Dear professor Harrell, I probably have the same problem as Haleh Ghaem Maralani. I am using the rms package and the rcspline.plot function to assess the relation of a continuous predictor to the log hazard function. I would like to use the "adj" statement, for example using this test dataset: http://r.789695.n4.nabble.com/file/n3058505/file.csv test <-read.csv("file.csv",header=TRUE) rcspline.plot(test$factor, test$Time,model="cox", adj=cbind(test$adj1, test$adj2), xrange=c(0,3),ylim=c(-1,2),event=test$event,nk=4,knots=c(0.8,1.0,1.5,2.0),showknots=TRUE,plotcl=FALSE,statloc="none",subset=test$SEX=="2",lty=2) Then I get the following Error. x -0.7860188 3.4871734 -4.6087226 -0.6761077 -0.9358280 [1] -3686.955 -3646.681 Error in pchisq(q, df, lower.tail, log.p) : Non-numeric argument to mathematical function Could you please help us understanding how to use the adj statement? Bart Ferket, MD, dept. Epidemiology, ErasmusMC Rotterdam -- View this message in context: http://r.789695.n4.nabble.com/rcspline-problem-tp3501627p4637039.html Sent from the R help mailing list archive at Nabble.com.
rcspline.problem
3 messages · Bart Ferket, Peter Ehlers
On 2012-07-19 07:10, Bart Ferket wrote:
Dear professor Harrell, I probably have the same problem as Haleh Ghaem Maralani. I am using the rms package and the rcspline.plot function to assess the relation of a continuous predictor to the log hazard function. I would like to use the "adj" statement, for example using this test dataset: http://r.789695.n4.nabble.com/file/n3058505/file.csv test <-read.csv("file.csv",header=TRUE) rcspline.plot(test$factor, test$Time,model="cox", adj=cbind(test$adj1, test$adj2), xrange=c(0,3),ylim=c(-1,2),event=test$event,nk=4,knots=c(0.8,1.0,1.5,2.0),showknots=TRUE,plotcl=FALSE,statloc="none",subset=test$SEX=="2",lty=2) Then I get the following Error. x -0.7860188 3.4871734 -4.6087226 -0.6761077 -0.9358280 [1] -3686.955 -3646.681 Error in pchisq(q, df, lower.tail, log.p) : Non-numeric argument to mathematical function Could you please help us understanding how to use the adj statement? Bart Ferket, MD, dept. Epidemiology, ErasmusMC Rotterdam
[You're replying to a year-old post; it would probably have
been better to start a new thread.]
I think that there may be a bug in rcspline.plot that
may be easily fixed. Grab the code of rcspline.plot()
and edit it as follows:
1. Find the line with
adj.df <- attr(v, "rank")
and replace it with
adj.df <- qr(v)[["rank"]]
2. Save the function as "myrcspline.plot".
3. Fix the evironment of your new function:
environment(myrcspline.plot) <- environment(rcspline.plot)
Now use myrcspline.plot in your analysis. Works for me, but
I'm no expert in such models and don't what side effects
this change might have.
Peter Ehlers
Dear Peter, This indeed resolves the problem. Many thanks. My apologies for not starting a new thread. I am a new R user and not yet fully integrated into the R community. Kind regards, Bart Ferket -- View this message in context: http://r.789695.n4.nabble.com/rcspline-problem-tp3501627p4637181.html Sent from the R help mailing list archive at Nabble.com.