similar to: building phylogenetic trees

Hi Everyone, I am trying to work with a routine that is from the IMSL called BSVLS. I have the file as a .dll file. I have been trying to call the routine using the dyn.load function. I am working on a 32-bit windows 7 OS with 3 GB. For some reason i still keep getting the error message LoadLibrary %1 is not a valid Win32 application I looked at previous posting and they were all related to

Hi I am looking for a package that 1. reads in a phylogenetic tree in NEXUS format 2. given two members/nodes on the tree, can return the distance between the two using the tree. I came across the following packages on CRAN ouch, ape, apTreeShape, phylgr all of which seem to provide extensive range of functions for reading in a Nexus-format tree and performing phylogenetic analyses, tree

Hi all, I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5

>From time to time people request symbolic computations beyond what D() and deriv() etc can provide. A brief look at the internet shows that there are many more or less developed computer algebra packages freely available. Therefore, I wondered if it would be an idea to try to 'integrate' one of these packages in R, which I guess can be done in more or less elegant ways... I do not know

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

I have a matrix of similarity scores that I want to convert into a matrix of dissimilarity scores so that I can apply some clustering methods to the data. That is, high values in my matrix signify similarity and low values (zero being the lowest) signify no similarity. What functions/options in R or its packages are available for making this kind of transformation of a matrix?

Can you recommend an R library that will help me create a diagram of a phylogenetic tree on which specific images are placed at appropriate nodes of the tree? For example, I have specific image files associated with each member of the phylogenetic tree, and I would like to automate the display of the image next to the correct node of the tree. I can provide an image file with an example.

Hello, Is it possible to include information about phylogenetic relatedness among species (when species are replicates for each study within a meta-analysis) in a meta-anlaysis in the metafor package? Alternatively, I wonder if the method f Lajeunesse 2009 American Naturalist has been adopted in R in any fashion? Thanks, Scott Chamberlain [[alternative HTML version deleted]]

Hello, I am trying to carry out a phylogenetic autoregression to test whether my data show a phylogenetic signal, but I keep calculating bizzare R-squared values. My script is: > library(ape) > x <-

Take a look at lmekin() in the coxme package. The motivating data set for my development of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families. The random effect is an intercept per subject with sigma^2 K as its variance where K is the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice, etc). lmekin is a linear models front

Dear all, I would like to ask you the following: I have data about different manuscripts, together with data about the presence/absence of copying errors, in the days when manuscript were really manuscripts. I would ideally like to use the data to draw a phylogenetic tree, so that I can infer which ms was copied from which. The error presence/absence is coded in binary format. The plan is to use

Hello R users, Can any one please help me to find a way to build phylogenetic tree by R program from any distance matrix. Suppose I have a data like : MATRIX [1] '1' 0.0 [2] '2' 0.071 0.0 [3] '3' 0.036 0.286 0.0 [4] '4' 0.429 0.75 0.714 0.0 [5] '5' 0.679 0.179 0.214 0.536 0.0 [6] '6' 0.893 0.929 0.964 0.464 0.357 0.0 [7]

Hi all, I want to calculate distances between phylogenetic trees. I found functions for symmetric difference (e.g. in ape and in some other packages). In addition to this I also want to calculate quartets and nearest neighbor interchange distances; are there any functions for this? My apologies if they exist and I overlooked. best regards

Hello, I am trying to import a phylogenetic tree from Mesquite into R. When I use the read.nexus command I get the following message: Warning message: In matrix(x, ncol = 2, byrow = TRUE) : data length [589] is not a sub-multiple or multiple of the number of rows [295] A phylo object is created but I am unable to plot it (when I try R freezes) and I can tell by looking at the tip labels that

I'm trying to select a model under PCA using independent contrasts. Since PICs need to be forced through the origin I've been using lmorigin for the original regression, but it doesn't appear that stepAIC recognizes it. I keep receiving an error message - "Error in na.fail.default(list(Phenology = c(NA_integer_, NA_integer_, : missing values in object" I'm having

Hi, I'm trying to build a mixed-effects model in which I'd like to include either a distance matrix or a phylogenetic tree as a random effect. The troubles I've had are that: 1. Function lmer() in package lme4 only accepts a data frame column as a random factor and not a distance matrix. 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and ultrametric phylogenetic

Hi, Using Ape, I have constructed an object of class "phylo", using the method 'nj' (lets call the object 'tree_ja'). I also have a given subset of 'tree_ja' in a vector (lets call the vector 'subspecies'). What I want to do, is construct a nj tree - plot(tree_ja) - but have the species in vector 'subspecies' shown as red at the tips of the

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH available. The most important change is that the

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH available. The most important change is that the

dear group members, I am looking for a function that assess the stability of cluster. The result of hclust function is an hclust object which can be plot as a dendrogram. However to have confidence in the tree topology usualy bootstap is applied. I understand that I can apply bootstarp on the original data and then run hclust(dist() ) as much as I resampled but how to comapre the topologies the I