search for: popgen

Dear R-help As a novice to R I was seeking some advice with respect to using R to help solve a problem I have. I have a large number of infiles that need analysed. This can be done, I believe, using 2 separate R packages (popgen and ape) with the output from 'popgen' being used as input for 'ape'. What I would like to know is whether it is possible within R to write some script so that these files can be read from a folder outside the R space (say a folder within the C drive of my computer) and processed wi...

Hello, I'm in need of running a PVA and want to load {popbio}. However, I can't find it. I can't see where or how to load it. I have added repositories and changed the CRAN mirror site. I see {polynom} and {popgen} but no {popbio} between. What am I doing wrong? Thanks, Michelle [[alternative HTML version deleted]]

Dear r-helpers, I downloaded http://popgen.unimaas.nl/~jlindsey/rcode/rmutil.tar (it was originally .tgz, but got unzipped by my browser). Can anyone give me detailed instructions on installing this and Lindsey's other packages on R version 2.4.0 (2006-10-03)---(powerpc- apple-darwin8.7.0, locale: C)? ____________________________...

...27 \n 28 C 29 0 30 1 31 B Can you help me? Thanks Nicole Dr Nicole Soranzo Centre for Population Genetics and Human Health University College London Darwin Building Gower Street London WC1E 6BT Tel: +44 (0)20 7679 4397 Fax: +44 (0)20 7679 2887 E-mail: n.soranzo at ucl.ac.uk http://popgen.biol.ucl.ac.uk/ -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: FunctRes.txt Url: https://stat.ethz.ch/pipermail/r-help/attachments/20040331/3ce0dd9b/FunctRes.txt

Background: OS: Linux Mandrake 10.1 release: R 2.0.0 editor: GNU Emacs 21.3.2 front-end: ESS 5.2.3 --------------------------------- Colleagues Is there a function in R that is an equivalent of zoom in matlab? This is very useful for being able to magnify details in a plot. I have searched the help for "zoom", "interactive zooming", and "magnify". The R search

I'm trying to install the ordinal package (http://popgen.unimaas.nl/~plindsey/rlibs.html). I downloaded ordinal03.tgz and untarred it. rmutil was previously installed (and appears to work ok.) Then I installed ordinal: [root at localhost ~]# R CMD INSTALL /home/chippy/Download/ordinal * Installing to library '/usr/lib/R/library' * Installing *s...

Hi all, Does anyone know what happened to the dna library or the dotmatrix function? For the life of me, I can't find it anywhere with the exception of this reference: http://rss.acs.unt.edu/Rdoc/library/dna/html/dotmatrix.html Thanks! Jeff. http://www.nd.edu/~jspies/ [[alternative HTML version deleted]]

Hi All, I want to upload J K Lindsey's "repeated" in a LINUX OS.. I had tried the command.. [root@localhost Desktop] # R CMD INSTALL repeated.gz " WARNING: invalid package 'repeated' " *Installing to library '/usr/local/lib/R/library' ERROR: No packages

I would like to install the package "growth" as it contains the function "corgram" and some other presumably useful stuff for time series analysis. I can see it is in R standard library list: http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/doc/html/packages.html<http://hosho.ees.hokudai.ac.jp/%7Ekubo/Rdoc/doc/html/packages.html>

Hello! I must estimate the parameters of a exponential power density. There is the normalp package, but this works only for a shape parameter bigger than 1. But what should i do if the shape parameter is less than 1? (Sorry for my english) Thank you very much for help! -- View this message in context: http://www.nabble.com/Parameters-of-exponential-power-density-tp20774495p20774495.html Sent from

*Dear R-help: My name is Rodrigo and I have a question with nlme package in R to fit a mixed beta regression model. The details of the model are: Suppose that:* *j in {1, ..., J}* *(level 1)* *i in {1, ..., n_j}* *(level 2)* *y_{ij} ~ Beta(mu_{ij} * phi_{ij}; (1 - mu_{ij}) * phi_{ij}) y_{ij} = mu_{ij} + w_{ij} * *with* *logit(mu_{ij}) = Beta_{0i} + Beta_{1i} * x1_{ij} + b2 * x2_{ij}

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

Hi, Is there any package in R which i can use for Coalescent Theory/Genelogical Trees? Is this possible to use R function in C language? I would be very thankful to you. Regards, ++++++++++++++++++++++++++++++++++++++++++++++ MUHAMMAD FAISAL Department of Statistics and Decion Support system, University of Vienna,Austria:: Send Me Message at Yahoo Res. # +4314796696104, Cell #

Dear R-users, Do you know if we can use the function lme in R for log-normal distribution of parameters as used in Nonmem ? theta=theta0*exp(eta) In our model, the parameters follow the log-normal distribution so it's not reasonable to deal with normal distribution which gives us negative values in simulation Thanks for your help, Thu [[alternative HTML version deleted]]

Hello - I cannot get to www.alpha.luc.ac.be/~jlindsey/rcode.html<http://www.alpha.luc.ac.be/%7Ejlindsey/rcode.html>to obtain and install the repeated library for use of glmm(). Is the web page not active? Can you give me an alternative location to obtain the repeated library? Thank you, Becky Parker [[alternative HTML version deleted]]

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

Package mvtnorm provides dmvnorm, pmvnorm that can be used to compute Pr(X=x,Y=y) and Pr(X<x,Y<y) for a bivariate normal. Are there functions that would compute Pr(X<x,Y=y)? I'm currently using "integrate" with dmvnorm but it is too slow.

Thompson's Manual to Accompany Agresti's book refers to a package named "repeated". It's not on CRAN from what I can see. I have seen rpm's for it. Where is the best place to download this package? Rick B.

...I am not on the list, please could you answer to jerome.goudet at unil.ch? Many thanks in advance. R 2.4.0 Windows XP Matrix package version 0.9975-3 -- J?r?me GOUDET Dep. Ecology & Evolution Biophore, UNIL-Sorge UNIL-CH-1015 Lausanne Switzerland http://www.unil.ch/dee http://www.unil.ch/popgen Tel: +41 21 692 42 42 Fax: +41 21 692 42 65 Secr:+41 21 692 42 60 jerome.goudet at unil.ch

It's in the Venables & Ripley MASS (ed 3) book in the section on principal components. The context is as follows > ir <- rbind(iris[,,1], iris[,,2], iris[,,3]) > ir.species <- factor(c(rep("s",50),rep("c",50),rep("v",50))) (then they use brush(ir) which I guess is not an R function) and then > princomp(log(ir[1:4]),cor=T) (there is no [1:4]