search for: amackey

Hi, In support of reproducible research at my Institute, I seek an approach to re-creating the R environments in which an analysis has been conducted. By which I mean, the exact version of R and the exact version of all packages used in a particular R session. I am seeking comments/criticism of this as a goal, and of the following outline of an approach: === When all the steps to an workflow

...s="| enscript -Pbiochem_LJ5P" # the default argument for lpr is -P % ./script.pl --lpr=biochem_LJP # send other parameters to lpr (e.g. 2 copies); % ./script.pl --lpr="-Pwrp_ph56 -#2" # send pdf's to someone: % ./script.pl --pdf --email=amackey at virginia.edu --subject="Here's the latest version" DESCRIPTION R::Wrapper is meant to be a utility wrapper around the RS-Perl R module. It currently provides three main features: the first is a visually "cleaner" interface to the R module's calling interf...

I've posted a message twice to this list, and never seen it appear yet ... perhaps this one will go through ... ? -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey at pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697

...iven the trained HMM, I then wish to label new sequences via viterbi(). Am I missing the purpose of this package? I also read through the msm package docs, but my data doesn't really have a time coordinate on which the data should be "aligned". Thanks for any pointers, -Aaron <amackey@virginia.edu> [[alternative HTML version deleted]]

There are numerous tools like scons, make, ruffus, ant, rake, etc. that can be used to build complex pipelines based on task dependencies. These tools are written in a variety of languages, but I have not seen such a thing for R. Is anyone aware of a package available? The goal is to be able to develop robust bioinformatic pipelines driven by scripts written in R. Thanks, Sean

I have a 47k x 47k adjacency matrix that is very sparse (at most 30 entries per row); my textual representation therefore is simply an adjacency list of connections between nodes for each row, e.g. node connections A B C D E B A C D C A E D A E A F F E G H I'd like to import this into a dataframe of node/connection (character/vector-of-characters) pairs. I've experimented with

Is there anyway I can write a script which feed input datasource from stdin and let R process it (maybe frequency report) then output the report to stdout? I can't seem to find much info on documentation or FAQ on this topic. Thanks! Soichi Hayashi ********************************************************************** The information contained in this communication is confidential,

[ Not sure why, but the first time I sent this it never seemed to go through; apologies if you're seeing this twice ... ] I have some fully functional code that I'm guessing can be done better/quicker with some savvy R vector tricks; any help to make this run a bit faster would be greatly appreciated; I'm particularly stuck on how to calculate using "row-wise" vectors

I have a MLE task that for a small number of parameters finishes in a reasonable amount of time, but for my "real" case (with 17 parameters to be estimated) either takes far too long (over a day), or fails with "computationally singular" errors. So a) are there any parallel implementations of optim() (in R or otherwise) and b) how can I make my function more robust?