similar to: working with taxonomic trees: sampling

I've a data frame with this structure: 'data.frame': 1987 obs. of 11 variables: $ site : Factor w/ 24 levels "B(W)","BC-1",..: 1 1 2 2 2 1 1 1 ... $ sampdate : Date, format: "2000-07-18" "2000-07-18" ... $ tclass : Factor w/ 8 levels "Annelida","Arachnida",..: 1 5 5 5 5 ... $ torder : Factor

Doug, I thought perhaps that you might be interested in the comparison of lme to the results for the same models fitted by Richard Jones' carma (I just wrote the R interface to his Fortran code). The code to run the example from the lme help and for the equivalent with carma is in the file below. The two main differences in results are 1. the random coefficients covariance matrix is quite

Hi all, I would love to plot my data with R. I have abundance and frequency of fungal taxonomic data that should be plotted in the same graph. In Microsoft Excel is that possible but the graphic result is, as always, very poor. Is there a function that may let me plot these data in R? I have a matrix made of two columns, on is the relative abundance and the other is the relative frequency for

Hello, I have a problem to treat my data. I seek the orders being able to treat under sampling: I have X samples divided into 10. How to take, in a random way, under sample from the 1st sample, and in addition, one under sample of the 2nd sample, and so on to X to calculate the average taxonomic richness of the selection. Then I would like to know how to renew the experiment by taking

Hi there, I am just starting in R and this might be a very basic question. I applied one on the examples of pairs() to my own data. The examples shows scatter plots on one side of the matrix and the correlation coefficients on the other which works well. I then modified it slightly because I want different colors in the plots. Now i am getting the error of unused arguments, because the color

Dear all, I run a loop wrapped in try(), and for each of the rows where "try-error" is true I want to fill that row with NA (at the moment it is omitted). So I would expect to get a dataframe with 1000 rows some of which would be empty, but instead I get a dataframe with 995 rows. In this case missing 5 rows were omitted. Any suggestions? Thanks, Olga ----------------

Dear all, I'd like to introduce a new R package called *phylogram,* for working with evolutionary trees as deeply-nested lists known as "dendrogram" objects. The package provides functions for importing and exporting phylogenetic trees in the Newick parenthetic text format, as well as several functions for command-line tree manipulation. With an emphasis on speed and computational

The new package RFLPtools is available on CRAN. RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further

The new package RFLPtools is available on CRAN. RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further

Hi List, I am looking for a variable selection procedure with a forward-backward selection method. Firstly, it is meant to work with the cophenetic correlation coefficient (CPCC) and intended to find the variable combination with the highest cophenetic correlation. Secondly, it is aimed at Gower metric with wards method (though this could be easily extended) aimed at categorical data. What I

CRAN (and crantastic) updates this week New packages ------------ * DCGL (1.0) Bao-Hong Liu http://crantastic.org/packages/DCGL Functions for basic differential coexpression analyses: gene filtering, link filtering, DCG (Differentially-Coexpressed Gene) identification and DCL (Differentially-Coexpressed Links) identification.Two algorithms,named DCP and DCe, are provided for

CRAN (and crantastic) updates this week New packages ------------ * bisectr (0.0.2) Maintainer: Winston Chang Author(s): Winston Chang <winston at stdout.org> License: GPL-2 http://crantastic.org/packages/bisectr Tools to find bad commits with git bisect * CUMP (1.0) Maintainer: Xuan Liu Author(s): Xuan Liu <liuxuan at bu.edu> and Qiong Yang <qyang at bu.edu>

CRAN (and crantastic) updates this week New packages ------------ * disclapmix (0.1) Maintainer: Mikkel Meyer Andersen Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen License: GPL-2 http://crantastic.org/packages/disclapmix disclapmix makes inference in a mixture of Discrete Laplace distributions using the EM algorithm. * EstSimPDMP (1.1) Maintainer: Unknown Author(s):