similar to: phangorn and calculation of a rate matrix

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

Dear subscribers of R-devel I am experiencing that R crashes (further details are given below) in some complex matrix calculations when EISPACK=TRUE has been specified in eigen(). I discovered the behaviour some months ago just after the release of R-2.2.0, and it has been lying on my desk since. I apologise for not having nailed the problem down to a simple function call, but I thought I

Hi all, I've read the emails of Dan, Deepayan and Sundar about adding error bars to the lattice plots ( https://stat.ethz.ch/pipermail/r-help/2006-October/114883.html), but I still have the problem when I want to adding error bars to barchart. I tried both the solution of Deepayan and Sundar but without luck. Here is my code (I changed prepanel.ci and panel.ci a little to plot bars

Hi, I have a CSV file with various biological reactions. Subscripts, superscripts, and italics are encoded in carats, and I was wondering if R can actually recognize those and print actual superscripts, etc. Here's an example: <i>S</i>-adenosyl-L-methionine + rRNA = <i>S</i>-adenosyl-L-homocysteine + rRNA containing

Hi, I've written a function which I load with a source command. The function requires a certain library, phangorn, to work. I would like the function to check if phangorn is loaded as a library before running. For some reason, just putting require(phangorn) into the sourced function doesn't do anything. This must be simple, but I can't figure it out! Any help appreciated...

Hello, I was simply doing a graph, but an error repeatdly occurs. Any idea why? (this only happens in the latest R version, I am a windows user). Thank you, Marta library(Hmisc) > example(xYplot) xYplot> d <- expand.grid(x = seq(0, 2 * pi, length = 150), p = 1:3, shift = c(0, pi)) xYplot> xYplot(sin(x + shift)^p ~ x | shift, groups = p, data = d, type = "l")

Hello All! I'm a new R user, with no much experience. I have a R script (downloaded from internet) which has user interaction using "readline()" function. So as I have to run it repeatdly (with some different options) I was planning to do it on a BATCH mode. Is there any way to answer the "readline()" questions from a batch file? How do I do that? I'm using R under

Hi all, I am a phylogenetic student, I'm running SH test to examine free (tree1) and constrained (tree2) trees using R phangorn package. The outputs are like the following and i'm confused how should i interpret them!!!   Trees      ln L           Diff ln L    p-value [1,]     1 -1422.921   0.00000  0.4952 [2,]     2 -1457.282  34.36085  0.0201 Why it gives us two p values? Would you

Dear colleagues, dear members of the R Core Team, This was an issue raised by Prof. Brian Ripley and sent privately to all developers of CRAN packages that suggest Bioconductor packages (see original message below). As mentioned in my message enclosed below, it was easy for me to fix the error in examples (new version not submitted to CRAN yet), but it might turn into a major effort for the

Thanks a lot, I?aki, this is a perfect solution! I already implemented it and it works great. I'll wait for 2 more days before I submit the revised package to CRAN - in order to give others to comment on it. Best regards, Ulrich On 01/22/2018 10:16 AM, I?aki ?car wrote: > Re-sending, since I forgot to include the list, sorry. I'm including > r-package-devel too this time, as it

Re-sending, since I forgot to include the list, sorry. I'm including r-package-devel too this time, as it seems more appropriate for this list. El 22 ene. 2018 10:11, "I?aki ?car" <i.ucar86 at gmail.com> escribi?: > > > El 22 ene. 2018 8:12, "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at> > escribi?: > > Dear colleagues, dear members of

On 01/22/2018 08:40 AM, Ulrich Bodenhofer wrote: > Thanks a lot, I?aki, this is a perfect solution! I already implemented > it and it works great. I'll wait for 2 more days before I submit the > revised package to CRAN - in order to give others to comment on it. It's very easy for 'pictures of code' (unevaluated code chunks in vignettes) to drift from the actual

When I try to go to http://cran.us.r-project.org I get sent to a location called "domains 4 sale" or something of that ilk, indicating that some "URL scavenger" has flagged it as expired. Has something happened, or is it just wishful thinking on some scavenger's part that the URL is no longer pointing to the US CRAN mirror? Try this link:

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

Dear R experts, recently I started developing a Rcpp package "OpenMPTest". Within that package I want to use OpenMP, as in the following code example: // header file #include <omp.h> using namespace Rcpp ; RcppExport SEXP testOpenMP( SEXP nThreads ) ; // cpp file SEXP testOpenMP( SEXP nThreads ) { BEGIN_RCPP NumericVector numberThreads = NumericVector( nThreads );

CRAN (and crantastic) updates this week New packages ------------ * EffectStars (1.0) Maintainer: Unknown Author(s): Gunther Schauberger License: GPL-2 http://crantastic.org/packages/EffectStars The package provides functions to visualize regression models with categorical response. The effects of the covariates are plotted with star plots in order to allow for an optical

CRAN (and crantastic) updates this week New packages ------------ * allan (1.0) Alan Lee http://crantastic.org/packages/allan Automates Large Linear Analysis Model Fitting * andrews (1.0) Jaroslav Myslivec http://crantastic.org/packages/andrews Andrews curves for visualization of multidimensional data * anesrake (0.3) Josh Pasek http://crantastic.org/packages/anesrake This

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Full_Name: Tim Middelkoop Version: 0.64.0 OS: IRIX 6.3 on O2 Submission from: (NULL) (128.119.88.192) Various IRIX complile issues src/nmath/pnt.c IRIX cc does not like double negatives Makeconf,config.site,etc/Makeconf f77 pic hack, should change Makeconf.in or other... change -PIC with -KPIC enjoy, tim... === diff -ru orig/R-0.64.0/src/nmath/pnt.c R-0.64.0/src/nmath/pnt.c ---