similar to: Interaction contrasts or posthoc test for glm (MASS) with ANOVA design

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

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

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 :

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 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

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, 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) -

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

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,

Hello: I need to take a species-sample matrix and transpose it to the format used by PC-ORD for analysis. Unfortunately, the number of species is very large (>5000), and so this operation cannot be performed simply in an application like Excel, which has a 255 column limit. So, I wrote relatively simple code in R that I hoped would do this (appended below). But there are glitches. The

Hello. We have some questions concerning the statistical analysis of a dataset. We aim to compare the sample means of more than 2 independent samples; the sample sizes are unbalanced. The requirements of normality distribution and variance homogeneity were not met even after transforming the data. Thus we applied a nonparametric test: the Kruskal-Wallis-test (H-Test). The null hypothesis was

Hi there, I was hoping to post this message. Im hoping I;ve got the right spot?! Hi there, sorry for basic question but im very new to R. Im trying to run a lme model with two categorical variables, each having 6 (for the explanatory variable C.f) and 5 levels (for expl. variable D.f) respectively. The lme runs fine, summary and anova commands are ok. But now i've tried running posthoc

dear all, I want to perform a posthoc test for my ANCOVA: a1<-aov(seeds~treatment*length) With summary(glht(a1, linfct = mcp(treatment = "Tukey"))) R tells me: "covariate interactions found -- please choose appropriate contrast" How do I build these contrasts? Ideally, I would like to have the posthoc test for the ANCOVA including a block-effect

Dear List, are there post-hoc tests like Scheffe, LSD, etc. available after ANOVA test is performed with significant F-statistic? I have tried help.search("Scheffe"), but "No documentation found" (and I have most of packages installed). Probably there are such tests in R, and I am just searching badly... My second question is: Which test/method I should use for ANOVA-like

Hi All, I have performed a 3-way ANOVA analysis for my experimental data using aov function. My simple R funtion for this is: 3aof <- function(x){ m <- data.frame(R,S,T, x); anova(aov(x ~ R+S+T+R*S+R*T+S*T+R*S*T, m) ) } Now, I am getting P values for all the main and interactions effects. If I want to perform postdoc test on one of my main effects, say T, what method I should use (i have

Hi, I have analyzed my data using log-linear model as seen below: > yes.no <- c("Yes","No") > tk <- c("On","Off") > ats <- c("S","V","M") > L <- gl(2,1,12,yes.no) > T <- gl(2,2,12,tk) > A <- gl(3,4,12,ats) > n <- c(1056,4774,22,283,326,2916,27,360,274,1770,15,226) >

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