similar to: R for Windows crash on new laptop

I realized that the script I included in my original post (see below) was written for an older version of rmetasim and will not work with the current version. The only change that need be made to get my script to run with the latest release of rmetasim is to change the command 'simulate.landscape()' to 'sim.landscape()'. My apologies to anyone who tried to use my script and

Hello, I am trying to do some simulation using the rmetasim package and I've run to this problem. --beginning of error msg-- Error in "[<-"(`*tmp*`, slice[l, ], slice[l, ], value = c(0.200000002980232, : number of items to replace is not a multiple of replacement length --end of error msg-- Here is the script I used. --script starts here-- ## load 'rmetasim'

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

I've been trying to learn about dynamically loading subroutines in R. Ultimately I would like to use this approach to implement some simulations. For the moment though, I've run into a problem compiling c++ code and loading it into R. The 'C/C++' and 'R'code below works fine when compiled and linked with gcc, but gives an error when the library is compiled and linked with

Dear prof. Harrell, I'm not able to use the force option with fastbw, here an example of the error I've got (dataset stagec rpart package): > fitstc <- cph(Surv(stagec$pgtime,stagec$pgstat) ~ age + eet + g2 + grade + gleason + ploidy, data=stagec) > fbwstc <- fastbw(fitstc,rule="aic",type="individual") > fbwstc Deleted Chi-Sq d.f. P Residual d.f.

Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. thanks, Claire -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17065607.html Sent from the R help mailing list archive at

I am receiving the above error ( full r session output below) the script runs OK in windows. and "genotypes" and "ploidy" are both correct arguments any suggestions would be most welcome Nevil Amos MERG/ACB Monash University School of Biological Sciences > library(Geneland) Loading required package: RandomFields Loading required package: fields Loading required

Hello, I use rpart to predict survival time and have a problem in interpreting the output of ?estimated rate?. Here is an example of what I do: > stagec <- > read.table("http://www.stanford.edu/class/stats202/DATA/stagec.data", > col.names=c("pgtime", "pgstat", "age","eet", "g2", "grade", "gleason", >

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

My data looks like this: > data name G_hat_0_0 G_hat_1_0 G_hat_2_0 G_0 G_hat_0_1 G_hat_1_1 G_hat_2_1 G_1 1 rs0 0.488000 0.448625 0.063375 1 0.480875 0.454500 0.064625 1 2 rs1 0.002375 0.955375 0.042250 1 0.000000 0.062875 0.937125 2 3 rs2 0.050375 0.835875 0.113750 1 0.877250 0.115875 0.006875 0 4 rs3 0.000000 0.074750 0.925250 2 0.897750 0.102000

On Fri, 16 Jan 2009, r-help-request at r-project.org wrote: > Date: Thu, 15 Jan 2009 13:29:03 +0100 > From: Pablo G Goicoechea <pgoikoetxea at neiker.net> > Subject: Re: [R] How to create a chromosome location map by locus ID > To: Sake <tlep.nav.ekas at hccnet.nl> > Cc: r-help at r-project.org > Message-ID: <496F2C0F.3040304 at neiker.net> > Content-Type:

Hi everyone, I have an issue with a data conversion. First, I tried it with the reshape-package, but since it's quite a while that I used it, I feel kind of rusty... I have a data.frame like this: id Sample.Name Marker Allele.1 Allele.2 sample_id species 1 01_primer01 Dalb01 165 179

Hello, I have a data-frame in which one-column is a factor: > str(data); `data.frame': 194 obs. of 8 variables: $ Type : Factor w/ 3 levels "Nuclear-Rec..",..: 1 2 2 2 2 2 2 2 2 2 ... $ Locus : num 0.000571 0.004000 0.001429 0.004857 0.007429 ... And I'd like to make a boxplot of the data$Locus values, where each level of the factor gets its own

Dear R user: Now I am studying "matrix population models" and Rmetasim package,but I find it's very difficult to understand this model fully and can't find a good teacher.My question is that:Now I do some research about one marine shrimp: Penaeus chinensis, it's life cycle is one year. after it breed it's offsprings, it will died. This shrimp's life cycle is dicrete

Hi Guys, I have this part of a program: library(survival) Gastric <- cbind.data.frame(Gp=c(rep(1,45),rep(0,45)), ### 2nd gp 0 time=c(1,63,105,129,182,216,250,262,301,301,342,354,356,358, 380,383, 383,388,394,408,460,489,499,523,524,535,562,569,675,676, 748,778,786,797,955,968,1000,1245,1271,1420,1551,1694,2363,2754,2950,

Dear R users, I am sorry to disturb you! But I really need your help for the usage of sigPathwy. Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really

Hi all, I've been looking in R for an EM algorithm adjusted for multiple-locus haplotypes frequencies, but failed in 100%. Has anyone heard of anything of this kind in R? Thanks in advance, Marcin