Dear Dr ;
I am a PhD student at Epidemiology department of National University of
Singapore. I used R command (rcspline.plot) for plotting restricted cubic
spline ??? the model is based on Cox. I managed to get a plot without
adjustment for other covariates, but I have a problem regarding to
adjusting the confounders.
I applied below command to generate the matrix for covariates.
m=as.matrix(age,sex) or m1=matrix(age,sex) or m2=cbind(age,sex)
But, when I input ..... adj=m, or adj=m1, or adj=m2...... in the model, R
gives below error:
Error in pchisq(q, df, lower.tail, log.p) :
Non-numeric argument to mathematical function
In addition: Warning message:
In coxph.fit(cbind(x, xx, adj), cbind(y, event), strata = NULL, :
Loglik converged before variable 1,2,3,4 ; beta may be infinite.
I would be grateful if you take my issue into your consideration and help me
on this case
Sincerely Yours
Haleh Ghaem
PhD student, NUS
Please follow the posting guide. You didn't state which package you are using and didn't include a trivial self-reproducing example that causes the error. For your purpose the rms package is going to plot restricted cubic spline fits (and shaded confidence bands) more flexibly. Frank Haleh Ghaem Maralani wrote:> > Dear Dr ; > > > I am a PhD student at Epidemiology department of National University of > Singapore. I used R command (rcspline.plot) for plotting restricted > cubic > spline ??? the model is based on Cox. I managed to get a plot > without > adjustment for other covariates, but I have a problem regarding to > adjusting the confounders. > > I applied below command to generate the matrix for covariates. > > m=as.matrix(age,sex) or m1=matrix(age,sex) or m2=cbind(age,sex) > > But, when I input ..... adj=m, or adj=m1, or adj=m2...... in the > model, R > gives below error: > > > Error in pchisq(q, df, lower.tail, log.p) : > > Non-numeric argument to mathematical function > > In addition: Warning message: > > In coxph.fit(cbind(x, xx, adj), cbind(y, event), strata = NULL, : > > Loglik converged before variable 1,2,3,4 ; beta may be infinite. > > > I would be grateful if you take my issue into your consideration and > help me > on this case > > > Sincerely Yours > > > Haleh Ghaem > > PhD student, NUS > ______________________________________________ > 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. >----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/rcspline-problem-tp3501627p3502623.html Sent from the R help mailing list archive at Nabble.com.
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
--
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http://r.789695.n4.nabble.com/rcspline-problem-tp3501627p4637039.html
Sent from the R help mailing list archive at Nabble.com.