search for: taxonom

Dear all, I am working with taxonomic data, represented as a list of classes, orders, families, genera and finally species. > class(mydata) [1] "data.frame" > mode(mydata) [1] "list" > names(mydata) [1] "tclass" "torder" "tfamily" "tgenus" "tspecie...

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 f...

Hi, I was recently misfortunate enough to have to use regular expressions to sort out some data in R. I'm working on a data file which contains taxonomical data of bacteria in hierarchical order. A sample of this file can be generated using: tax.data <- read.table(header=F, con <- textConnection(' G9SS7BA01D15EC Bacteria(100) Cyanobacteria(84) unclassified G9SS7BA01C9UIR Bacteria(100) Proteobacteria(94) Alphaproteobact...

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 this time 2, 3... X under samples at the same time, always in a random way. Thank you in advance for your answer. Manue. [[alternative HTML version deleted]]

...ix, txt, sep="") + if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt) + text(0.5, 0.5, txt, cex = cex.cor * r) + } > pairs(pep[9:18],cex.labels = 0.6, pch = 21, bg = c("red", "blue", "green", > "yellow","brown")[unclass(pep$taxonomic.position)], lower.panel=panel.cor) thanks, Herwig -- View this message in context: http://www.nabble.com/Error-%3A-unused-arguments-in---pairs%28%29-tp21283398p21283398.html Sent from the R help mailing list archive at Nabble.com.

...... $ basin : Factor w/ 2 levels "H","O": 2 2 2 2 2 2 2 2 2 2 ... When I create a bar chart for tclass by stream the resulting bars appear to have multiple segments (see attached pdf) from this command: barchart(quant ~ tclass | stream, data = benthos, main = 'Taxonomic Classes', xlab = 'Class Name', ylab = 'Number/square meter', scales = list(x = list(rot = 90))) and I want to understand what the segments represent. I thought the formula 'quant ~ tclass' would produce one bar per class. I cannot find the answer in the ?barchart help...

...y, functions to check the data quality of molecular fingerprints are available. To identify the organisms represented by the extracted fragment patterns (e.g.\ RFLP genotypes), RFLPtools includes a function to compare samples with fragment patterns stored in a reference dataset, from which the taxonomic affiliations are already known. To identify unknown samples in scientific projects, DNA sequences are used, and the gained DNA sequences are compared to existing sequence data via alignments tools, as standalone BLAST. RFLPtools offers tools to generate groups based on tabular report files of...

...y, functions to check the data quality of molecular fingerprints are available. To identify the organisms represented by the extracted fragment patterns (e.g.\ RFLP genotypes), RFLPtools includes a function to compare samples with fragment patterns stored in a reference dataset, from which the taxonomic affiliations are already known. To identify unknown samples in scientific projects, DNA sequences are used, and the gained DNA sequences are compared to existing sequence data via alignments tools, as standalone BLAST. RFLPtools offers tools to generate groups based on tabular report files of...

...mphasis on speed and computational efficiency, the *phylogram* package also includes tools for rapidly computing distance matrices, and building large trees using fast alignment-free k-mer counting and divisive clustering. While not guaranteed to produce sufficiently accurate phylogenetic trees for taxonomic purposes, this offers an efficient means of clustering large trees for a variety of other applications including tree-based sequence weighting, guide trees for progressive multiple sequence alignment, and other recursive operations such as classification tree learning. Any feedback is warmly wel...

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>

At last year''s Xen North America Summit in Boston, I gave a talk about memory overcommitment in Xen. I showed that the basic mechanisms for moving memory between domains were already present in Xen and that, with a few scripts, it was possible to roughly load-balance memory between domains. During this effort, I discovered that "ballooning" had a lot of weaknesses, even though

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):