similar to: Correlation matrices

Hello again, I was too quick before. What I was looking for was a function that constructs the design (or incidence) matrix (X in a linear model) from a factor. Uwe Ligges suggested using model.matrix and this does almost what I want, but it is first necessary to construct a data variable. It also asigns ones to all rows of the first column (because this is set to be the contrast, not really what

Hello, I wonder if someone could send me suggestions on how to solve the following problem: I have a vector of an arbitrary size (ex. data<-c(10,10,11,10,12,11,10,12,11,11,10,11)) and use the table function, which gives the following result 10 11 12 5 5 2 that''s fine, but what I would like to do now is: construct new classes based on the number of classes from table, 10

Hello, I wonder if someone could help me with the following: I have generated 10 000 values from rnorm and now I want to randomly replace 500 of those with NA. The problem is that values indexed between 6-10,16-20,26-30.... only should be considered for replacement. Any suggestions? Patrik Waldmann -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing

I wonder if someone could help me adjusting the following code to parallelized snow code: #Creating a data set (not needed to be parallel) n<-100 p<-100 x<-matrix(rnorm(n*p),p) y<-rnorm(n) # Bootstrapping nboot<-1000 alpha<-0.05 rhoboot <- array(0, dim=c(p,nboot)) bootranks <- array(0, dim=c(p,nboot)) bootsamples <- array( floor(runif(n*nboot)*n+1), dim=c(n,nboot)) for

Hello, are there any functions in R for estimation of the mode of a MCMC-chain? Best, Patrik Waldmann [[alternate HTML version deleted]]

Hello, I have an unbalanced data set with some factors and several variables. The missing values are spread unequally over the variables. Because of the unbalanced structure have i tried NLME, but I cannot understand how I should set up the na.omit. I would not like to use na.omit before setting up the model, as that would exclude too many observations (on the whole structure). Lets say I have

I haven't found a function that directly calculates the matrix inverse, does it exist? Otherwise what would be the fastest way to do it? Patrik Waldmann -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the

Hi Now a more theoretical question. I have two correlation matrices - one of a set of variables under a particular condition, the other of the same set of variables under a different condition. Is there a statistical test I can use to see if these correlation matrices are "different"? Thanks Mick

Dear R'ers, When I used S-plus i wrote a small program for a Mantel-Haenszel test for trend (I think it worked). Unfortunately I can't get it working in R. It appears as if my use of 'el' is the problem but I can't sort it out. Error in apply(array, c(, 2, 3), function(el) el * 1:s) : argument is missing, with no default Further down in the program I use 'el'

I would like to perform partial mantel tests on only within group values, with "between group" values assigned to NA. This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a "matrix is not square error. is it possible to perform this test in ecodist? many thanks

> Background: > OS: Linux Ubuntu Dapper > release: R 2.3.0 > editor: GNU Emacs 21.4.1 > front-end: ESS 5.2.3 > ----------------------------- > Colleagues > I have two spatial datasets (latitude, longitude, fish eggs) and (latitude, longitude, fish larvae) at the same 280 stations (i.e. 280 cases). I want to determine if the 2 datasets are spatially correlated. In other

Dear all, Does anyone knows why the results of a BIOENV (PRIMER v. 6.1.15) are diferent of the bioenv() + mantel() in vegan? Not the spearman correlation, indeed the pseudo-p value. I know that the approach bioenv() + mantel() is biased. So, how the BIOENV (PRIMER) ends with larger p values (permutated). Acctualy how the permutation test in BIOENV (PRIMER) is conducted. The user guide does not

Dear R users, I am having a problem performing the mantel test (both with functions mantel {vegan} and mantel.test {ape}) due to I believe the presence of NAs on my distance matrices, which look like e.g.: NA 1 2 1 2 3 NA 4 5 6 and 1 1 2 2 3 4 5 6 7 8 Would any of you have a solution for that? Thank you for much for your help! Marcia Rocha -- View this message in

Does anyone know of an R function for computing the Greenland-Robins variance for Mantel-Haenszel relative risks? Thanks Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Dear all, Dose anyone know whether there is a good R packege or program for Mantel's randomization test? Thanks in advance. ------------------------ Takashi Mizuno zoono at sci.osaka-cu.ac.jp Plant Ecology Lab. Osaka City University ------------------------ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

I want to import my zpool''s from FreeBSD 8.0 in OpenSolaris 2009.06. After reading the few posts (links below) I was able to find on the subject, it seems like it there is a differences between FreeBSD and Solaris. FreeBSD operates on directly on the disk and Solaris creates a partion and uses that... is that right? Is it impossible for OpenSolaris to use zpool''s from FreeBSD?

https://bugzilla.mindrot.org/show_bug.cgi?id=2331 Bug ID: 2331 Summary: ssh-copy-id -i id_new.pub fails to copy that id, also: wrong error msg Product: Portable OpenSSH Version: -current Hardware: All OS: Linux Status: NEW Severity: major Priority: P5 Component:

Dear Dr.Goslee and anyone may intrested in matrix manipulate, I am using your ecodist to do mantel and partial mantel test, I have locality data and shape variation data, and the two distance matrixs are given as belowings. When I run the analysis, it is always report that the matrix is not square, but I didn't know what's wrong with my data. Would you please help me on this. I am quite

Dear all, Has anyone written R code for partial Mantel Tests- as described for instance in Legtendre & Legendre (1998) ? In other words, in a community ecology analysis, I would like to calculate the correlation between two dissimilarity matrices, controlling for a third distance matrix representing geographical distances between sites. Thanks! Christophe Bouget Biodiversité et gestion des

Hi, I am trying to use a mantel test on two distance matrices. The code I have entered for each is: Gen_dists <- read.csv(file.choose(), stringsAsFactors = FALSE, na.strings = c(" "), fill = T,