similar to: Calculate an equation

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

Hello, I have a matrix with the distances among sites. And I have another matrix with the presence and absence of each species in each site. I would like to test the spatial autocorrelation among sites. I have tried to use the function gearymoran of the ade4 package, but error messages keep popping up. Do you know any function for me to test the spatial autocorrelation of my data? Thanks,

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

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

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

For the little C test program where a constant is stored in memory and also used as a parameter: #include <stdint.h> uint64_t val, *p; extern uint64_t xtr( uint64_t); uint64_t caller() { uint64_t x; p = &val; x = 12345123400L; *p = x; return xtr(x); } clang (3.2, 3.3 and svn) generates the following X86 code (at -O3): caller: movq

Hello. I am in a habit of compiling daily snapshots of R-devel and R-patched on my Windows XP workstation. I have cygwin environment with up-to-date RTools and MiKTeX. I run cygwin and MiKTeX upadaters pretty often (every couple of days) so both of them are reasonably current. Recently I noticed a small annoyance when compiling R-dvel. It started happening right after I updated to the new

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

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 :

We have received an email in Ubuntu alerting us that something strange was going on during the r-base 2.7.1 rc build (see [1]). It seems that there is an error during the convertion of R-FAQ.texi to pdf. The following excerpt, taken from [2], shows the problem: /bin/sh: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs

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,

> I expected that this optimization would be picked > up in a cse, gvn, machine-cse or even peepholing pass. > > Comments? At the LLVM IR level this is represented as define i64 @caller() #0 { entry: store i64* @val, i64** @p, align 8, !tbaa !0 store i64 12345123400, i64* @val, align 8, !tbaa !3 %call = tail call i64 @xtr(i64 12345123400) #2 ret i64 %call } Which is

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

Full_Name: Martin O'Gorman Version: OS: Submission from: (NULL) (84.176.63.149) I have been looking at the PPC package and have a question. As the input data is comma separated, shouldn?t the command to read in the raw (no batch) mass spec data indicate that sep=?,? (marked below) ? Otherwise, the data read in is the pair of values (m/z,intensity). It is not obvious why that should be.

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

Hi Everybody, i again have the problem in using tune.knn(), its giving an error saying missing values are not allowed.... again here is the script for BreastCancer Data, library(e1071) library(mda) trdata<-data.frame(train,row.names=NULL) attach(trdata) xtr <- subset(trdata, select = -Class) ytr <- Class bestpara <-tune.knn(xtr,ytr, k = 1:25, tunecontrol = tune.control(sampling

On Aug 2, 2013, at 1:37 PM, Rafael Espíndola <rafael.espindola at gmail.com> wrote: >> I expected that this optimization would be picked >> up in a cse, gvn, machine-cse or even peepholing pass. >> >> Comments? > > > At the LLVM IR level this is represented as > > define i64 @caller() #0 { > entry: > store i64* @val, i64** @p, align 8, !tbaa

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