Re: [R] Rms package - problems with fit.mult.impute
Thank you Frank! Now it works perfectly fine. Regards Lina Message: 73 Date: Thu, 23 Jun 2011 14:13:06 -0700 (PDT) From: Frank Harrell f.harr...@vanderbilt.edu To: r-help@r-project.org Subject: Message-ID: 1308863586428-3621045.p...@n4.nabble.com Content-Type: text/plain; charset=UTF-8 There is a problem passing x in the ... arguments to fit.mult.impute when the function has a formal argument starting with x (xtrans). To get around this specify xtrans=a to fit.mult.impute instead of just listing a. Frank Lina Hellstr?m wrote: Hi! Does anyone know how to do the test for goodness of fit of a logistic model (in rms package) after running fit.mult.impute? I am using the rms and Hmisc packages to do a multiple imputation followed by a logistic regression model using lrm. Everything works fine until I try to run the test for goodness of fit: residuals(type=c(gof)) One needs to specify y=T and x=T in the fit. But I get a warning message when I do that with fit.multiple.impute. a-aregImpute(~med.hist.err+ med.discr+newLiving+No.drugs+Days.categ+Los+Age+Ward+Sex, n.impute=20, nk=0,data=med.err) ddist-datadist(Age,No.drugs,Days.categ, Sex, Living, Ward) options(datadist=ddist) fmi-fit.mult.impute(med.hist.err~Age+No.drugs+Days.categ+Sex+Living+Ward, fitter=lrm, x=T, y=T,a,data=med.err) Error in 1:n.impute : NA/NaN argument In addition: Warning message: In 1:n.impute : numerical expression has 18 elements: only the first used It works to do the fit.mult.impute without x and y=T but then I get the following warning message when running residuals gof-residuals(fmi, type=c(gof)) Error in residuals.lrm(fmi, type = c(gof)) : you did not specify y=T in the fit It was no problem to do the goodness of fit test when I ran the lrm on my complete data set without multiple imputation and fit.mult.impute. model.lrm-lrm(med.hist.err~Age+No.drugs+Days +Sex+Living+Ward, x=TRUE, y=TRUE) gof-residuals(model.lrm, type=c(gof)) Thanks Lina _ PhD student Linnaeus University Sweden [[alternative HTML version deleted]] __ R-help@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.
[R] Rms package - problems with fit.mult.impute
Hi! Does anyone know how to do the test for goodness of fit of a logistic model (in rms package) after running fit.mult.impute? I am using the rms and Hmisc packages to do a multiple imputation followed by a logistic regression model using lrm. Everything works fine until I try to run the test for goodness of fit: residuals(type=c(gof)) One needs to specify y=T and x=T in the fit. But I get a warning message when I do that with fit.multiple.impute. a-aregImpute(~med.hist.err+ med.discr+newLiving+No.drugs+Days.categ+Los+Age+Ward+Sex, n.impute=20, nk=0,data=med.err) ddist-datadist(Age,No.drugs,Days.categ, Sex, Living, Ward) options(datadist=ddist) fmi-fit.mult.impute(med.hist.err~Age+No.drugs+Days.categ+Sex+Living+Ward, fitter=lrm, x=T, y=T,a,data=med.err) Error in 1:n.impute : NA/NaN argument In addition: Warning message: In 1:n.impute : numerical expression has 18 elements: only the first used It works to do the fit.mult.impute without x and y=T but then I get the following warning message when running residuals gof-residuals(fmi, type=c(gof)) Error in residuals.lrm(fmi, type = c(gof)) : you did not specify y=T in the fit It was no problem to do the goodness of fit test when I ran the lrm on my complete data set without multiple imputation and fit.mult.impute. model.lrm-lrm(med.hist.err~Age+No.drugs+Days +Sex+Living+Ward, x=TRUE, y=TRUE) gof-residuals(model.lrm, type=c(gof)) Thanks Lina _ PhD student Linnaeus University Sweden [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Rms package - problems with fit.mult.impute
There is a problem passing x in the ... arguments to fit.mult.impute when the function has a formal argument starting with x (xtrans). To get around this specify xtrans=a to fit.mult.impute instead of just listing a. Frank Lina Hellström wrote: Hi! Does anyone know how to do the test for goodness of fit of a logistic model (in rms package) after running fit.mult.impute? I am using the rms and Hmisc packages to do a multiple imputation followed by a logistic regression model using lrm. Everything works fine until I try to run the test for goodness of fit: residuals(type=c(gof)) One needs to specify y=T and x=T in the fit. But I get a warning message when I do that with fit.multiple.impute. a-aregImpute(~med.hist.err+ med.discr+newLiving+No.drugs+Days.categ+Los+Age+Ward+Sex, n.impute=20, nk=0,data=med.err) ddist-datadist(Age,No.drugs,Days.categ, Sex, Living, Ward) options(datadist=ddist) fmi-fit.mult.impute(med.hist.err~Age+No.drugs+Days.categ+Sex+Living+Ward, fitter=lrm, x=T, y=T,a,data=med.err) Error in 1:n.impute : NA/NaN argument In addition: Warning message: In 1:n.impute : numerical expression has 18 elements: only the first used It works to do the fit.mult.impute without x and y=T but then I get the following warning message when running residuals gof-residuals(fmi, type=c(gof)) Error in residuals.lrm(fmi, type = c(gof)) : you did not specify y=T in the fit It was no problem to do the goodness of fit test when I ran the lrm on my complete data set without multiple imputation and fit.mult.impute. model.lrm-lrm(med.hist.err~Age+No.drugs+Days +Sex+Living+Ward, x=TRUE, y=TRUE) gof-residuals(model.lrm, type=c(gof)) Thanks Lina _ PhD student Linnaeus University Sweden [[alternative HTML version deleted]] __ R-help@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/Rms-package-problems-with-fit-mult-impute-tp3619814p3621045.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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.
