similar to: Getting the through items from a has_many :through :uniq relationship

In this real example (below), all four of the replicates in one treatment combination had zero failures, and this produced a very high standard error in the summary.lm. =20 Just adding one failure to one of the replicates produced a well-behaved standard error. =20 I don't know if this is a bug, but it is certainly hard for users to understand. =20 I would value your comments=20 =20 Thanks =20

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

Hi everyone, I would like to fit a predictive model to my data in order to compare absorbance readings to a toxin standard. This data was obtained by exposing red blood cells to different toxin concentrations, which lead to the lysis of the red blood cells, increasing the absorbance (hemoglobin is freed). The data has a sigmoid shape (see below), so I thought about fitting a logistic model to the

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

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

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 :

Hi List, I''m trying to get my ListCtrl to work. Currently I''ve managed to fill my ListCtrl with items, but I think it''s not the most beautiful way: class MyList < Wx::ListCtrl def initialize(parent, *args) super(parent, :style => Wx::LC_REPORT|LC_HRULES ) create_layout fill_list end def create_layout self.insert_column(0, "Name")

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

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) -

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

> Can you file a bug with some example outputs that are unrelated to the search string? Here is the example (see attachment). This example does the following: 1)First, it indexes text from the "text.txt" file (see attachment) (actually, this is the text of the following book: "Abbas, Lichtman. Basic immunology"). 2)Next, it searches for the "extracellular

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

I have 11 vectors representing insect survival probabilities in response to different levels of toxins at 10 concentrations lx100=c(1,1,1,.8,.5,.4,.2,0) day100=c(0,1,2,3,4,5,6,7,8) lx90=c(1,1,1,1,.9,.8,.6,.4,.2,.1,0) day90=c(0,1,2,3,4,5,6,7,8,9,10) #...and so on10% and a zero (control) series lx0=c(1,1,1,1,1,1,.9,.9,.8,.8,.6,.5,.4,.3,.2,.1,.1,0)

Hi i would like to use some graphs or tables to explore the data and make some sensible guesses of what to expect to see in a glm model to assess if toxin concentration and sex have a relationship with the kill rate of rats. But i cant seem to work it out as i have two predictor variables~help?Thanks.:) Here's my data. >

Hi guys My data is Tasmania txt There are *N *= 16 samples, consisting of 8 replicate cores (taken from different areas across the sandflat) from each of 2 natural 'treatments' (either disturbed "D" or undisturbed "U" by soldier crab burrowing activity. The abundances of each of *p *= 56 species were recorded from each core (variables 1 to 39 in the file are