similar to: ape comparative analysis query

Hello all, I have a *.csv file that looks like this (actual file is orders of magnitude larger): Site taxa no.ind forest LMA 1 forest LCY 1 forest SCO 1 meadow LMA 2 meadow LCY 1 meadow PNT

Hello, I'm doing a comparative analysis of mammal brain and body size data. I'm following Charlie Nunn and Natalie Cooper's instructions for "Running PGLS in R using caper". I run into the following error when I create my comparative dataset, combining my phylogenetic tree (mammaltree) and taxon measures (mammaldata): "Error in phy$node.label[which(newNb > 0) -

Dear all, I was wondering if you could help me with the following. I want to do calculate this equation: Ps(t)= (?_(r=1)^N Xtr* 1/?drs)/(?_(r=1)^N 1/?drs) Ps(t) ? Probability that taxon t will occur at site s (300 sites s) N ? Number of sites = from 1 to 49 Xtr ? Value for taxon t at site r (I have this information in a table, 40 taxa (columns) t, 49 sites r) drs ? Distance from site r to

Hello I apologise for the length of this entry but please bear with me. In short: I need a way of subsampling communities from all possible communities of n taxa taken 1:n at a time without having to calculate all possible combinations (because this gives me a memory error - using combn() or expand.grid() at least). Does anyone know of a function? Or can you help me edit the combn or

Dear R users, i am fairly new to R and am having trouble creating code to solve a problem. I've searched the list, combed Crawley's 'R book' and several others, but can't quite find what i want. I want to generate permutations of various 'blocks' of 14 numbers. Each number within a block is a character state for a particular biological taxon. In the example below, for

Getting the through items from a has_many :through :uniq relationship In a nutshell, I have been using the has_many :through :uniq relationship, and I want a DRY way to list the join model objects. Currently, my objects include taxon objects, toxin objects, data_object objects, and taxon_toxin_citation objects ("citation" is another word for data_object). A taxon has many data objects,

Dear R community, I am running R 2.0.1 on a Windoze XP OS. I recently upgraded from R 1.9x to 2.0.1 and I am currently upgrading a my personal function packages. My other packages compiled without a hitch but I am having a difficult time with my largest package. Can someone please help me with the following error message "Error in parse(file, n, text, prompt) : syntax error on line

R users, I recently upgraded (?) to Windows XP from 2000. I am trying to build an R package. I have done this many times on my old system and I am not sure why it is not working in XP. To build the package I call a bat file that specifies all the necessary paths -- but the "build" file (which appears to be a perl script) is looking for a "src" subdirectory in the src

Let's say I would like to look inside the function corBrownian in library (ape). When I type in the function name I get the following, which is not nearly the detail that goes into this function. I am wondering how to begin cracking this function open (and others) so I can learn more about it and perhaps code my own corClass one day. Thanks. > corBrownian function (value = 1, phy, form

Dear R experts I am running a negative-binomial GLM (glm.nb) to test the null hypotheses that species 1 and 2 are equally abundant between site 1 and site2, and between each other. So, I have a 2x2 factorial design with factors Site (1,2) and Taxon (1,2). Since the Site:Taxon interaction is significant, I need to do the equivalent to a "post-hoc test" for ANOVA, however, the same tests

Hi Derek, I was getting this too, with three tables, called taxa, databases and references I found I could add an irregular pluralisation for taxa: Inflector.inflections do |inflect| inflect.irregular ''taxon'', ''taxa'' end to the environment.rb, but no amount of modification there would allow databases and

I would like to revisit a problem that was discussed previously (see quoted discussion below). I am trying to do the same thing, using a string to indicate a column with the same name. I am making "foo" a string taken from a list of names. It matches the row where "item" = 5, and picks the corresponding "taxon" > foo <- list$taxon[match(5,list$item)] Let's

Hello, I've got a matrix consisting of one column with n rows. Each field in the matrix is filled with a character vector. I would like to convert this matrix into a character vector containing the B03_MAH-type entries from the beginning of each row and a data.frame that contains the numeric data, but I am stuck. I have tried to use textConnection with sep = " " but since

taxa <- (structure(list(Date = structure(c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("2006/04", "2006/05", "2006/07", "2006/10", "2006/12", "2007/02", "2007/04", "2007/06", "2007/08", "2007/10", "2007/12", "2008/01"), class =

I don't see what's missing in my statements to add rows to a data frame and someone else will probably see what needs to be added to the statements. The data frame has this structure (without any data): $ PHYLUM : chr $ SUBPHYLUM : chr $ SUPERCLASS : chr $ CLASS : chr $ SUBCLASS : chr $ INFRACLASS : chr $ SUPERORDER : chr $ ORDER : chr $ SUBORDER :

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page, from vegan package): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't accept a

Hi This question is far less simple than the title suggests, please read carefully, thanks. I have 2 sets of data, both read into R >data1<-read.table ("1.txt", header=T, sep="\t") >data2<-read.table ("2.txt", header=T, sep="\t") >data1 Taxon stage1 stage2 stage3 stage4 T1 0 0 1 1 T2 0

Hello. Does anyone know of an existing function that takes a list in the form of: Plot1 Species1 Abundance1 Plot1 Species2 Abundance2 Plot2 Species1 Abundance1 Plot2 Species3 Abundance3 . . . PlotN SpeciesN AbundanceN and translates into a matrix in the form of Species1 Species2.... SpeciesN Plot1 Abundance1 Abundance2... AbundanceN Plot2 Abundance1

Hello, How can I create a symmetric contingency table from two categorical vectors having different length of levels? For example one vector has 98 levels TotalData1$Taxa.1 [1] "Aconoidasida" "Actinobacteria (class)" "Actinopterygii" "Alphaproteobacteria" [5] "Amoebozoa"