search for: phangorn

...ot;,"d","e","g","h","i","k","l","n","q","r" instead of the conventional nucleotide codes). My intention is to calculate the ratematrix (which is a 12x12 matrix) for this special aligment with ape and phangorn, however I've repeatdly fail to do it. The aligment is in a phyDat object containing 30 sequences and 12 states (by using "user-defined" character states consisting on the 12 letters indicated above). I follow the steps described in the phangorn-specials vignette but the ratematrix (u...

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 nucl...

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... Cheers! Nick -- ==...

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 likelih...

...gt;> >> ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT NMF PlackettLuce >> ProFit ProFound RNAseqNet SIBERG antaresRead apcluster cherry clValid coloc >> colorhcplot entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin loon >> nscancor ordinalgmifs penalized phangorn propr shiftR switchr tcgsaseq >> tileHMM tmod >> >> then give ERRORs or (new) WARNINGs on their checks. Please correct ASAP, >> and by Feb 20 to safely retain the package on CRAN. >> >> > ______________________________________________ > R-devel at r-projec...

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 please help me with that? Regards,...

...se GenCAT GiANT >> ??????????? NMF PlackettLuce ProFit ProFound RNAseqNet SIBERG >> ??????????? antaresRead apcluster cherry clValid coloc colorhcplot >> ??????????? entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin >> ??????????? loon nscancor ordinalgmifs penalized phangorn propr shiftR >> ??????????? switchr tcgsaseq tileHMM tmod >> >> ??????????? then give ERRORs or (new) WARNINGs on their checks. >> ??????????? Please correct ASAP, and by Feb 20 to safely retain the >> ??????????? package on CRAN. >> >> >> ??????? ___...

...ting), packages > > ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT NMF > PlackettLuce ProFit ProFound RNAseqNet SIBERG antaresRead apcluster > cherry clValid coloc colorhcplot entropart filematrix fuzzyforest > fuzzyjoin glycanr hexbin loon nscancor ordinalgmifs penalized phangorn > propr shiftR switchr tcgsaseq tileHMM tmod > > then give ERRORs or (new) WARNINGs on their checks.? Please correct > ASAP, and by Feb 20 to safely retain the package on CRAN. >

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

...CorShrink GRANBase GenCAT GiANT > NMF PlackettLuce ProFit ProFound RNAseqNet SIBERG > antaresRead apcluster cherry clValid coloc colorhcplot > entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin > loon nscancor ordinalgmifs penalized phangorn propr shiftR > switchr tcgsaseq tileHMM tmod > > then give ERRORs or (new) WARNINGs on their checks.? > Please correct ASAP, and by Feb 20 to safely retain the > package on CRAN. > > > __________________________________...

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

...amr (1.47), panel (1.0.7), paran (1.4.3), parser (0.0-10), partDSA (0.7.1), partitions (1.9-8), party (0.9-9997), PBSmapping (2.61.9), PBSmodelling (2.61.210), pcalg (1.0-2), pcaPP (1.8-1), pedigree (1.3.1), pegas (0.3-2), penalized (0.9-31), pendensity (0.2.3), pgfSweave (1.0.5), pgirmess (1.4.6), phangorn (1.0-2), phyclust (0.1-7), picante (1.1-1), playwith (0.9-52), plink (1.2-3), plm (1.2-4), plotrix (2.9-5), plsdof (0.2-1), plspm (0.1-6), plyr (1.0.3), pmml (1.2.22), poLCA (1.2), polycor (0.7-8), pomp (0.31-1), potts (0.5), prefmod (0.8-21), prim (1.0.8), ProbForecastGOP (1.3.2), profdpm (2.0), p...