similar to: peering inside functions in a package?

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch

Hi, I have been using the function lme() of the package nlme to model grouped data that is auto-correlated in time and in space (the data was collected on different days via a moving monitor). I am aware that I can use the correlation classes corCAR1 and corExp (among other options) to model the temporal and spatial components of the auto-correlation. However, as far as I can tell, I can only

dear list, I am wondering if one can find examples and/or more detailed descriptions of modifications needed when going beyond standard corStruct classes (i.e. those already provided for use in lme/nlme)? When I looked at pages 238-239 of Pinheiro/Bates (2000): Mixed-effects models in S and S-plus, I found that I would need a bit more explicit guidance what to do for implementing a new

Dear all, I am trying to define my own corStruct which is different from the classical one available in nlme. The structure of this correlation is given below. I am wondering to know how to continue with this structure by using specific functions (corMatrix, getCovariate, Initialize,...) in order to get a structure like corAR1, corSymm which will be working for my data. Thanks in advance.

Full_Name: Benjamin Tyner Version: 2.6.0 RC 2007-10-01 r43043 OS: WinXP Submission from: (NULL) (171.161.224.10) platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status RC major

Let me modify my question about user-defined covariance structures for LME models: Can somebody tell me how I can see the code for the definition of the correlation structures that come with the NLME package. Specifically I like to see the code for the functions coef, corMatrix, and intialize for any of the pre-defined correlation structures, and use this as a template to define a new correlation

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

Dear list, I am trying to plot a radial dendrogram using the ape package, which requires my data to be of class 'phylo'. Currently I have my dendrogram stored as an object of class 'dendrogram' which was produced from an outside bit of C code, but was made into an object of class 'igraph.eigenc' and converted to a dendrogram using 'as.dendrogram()' from the igraph

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

I have spatial data on a sphere (the Earth) for which I would like to run an gls model assuming that the errors are autcorrelated, i.e. including a corSpatial correlation in the model specification. In this case the distance metric should be calculated on the sphere, therefore metric = "euclidean" in (for example) corSpher would be incorrect. I would be grateful for help on how to

Hello. I'd like to compute the associate vector of distances between leaves in a binary non-rooted tree. The definition of a distance between two leaves in a binary non-rooted tree is the number of edges in the path joining the two leaves. I've tried the ape package but I'm unable to find this vector. For example, using rtree(5,rooted=F) I've obtained the following tree: $edge

This is an OpenPGP/MIME signed message (RFC 2440 and 3156) --------------enig308510A16A445880F353C5C9 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable to trigger the bug: plot(0:1,0:1) text(0.5,0.5,"abc",srt=3D-1e-9) this doesn't happen for positive, small srt, or for negative srt with magnitude greater than about 1e-8 (the example in

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

Hi, I'm doing hierarchical clustering, and want to export my dendrogram to a tree-viewing/editing software. I can do this by converting the data to Newick format (hc2Newick in ctc package), but I can't get branch lengths to show in the resulting phylogram. I figured it might help to convert my hclust object into a phylo object (as.phylo in ape package), but the following lines give me

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

Having a problem running the ace command in ape. After reading my table into R and then putting the names of the rows in the table in same order as the tree I can't get ace to run and get the message Erreur dans as.matrix(x) : dims [produit 25] ne correspond pas ? la longueur de l'objet [0] This is the command I am using and each of the vectors used in the snalysis.

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"

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,

Hi, I was recently splitting some massive phylo class objects with extract.clade() and noticed what appears to be a bug in how tip labels are copied from the full tree to the pruned tree. This possible bug was also mentioned here: http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html An example: library(ape) set.seed(5) x <- matrix(rnorm(100), ncol=10) p <-

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