= mydata > compar.gee(alt ~ R,

objcopy needs "output-target" and "binary-architecture" parameters which makes it necessary to keep a list of known architectures. The bin2s.pl script generates input for the GNU assembler which should produce an object file that is equivalent to that produced by objcopy. I have successfully tested the change on an amd64 Debian/unstable system. --- helper/Makefile.am |

Folks I'm trying to use xfs_quota to keep track of disk space usage for my users. The documentation states that I should specify "uquota" as an option on the mount data in /etc/fstab. Yet, I cannot find the entry in fstab that corresponds to the Logical Volume that ends up being mounted on /home1. The system in question was installed on a single disk system. Later, after

I am not sure whether this would work or if there are other limitations that would block this very simplistic porting strategy to work. Since it looks so easy on paper, I expect it to be more complicated otherwise it would probably already have been done. According to the LLVM FAQ the important dependencies for LLVM are a unix-type shell and sed [1], but those dependencies are provided by APE

Hello All, I have a toy dataframe like this. It has 8 columns separated by tab. Name SampleID Al1 Al2 X Y R Th rs191191 A1 A B 0.999 0.09 0.78 0.090 abc928291 A1 B J 0.3838 0.3839 0.028 0.888 abcnab A1 H K 0.3939 0.939 0.3939 0.77 rx82922 B1 J K 0.3838 0.393

Dear all, I was testing the wonderful package APE. However upon testing a particular Newick's format tree - which I think to be a non-binary tree - it yields different result as expected. > library(ape) > tree.hiv <- read.tree(text="(rat,mouse,(human,chimp));") > is.binary.tree(tree.hiv) [1] TRUE Was that a bug in APE package? - Gundala Viswanath Jakarta - Indonesia

Hello all, I was checking the newest update of my library before submitting it to CRAN, using R 2.15.0 and Rtools for Windows 215 using Rcmd in the Command Prompt, on my x64 Windows7 laptop. I recently heard that for checking packages for CRAN submission one should use the option --as-cran; previously I was submitting packages, so I was trying that for the first time. The check proceeds fine

I have the following script (also attached): #!/usr/bin/Rscript spec=matrix(c( 'verbose', 'v', 1, "integer", 'help' , 'h', 0, "logical" ),ncol=4, byrow=TRUE) spec.dim=dim(spec) spec.opt.long=spec[,1] spec.opt.short=spec[,2] spec.opt.l <- spec.dim[1] infile <- "test.dat" args=commandArgs(TRUE); l=length(args) self =

Here it is: read.inputs<-function(infile) { for (counter in 1:length(input.list)) { seek(infile,where=0,origin='start') newline<-readLines(infile,n=1) while(length(newline)>0) { if(!is.na(grep(as.character(input.list[[counter]][1]),newline)[1])) { break } newline<-readLines(infile,n=1) } if (length(newline)>0)

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hi all, Please a moment to look my source code, this is very similar to example of the documentation. I added FIXED_POINT flag. My source code compile and build but not decode correctly (the error may be in the while). I work with eVC 4.0 and pocket pc 2003. Someone know what is the error? Thanks. Rodrigo. #include "speex.h" #define FRAME_SIZE 160 void CPlayerDlg::OnButton3() {