search for: mackey

I could use some help generating a time series for the Mackey-Glass equation: dx/dt = 0.2 x(t-tau)/(1 + x(t-tau)^10) - 0.1 x(t) for the case there tau = 17. I tried the "ddesolve" package but the dde(...) function seems to hang, not producing anything. Can someone show me the R script how to do this? - Mike Beddo [[alternative HTML vers...

[ 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

...the other hand, RODBC worked more or less magically once I set up the data sources. What is your success using ROracle and why would it be preferable to RODBC ? -Avram On Thursday, September 11, 2008, at 12:47PM, "Coey Minear" <cminear at securecomputing.com> wrote: >Aaron Mackey writes: > > I guess I'd do it something like this: > > > > dbGetQuery(con, "CREATE TEMPORARY TABLE foo ( etc etc)") > > sapply(@userids, function (x) { dbGetQuery(con, paste("INSERT INTO foo > > (userid) VALUES (", x, ")")) }) > &g...

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

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

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

Hi. I have asked this question before and Aaron J. Mackey and Tony Plate gave me some great insight but I still can't figure out how to do what I am trying to accomplish. So let me ask again... What I am trying to do is to make R read data from pipe (stdin). Say I have following files on my directory my.dat apple 1 orange 2 gra...

There's got to be a better way to use order() on a matrix than this: > y 2L-035-3 2L-081-23 2L-143-18 2L-189-1 2R-008-5 2R-068-15 3L-113-4 3L-173-2 398 1 1 2 2 1 1 2 2 857 1 1 2 2 1 2 2 2 911 1 1 2 2 1 2 2 2 383 1 1

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

...="| 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...

My apologies if this is a FAQ, I searched the mailing list archives before posting. Background: I am a long time user of SPlus, and a recent user of R. My work normally involves converting the raw output of something interesting into data to be analyzed in S/R, for which I use Perl extensively. I then import the data into S/R, perform the analyses I need, dumping the values into a new file,

I have a fairly large model: > length(Y) [1] 3051 > dim(covariates) [1] 3051 211 All of these 211 covariates need to be nested hierarchically within a grouping "class", of which there are 8. I have an accessory vector, " cov2class" that specifies the mapping between covariates and the 8 classes. Now, I understand I can break all this information up into individual

Dear All, I want to generate survival curve with cox model but I want to estimate the coefficients using glmnet. However, I also want to include a strata() term in the model. Could anyone please tell me how to have this strata() effect in the model in glmnet? I tried converting a formula with strata() to a design matrix and feeding to glmnet, but glmnet just treats the strata() term with one

I have a dataset that looks like this (many other variables not shown. including a unique row identifier "id"): > summary(hits) query lib coverage percid Length:80664 Length:80664 Min. :0.080 Min. :0.2250 Mode :character Mode :character 1st Qu.:0.980 1st Qu.:0.8160 Median :1.000

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?

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,

I have x, y, z data. The x, y fields dont change but Z does. How do I add a very small number onto the end of each x, y data point. For example: Original (X) Original (Y) Original (Z) 15 20 30 15 20 40 New (X) New (Y)

....com> [MN10300] David Hubbard <david.c.hubbard@gmail.com> David Härdeman <david@hardeman.nu> David J. Choi <david.choi@micrel.com> David Jeffery <djeffery@redhat.com> David L Stevens <dlstevens@us.ibm.com> David Liu <dwliu@qca.qaulcomm.com> David Mackey <tdmackey@twitter.com> David McCullough <david_mccullough@mcafee.com> David McCullough <ucdevel@gmail.com> David McCullough <ucdevel@gmail.com> (ARM only) David Milburn <dmilburn@redhat.com> David Miller <davem@davemloft.net> David Moore <david.moo...

....com> [MN10300] David Hubbard <david.c.hubbard@gmail.com> David Härdeman <david@hardeman.nu> David J. Choi <david.choi@micrel.com> David Jeffery <djeffery@redhat.com> David L Stevens <dlstevens@us.ibm.com> David Liu <dwliu@qca.qaulcomm.com> David Mackey <tdmackey@twitter.com> David McCullough <david_mccullough@mcafee.com> David McCullough <ucdevel@gmail.com> David McCullough <ucdevel@gmail.com> (ARM only) David Milburn <dmilburn@redhat.com> David Miller <davem@davemloft.net> David Moore <david.moo...

....com> [MN10300] David Hubbard <david.c.hubbard@gmail.com> David Härdeman <david@hardeman.nu> David J. Choi <david.choi@micrel.com> David Jeffery <djeffery@redhat.com> David L Stevens <dlstevens@us.ibm.com> David Liu <dwliu@qca.qaulcomm.com> David Mackey <tdmackey@twitter.com> David McCullough <david_mccullough@mcafee.com> David McCullough <ucdevel@gmail.com> David McCullough <ucdevel@gmail.com> (ARM only) David Milburn <dmilburn@redhat.com> David Miller <davem@davemloft.net> David Moore <david.moo...