Dear all, I have been using the contrast library in my teaching for the last couple of years and am right in the middle of this year's round. In the last week R has been updated to version 2.14.0 on our computers. This has had the unfortunate effect of meaning the contrasts library no longer works, as the Design library is no longer available. I wonder if anyone has a fix for this...or alternatively can tell me another package that is as simple to use (the students won't cope with anything more complicated - we're all biologists not statisticians). I hope someone can help. Here is a typical bit of code I'm currently running so you can see what I'm trying to do: exptime is a covariate and both infstat and status are factors mod<-glm(propalive~exptime+infstat+status+ infstat:status, data=dat) library(contrast) contrast(mod3, a = list(status = levels(dat$status), infstat="control", exptime=8230), b = list(status = levels(dat$status), infstat="infected",exptime=8230)) any help gratefully received, Jo Dr Joanne Lello Cardiff University School of Biosciences Organism and Environment Group Biomedical Sciences Building Museum Avenue Cardiff CF10 3AX Tel: 02920 875885 E-mail: lelloj@cardiff.ac.uk [[alternative HTML version deleted]]
On another list it was reported that a new version of contrast was uploaded to CRAN earlier today that makes use of Design's replacement "rms". Wait a day or two and then download this updated version and rms. http://www.mail-archive.com/r-sig-mac at r-project.org/msg00924.html Michael On Thu, Nov 24, 2011 at 12:23 PM, Joanne Lello <LelloJ at cardiff.ac.uk> wrote:> Dear all, > > I have been using the contrast library in my teaching for the last couple > of years and am right in the middle of this year's round. In the last week > R has been updated to version 2.14.0 on our computers. This has had the > unfortunate effect of meaning the contrasts library no longer works, as > the Design library is no longer available. I wonder if anyone has a fix > for this...or alternatively can tell me another package that is as simple > to use (the students won't cope with anything more complicated - we're all > biologists not statisticians). > > I hope someone can help. > > Here is a typical bit of code I'm currently running so you can see what > I'm trying to do: > > exptime is a covariate and both infstat and status are factors > > mod<-glm(propalive~exptime+infstat+status+ > ? ? ? ?infstat:status, > ? ? ? ?data=dat) > > library(contrast) > > contrast(mod3, > ? a = list(status = levels(dat$status), infstat="control", exptime=8230), > ? b = list(status = levels(dat$status), infstat="infected",exptime=8230)) > > any help gratefully received, > > Jo > > Dr Joanne Lello > Cardiff University > School of Biosciences > Organism and Environment Group > Biomedical Sciences Building > Museum Avenue > Cardiff > CF10 3AX > Tel: 02920 875885 > E-mail: lelloj at cardiff.ac.uk > ? ? ? ?[[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Note that you can do what you specified using only the rms package: require(rms) f <- Glm(propalive~exptime+infstat*status, data=dat) contrast(f, a = list(status = levels(dat$status), infstat="control", exptime=8230), b = list(status = levels(dat$status), infstat="infected",exptime=8230)) Frank Joanne Lello wrote> > Dear all, > > I have been using the contrast library in my teaching for the last couple > of years and am right in the middle of this year's round. In the last week > R has been updated to version 2.14.0 on our computers. This has had the > unfortunate effect of meaning the contrasts library no longer works, as > the Design library is no longer available. I wonder if anyone has a fix > for this...or alternatively can tell me another package that is as simple > to use (the students won't cope with anything more complicated - we're all > biologists not statisticians). > > I hope someone can help. > > Here is a typical bit of code I'm currently running so you can see what > I'm trying to do: > > exptime is a covariate and both infstat and status are factors > > mod<-glm(propalive~exptime+infstat+status+ > infstat:status, > data=dat) > > library(contrast) > > contrast(mod3, > a = list(status = levels(dat$status), infstat="control", exptime=8230), > b = list(status = levels(dat$status), infstat="infected",exptime=8230)) > > any help gratefully received, > > Jo > > Dr Joanne Lello > Cardiff University > School of Biosciences > Organism and Environment Group > Biomedical Sciences Building > Museum Avenue > Cardiff > CF10 3AX > Tel: 02920 875885 > E-mail: lelloj at .ac > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@ mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/The-contrast-and-Design-libraries-tp4106321p4109210.html Sent from the R help mailing list archive at Nabble.com.
On Thu, Nov 24, 2011 at 9:23 AM, Joanne Lello <LelloJ at cardiff.ac.uk> wrote:> Dear all, > > I have been using the contrast libraryThey're packages! [snip] For the sake of the good Martin Maechler, Josh -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/