similar to: Simple GLS regression with CAPER

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 there, > > I am using the function pgls in the CAPER package, everything seems to run > fine except for one of my variables. > When using this variable as continuous the anova works without problem, > but if using the same variable as factor (in fact, this is what it is), the > program returns this answer: > > Error in terms.formula(formula, data = data) : >

## I clicked the send-button too quickly, before changing the title of the message etc... Sorry.## I am running following phylogenetic analyses with the caper package: data=read.table(file="data.txt",header=T,sep="\t") tree = read.nexus("Tree.nex") primate = comparative.data(phy=tree, data=data,              names.col=Species, vcv=TRUE, na.omit=FALSE,

I can get btrfs to throw a kernel bug easily by running btrfs fi defrag on some files in 3.9.0: May 7 01:57:33 caper kernel: [ 0.000000] Linux version 3.9.0-030900-generic (apw@gomeisa) (gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) ) #201304291257 SMP Mon Apr 29 16:58:15 UTC 2013 ... May 7 02:09:21 caper kernel: [ 726.745485] ------------[ cut here ]------------ May 7 02:09:21 caper

Hello there, I'm trying to do lots of plots in one for-loop. But somehow ggplot does not evaluate arguments as expected. Here is an example: library(lattice) library(ggplot2) pl <- list() pl2 <- list() cDat <- as.data.frame(cbind(x1=0:100,x2=0:10,x3=1:20)) for(obs in c("x1", "x2")) { pl[[obs]] <- xyplot(cDat[,obs] ~ cDat[,"x3"], main=obs)

Help! I am a new R user. It has been slow getting up to speed, but definitely rewarding. I have come up against a problem I can't handle. I would very much appreciate any help. I am writing a vector auto regression (VAR) function that utilizes existing R statistical functions. I would like to use the step function to do step-wise elimination on each univariate time series model. No

I'm puzzled by the following problem, which appears when attempting to run an analysis on part of a dataset: If I try: csubset <- dat$Diagnosis==0 cont <- lme(fixed=cform, random = ~1|StudyName, data=dat,subset=csubset,na.action=na.omit) Then I get: Error in eval(expr, envir, enclos) : Object "csubset" not found But if I do

Hi, Try these scripts to build llvm and llvm-gcc. It's the ones I use and I managed to get them to work when I saw another build script using those CFLAGS. They compile llvm and stuff using only x86_64, but you can then generate code for i386 (just use a different backend). The configuration options are at the top of the scripts and they install llvm and llvm-gcc to ~/llvm. Regards,

Greetings, I am having trouble getting the Kaleidoscope example to build from tutorial #3 on Mac OS X 10.6.2. I didn't have too much trouble getting llvm-2.6 and llvm-gcc-frontend to build. Thanks for the help. Here are the steps I followed: Environment variables for build export LLVMOBJDIR=/opt/llvm export TARGETOPTIONS='--with-arch=nocona --with-tune=generic' export

Dear moderator, If possible I would like to send in the following question for R-help: I am analyzing a small data set using PGLS with phylogenetic uncertainty taken into account and thereby including 100 potential phylogenetic tree scenarios. I've managed to run models on all of the different trees and performed model averaging to get parameter estimates for the intercept and most of the

Following up on this -- on my system, I have 69 packages installed that appear to provide something like a confint() method: h <- help.search("confint", agrep = FALSE) p <- sort(unique(h$matches$Package)) length(p) ## [1] 69 p [1] "bamlss" "bbmle" "binom" "brglm2" [5] "broom"

Hi, I want to insert a key into each panel of a trellis plot, which I can do with a custom panel function that calles draw.key. The problem arises because I want the top right hand corner of the key to start in the top right hand corner of the panel. If you run my code below, you can see that the key appears in the center of each panel. This is because the default viewport in draw.key is the

Hello, I'm trying to develop a box plot of time series data to look at the range in the data values over the entire period of record. My data initially starts out as a list of hourly data, and then I've been using this code to make this data into the final ts array. # Read in the station list stn.list <- read.csv("/home/kbennett/fews/stnlist3", as.is=T, header=F) # Read in

Dear R experts, I have a labeled data set. Each data is assigned a binary label 0 or 1. Assume that I use some clustering algorithm to group the data by clusters (using some features of the data). Now I want to know how many data are labeled as 0/1 in each cluster. For example, assume that I have 9 labeled data grouped into three clusters. The ids of the clusters are 1, 2, and 3. The dataset is

Hello all, I what to print the banner plot that is output from the mona method in the cluster package but the problem is I dont want to print all that red ink. Here is an example: data(animals) ma <- mona(animals) ma ## Plot similar to Figure 10 in Struyf et al (1996) plot(ma) I can change the bar color by using the argument col=c(0,0) - plot(ma,col=c(0,0)) - but then the variable labels also

Hi all, Sorry for the re-post, I sent my previous e-mail before it was complete. I am trying to model seroprevalence using the differential equation: dP/dt = beta*seronegative*.001*(seropositive)-0.35*(0.999)*(seropositive)-r*seropositive. I would like to estimate my two parameters, beta and r, using maximum likelihood methods. I have included my code below:

Hi, I have a table for an 1 week exam result for many classes in school, like this: Day Class_ID Test Result 1 Monday 1 Paper Passed 2 Tuesday 1 Oral Passed 3 Friday 1 Paper Passed 4 Monday 3 Paper Passed 5 Sunday 3 Oral Passed 6 Monday 3

Hi, Is there any way to get the hessian matrix from the "constrOptim" function without supplying gradient function? Thanks. --------------------------------- Bring words and photos together (easily) with [[alternative HTML version deleted]]

Does winbind play well with NIS (or vice versa)? In my initial test, it doesn't seem that a machine that is running winbind will serve the user list over NIS to NIS clients. [ w2k3/ads ] --winbind--> [ Server 1 ] --NIS--> [ Server 2 ] I'd like to be able to authenticate connections (ssh/login) to Server 2 using the same logins as on Server 1 (samba) and the

Dear all, Very simple question, but apparently uneasy to solve in R: I have a sampling of a variable x: (3, 4. 5, 2, ...) I want to know: - the mean <x> -> mean(x) - the uncertainty on <x> -> std.error(x) ? Or sd(x)? - the standard deviation of x -> ? - the uncertainty on the standard deviation -> ? Anyone has an idea? Thanks in advance,