similar to: Subsetting data leads to funky plots

Hi all, I am wondering if anyone has written (or knows of) a function that will conduct a goodness-of-fit test for a gamma distribution. I am especially interested in test statistics have some asymptotic parametric distribution that is independent of sample size or values of fitted parameters (e.g., a chi-squared distribution with some fixed df), because I want to fit gamma distributions to

Hello! I'm a PhD student working with coral reef fish diversity in Mexico. I want to do species accumulation curves but I have differential sampling effort for each "sample". Do you know or have developed an R script that consider the differential effort of each sample? PRIMER and other programs use each pack of species as a replica without the possibility of telling the program that

How can I print a data.frame to a PDF with pdf()...dev.off() ____________ Paulo E. Cardoso [[alternative HTML version deleted]]

Dear David, you asked this question a while ago on the R mailing list and got no answer. I have the same problem and was wondering if you had found a solution Cheers Loic Loic Thibaut, PhD candidate, ARC Centre of Excellence for Coral Reef Studies, School of Marine Biology, James Cook University, Townsville, Qld, 4811, Australia. Tel + 61 747 815 735, Fax: + 61 747 251 570, email:

Hi I am experiencing a problem with the random number generator. When I call any function that involve RNG such as "runif" or "sample" I get this error: .Random.seed is not an integer vector but of type 'double' I can't coerce the random seed and it's recommended not to alter it anyway. Can anybody help me? Thanks and kind regards, Piero Visconti, PhD

For block effects with small variance, lmer will sometimes estimate the variance as being very close to zero and issue a warning. I don't have a problem with this -- I've explored things a bit with some simulations (see below) and conclude that this is probably inevitable when trying to incorporate random effects with not very much data (the means and medians of estimates are plausibly

Hi there, I have been having trouble running negative binomial regression (glm.nb) using library MASS in R v2.15.0 on Mac OSX. I am running multiple models on the variables influencing the group size of damselfish in coral reefs (count data). For total group size and two of my species, glm.nb is working great to deal with overdispersion in my count data. For two of my species, I am getting a

Hi all, I am fairly new to R and I am trying to run mvpart and create a MRT using explanatory variables and covariables. I've been following the procedures in Numerical Ecoogy with R. The command (no covariables) which works fine - ABUNDTMRT <- mvpart(abundance ~ .,factors,margin=0.08,cp=0,xv="1se",xval=nrow(abundance),xvmult=100,which=4) where abundance is 4th root

Hello, I recently started using the metafor package (version 1.6-0) in R (2.15.1, 64-bit Windows 7) and noticed that I was getting slightly different values when I manually calculated the standardized mean difference versus what escalc was giving me. Here''s a very simple example: escalc(measure="SMD", m1i=5,m2i=10,n1i=5,n2i=5,sd1i=1,sd2i=2,vtype="LS") The result

Hi guys: Sorry if this question is very basic. I?m learning basic matrix and vectors multiplication to develop a population matrix model for plants. I?m trying to multiply the elements of two vectors (each of the ?x? values by each of the ?y? values) to obtain a square matrix of xy values. f.e. x<-seq(5,205) y<-seq(5,20,5) stages<-c(?Sdl?, ?Juv?, ?Ad1?, ?Ad2?) If I just multiply xy as

Hi everyone, I know there have been several requests regarding subsetting before, but none of them really helps with my problem: I'm trying to subset only infected individuals from the REC2 data.frame: > str(REC2) 'data.frame': 362 obs. of 7 variables: $ RINGNO : Factor w/ 370 levels "BL17546","BL17577",..: 78 81 67 41 58 66 17 $ year : Factor w/ 8

Hi everyone, I am beginner using R but I try to learn more. I need this graphic or similar but instead of tropical and temperate are three ontogenetic states Larva Met Juv CTMAX CTMIN SP SP SP This is my scrip: Ex = subset(Expr, Outlayer=="N") Ex2 = subset (Ex, S0 == 1) Ex3

Have made a stacked area plot, but now want to manipulate the x axis: make in even increments (50) in order to suppress the tick marks (forming solid bar under plot). However, the plot functions do not seem to work, and I cannot find documentation for use of xat in stackpoly. This is a time series of data covering 579 years, and has been successfully converted from zoo to matrix. Data plotting

Dear all I have used the lda and predict functions to classify a set of objects of unknown origin. I would like to use a jackknife reclassification to assess the degree to which the outcomes deviate from that expected by chance. However, I can't find any function that allows me to do this. Any suggestions of how to generate the jackknife reclassification to assess classification accuracy?

> > just so you know, --enable-vorbis-updates is only a compile flag for the KH > > branch, not the mainline trunk. And I think it would be great to have this > > code be factored out of KH and integrated into the mainline trunk...This > > also seems like an odd thing to have as a compile flag, what was the > > motivation for that ? oddsock > That switch

I was recently testing R and RStudio on a high dpi 4K monitor under Windows and noticed that the plot window cannot be scaled or zoomed without affecting the relative sizing of all plot elements (line widths, font sizes, legend spacing etc). RStudio seems to try to overcome this by enabling dpi scaling for the plot window on high dpi screens, but this results in really fuzzy text and graphics

Dear list, I have two dissimilarity matrices, one for a training data set which I then clustered using PAM. The second is a diss matrix for a validation data set (an independent field sample). I have been trying to use knn to distinguish distances between the validation data set and the 6 mediods of the training data defined by using PAM. I continue to get error messages in regards to either the

Hi all, I am trying to model (continuous) spatial variation in a response variable as a function of one or more of several explanatory variables. I am principally interested in obtaining some measure of the relative "importance" of the explanatory variables. I have found several R libraries that are tailored to this sort of problem (geoR, geoRglm, gstat, etc.); however, as near

Thanks Petr. Comments below: At 03:40 PM 18/05/2007, Petr Klasterecky wrote: >Sean Connolly napsal(a): >>Hi all, >>I am wondering if anyone has written (or knows of) a function that >>will conduct a goodness-of-fit test for a gamma distribution. I am >>especially interested in test statistics have some asymptotic >>parametric distribution that is independent

Dear All, I've been using mcmcsamp() successfully with a few different mixed models but I can't get it to work with the following. Is there an obvious reason why it shouldn't work with a model of this structure ? *brief summary of objective: I want to test the effect of no-fishing marine reserves on the abundance of a target species. I have samples at coral reef sites inside and