similar to: problem with get() inside of lme()

Can any one help it will be very kind, loop statements I have this table and some more records, I want to reshape it V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 TP53 Dis1 Dis2 Dis3 Dis4 Dis5 Dis6 DCI New1 New2 New3 New4 FDI Hi2 H3 H4 GHD I1 I3 I4 I5 I6 I7 I8 I want my new table or matrix to be some thing like this V1 V2 V3 Tp53 Dis1 Dis2 Tp53 Dis1 Dis3 Tp53 Dis1 Dis4 Tp53 Dis1 Dis5 Tp53 Dis1 Dis6 Tp53 Dis2

Dear all, I wanted to create the mean using a algebra matrix. so I tried this one: > meanAnimals <- new3%*%factorial (Calculates the matrix multiplication of the new3 * factorial). But I get the following error message: Error in new3 %*% factorial : non-conformable arguments These are my matrices: > new3 [,1] [,2] [1,] 1.350 8.1 [2,] 465.000 423.0

hi, I have a question about merging two files. For example, I have two files, the first file is like the following: id trait1 1 10.2 2 11.1 3 9.7 6 10.2 7 8.9 10 9.7 11 10.2 The second file is like the following: id trait2 1 9.8 2 10.8 4 7.8 5 9.8 6 10.1 12 10.2 13 10.1 now I want to merge the two files by the variable "id", I only want

Hi all, I am a bit mystified by this error message that I get when I try to apply lmer() to a simple dataset with one between factor (age) and one within factor (item): "$ operator is invalid for atomic vectors" I'll just provide the code, because I don't see where the problem is: library(lme4) options(contrasts=c("contr.helmert","contr.poly")) data =

I am hoping someone will be kind enough to have a look at the following piece of code and tell me if there is a way to run lme() so it is a lot faster. The inner loop, j in 1:15000, takes about 2 hrs on my 2.8GHz dual Xeon 4GB RAM machine. The timings I have done show the dominant execution time is in lme. options(contrasts=c("contr.sum", "contr.sum"))

Dear R users, I am trying to read a huge file in R. For some reason, only a part of the file is read. When I further investigated, I found that in one of my non-numeric columns, there is one odd character responsible for this, which I reproduce bellow: In case you cannot see it, it looks like a right arrow, but it is not the one you get from microsoft word in menu "insert symbol". I

Hello, I am trying to help a colleague with an R problem (see below) to whit I can only generate a very inelegant solution. Any advice would be welcome. Thanks, Brian If you have two matrices, say a species by trait matrix (Matrix 1 below) and a plot by species matrix (Matrix 2 below), is there a straightforward way to prune one matrix so that the species list matches those in a

Hi there, I'm sure there's an easy answer to this, and I can't wait to see it. The question: is there an easy way to sort a data frame by it's row names? My dilemma: I've had to pull apart a data frame, run it through a loop to do some calculations and generate new variables, and then re-construct the chunks back into a data frame at the end. Doing this preserves the row

Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account. I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such

Dear all, Can anybody tell me how to export a 3d figure made with the plot3d function? I'm careless about whether it's still interactive or not in another format, as long I can get it out of R. Thanks! Alejandro Gonz?lez Departamento de Biodiversidad y Conservaci?n Real Jard?n Bot?nico Consejo Superior de Investigaciones Cient?ficas Claudio Moyano, 1 28014 Madrid, Spain Tel +0034

I have two questions related to plotting predicted values for a linear mixed model using xyplot: 1: With a groups= argument, I can't seem to get the key to appear inside the xyplot. (I have the Lattice book, but don't find an example that actually does this.) 2: With lme(), how can I generate confidence bands or prediction intervals around the fitted values? Once I get them, I'd

Hello all! Consider a dataset with a grouping structure, Group (factor) Several treatments, Treat (factor) Some sort of yield, Yield (numeric) Something, possibly important, measured for each group; GroupCov (numeric) To look for fixed effects from Treat on Yield, a first attempt could be: m1 <- lm(Yield ~ Treat) which gives, in a symmetric situation, the same estimated fixed effects as:

Dear R experts I was using kinship package to fit mixed model with kinship matrix. The package looks like lme4, but I could find a way to extract p-value out of it. I need to extract is as I need to analyse large number of variables (> 10000). Please help me: require(kinship) Generating random example data id <- 1:100 dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7,

Dear R-help I'm working on a large dataset which I have divided into 20 subsets based on similar features. Each subset consists of observations from different locations and I wish to use the location as a random effect. For each group I want to select regressors by a stepwise procedure and include a random effect on the intercept. I use stepAIC() and lme(). (The lmer()-function doesn't

Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features resolution (affy), I have a lot of probes to work with. I'm assuming it is correct to

On Mon, 2014-03-17 at 14:25 +1030, Rusty Russell wrote: > Erk, our tests are insufficient. Testbuilding an allmodconfig with this > now: Good idea. > diff --git a/include/linux/moduleparam.h b/include/linux/moduleparam.h [] > @@ -188,6 +188,9 @@ struct kparam_array > /* Default value instead of permissions? */ \ > static int __param_perm_check_##name

On Mon, 2014-03-17 at 14:25 +1030, Rusty Russell wrote: > Erk, our tests are insufficient. Testbuilding an allmodconfig with this > now: Good idea. > diff --git a/include/linux/moduleparam.h b/include/linux/moduleparam.h [] > @@ -188,6 +188,9 @@ struct kparam_array > /* Default value instead of permissions? */ \ > static int __param_perm_check_##name

This adds support for CONFIG_COMPAT_VDSO. As this will certainly raise questions, I left in the code needed for an alternative approach (which requires mode C code, but less build script changes). Signed-off-by: Jan Beulich <jbeulich@novell.com> Index: head-2007-02-27/arch/i386/Kconfig =================================================================== ---

This adds support for CONFIG_COMPAT_VDSO. As this will certainly raise questions, I left in the code needed for an alternative approach (which requires mode C code, but less build script changes). Signed-off-by: Jan Beulich <jbeulich@novell.com> Index: head-2007-02-27/arch/i386/Kconfig =================================================================== ---

This adds support for CONFIG_COMPAT_VDSO. As this will certainly raise questions, I left in the code needed for an alternative approach (which requires mode C code, but less build script changes). Signed-off-by: Jan Beulich <jbeulich@novell.com> Index: head-2007-02-27/arch/i386/Kconfig =================================================================== ---