similar to: phylo.pca

Dear all, I'm testing the effect of species and sex in my sample by using the principal component scores of a PCA analysis. I have 30 PCs and I tried to see if there is any significant difference from males to females, given that there is a significant effect of phylogeny (factor with several species). I didi it like this: Y<-PCA$pc.scores[,1:30] fit <- manova(Y ~ sp*sex)

Dear list users, I was wondering if there is any way to know, for an open graphical peripheric, the instruction that was used to call it. For example, if I create a plot using plot(runif(10)) is there any way to have the call returned to me? That would be especially usefull to know it there are any log axes, for example thanks t --------------------------------------- Timothée POISOT -

Hi, I am trying a two way anova with unequal sample sizes but results are not as expected: I take the example from Applied Linear Statistical Models (Neter et al. pp889-897, 1996) growth rate gender bone development 1.4 1 1 2.4 1 1 2.2 1 1 2.4 1 2 2.1 2 1 1.7 2 1 2.5 2 2 1.8 2 2 2 2 2 0.7 3 1 1.1 3 1 0.5 3 2 0.9 3 2 1.3 3 2 expected results are

>>>>> Francois Rousset <francois.rousset at umontpellier.fr> >>>>> on Tue, 3 Apr 2018 16:38:42 +0200 writes: > Dear list members, > If I install with R-devel r74500 on Windows (sessionInfo below) the > attached 'bugdemo' package with the single function > foo <- function() { > ? named <-

I have data set with binary responses. I would like to conduct polychoric principal component analysis (pPCA). I know there are several packages used in PCA but I could not find one that directly estimate pPCA and graph the individuals and variables maps. I will appreciate any help that expand these reproducible scripts. #How to conduct polychoric principal component analysis pPCA using #either

Dear R users, I am currently learning how to work with a new shared computer (a Mac pro) in our lab, that is dedicated to execute R code for large simulations (over a few days). We have a VNC option to remote control the computer, with a shared used session, but this is not really needed in most of the cases. I would like to do some ssh access. This is pretty straigthforward, and I am able to

I would like to see an example of a data matrix for cclust and how to import it to cclust. In fact, i don't know how to give my imput for cclust program! i test this file 1 0.23 1.52 2 0.52 1.25 3 0.13 1.89 4 0.78 1.11 i do >library(cclust) >x<-scan("test.matrice.phyl") >cclust(x,2,method="kmeans") i have this error message: Error in sample(length(x),

Hi, I'm interested in using pbtree (package phytools) to simulate a phylogeny, but would first like to understand how the simulation works (i.e. when does a split occur and how is the split chosen?). Can anyone point me to the model that is used? Thank you! [[alternative HTML version deleted]]

Dear list members, If I install with R-devel r74500 on Windows (sessionInfo below) the attached 'bugdemo' package with the single function foo <- function() { ? named <- c("bar"=TRUE) ? print(named) ? return(named) } then run > bugdemo::foo() [1] TRUE [1] TRUE The "bar" name is lost. It is not lost when I define foo in the R session instead of using

I'm not sure if this is the correct place to email for this kind of thing, but I couldn't find any other contact info. Also, I am new to llvm, so please try to be understanding. I keep getting an error when I try to compile a simple Hello World program (as a test)(error included below). The error is: Clang: warning: unable to find a Visual Studio installation; try running Clang from a

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo

--------------------- Doctoral Symposium of CISTI'2016 ------------------------- CISTI'2016 - 11th Iberian Conference on Information Systems and Technologies 15 - 18 june, 2016, Gran Canaria Island, Span http://www.aisti.eu/cisti2016/index.php/en/doctoral-symposium -------------------------------------------------------------------------------- The purpose of

--------------------- Doctoral Symposium of CISTI'2016 ------------------------- CISTI'2016 - 11th Iberian Conference on Information Systems and Technologies 15 - 18 june, 2016, Gran Canaria Island, Span http://www.aisti.eu/cisti2016/index.php/en/doctoral-symposium -------------------------------------------------------------------------------- The purpose of

================================= DOCTORAL SYMPOSIUM ==================================== CISTI'2014 - 9th Iberian Conference on Information Systems and Technologies Barcelona, Spain, June 18 - 21, 2014 http://www.aisti.eu/cisti2014/index.php/en/doctoral-symposium

================================= DOCTORAL SYMPOSIUM ==================================== CISTI'2014 - 9th Iberian Conference on Information Systems and Technologies Barcelona, Spain, June 18 - 21, 2014 http://www.aisti.eu/cisti2014/index.php/en/doctoral-symposium

Dear R users and Dear authors of the distr package and sequels I am trying to use the (very nice) package distrMod as I want to implement maximum likelihood (ML) fit of some univariate data for which I have derived a theoretical continuous density (pdf). As it is a parametric density, I guess that I should implement myself a new distribution of class AbscontDistributions (as stated in the pdf

Hello, The following code does'nt work for me. The last command reports an error. I have created a consensus tree using the consensus comand from phylo but cannot manipulate the phylo object afterwards to create a dendogram , by transforming the phylo object into a hclust object and then into a dendogram ?? Thanks for any help library(ade4) library(cluster) library(stats) library(ape)

Hi, I'm very much enjoying using the ape package to produce phylogenetic trees with colored branches (using edge.color). Is it also possible to specify that some branches should be drawn as dotted lines? That would be really useful. I've tried messing around with edge.width, but that doesn't seem to help me get dotted lines. thanks, Janet Young

Dear All, I get some problems using the 'phylo' and dissimilarity functions in R. I converted an output from 'hclust' into an order of phylo so as to be able to use the 'consensus' function on it. Each time I submit the consensus codes, my computer hangs. When I tried to see what the contents of the object converted into order phylo is, I get the message

Hello all, I'm now working with hclust objects and was hoping to perform some basic editing on them like: - Joining = the merging of two hclust objects (so they will share one root) - Splicing = So to cut/extract a branch out of an hclust object - that by itself will be an hclust object. I noticed I could extract one element of an hclust object by turning it into a dendrogram,