In examining the predict.coxph functions for the library I have with 2.7.1 versus the library with 2.9.1 I find a major rewrite of the function. A number of "internal survival functions" are no longer present so much of the code has changed. This makes identifying the specific problem beyond my capabilities. What I want to do, is generate predictions for specific combinations of covariates. The number of combinations I am interested in is different than the number of records in the original data file. Any help would be appreciated as some of the graphic routines I want to use on the data are only available in 2.8 or greater - meaning I am currently looking at trying to run two different versions of R to get the project done.
TIA, Michael Conklin -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Conklin Sent: Tuesday, August 18, 2009 8:26 PM To: r-help@r-project.org Subject: [R] Problem with predict.coxph We occasionally utilize the coxph function in the survival library to fit multinomial logit models. (The breslow method produces the same likelihood function as the multinomial logit). We then utilize the predict function to create summary results for various combinations of covariates. For example: mod1<-coxph(Depvar~Price:Product+strata(ID),data=MyDCMData2,na.action=na.omit,method="breslow") The model runs fine. Then we create some new data that is all combinations of Price and Product and retrieve the summary linear predictors. newdata=expand.grid(Price=factor(as.character(1:5)),Product=factor(as.character(1:5))) ## create a utility matrix for all combinations of prices and products totalut<-predict(mod1,newdata=newdata,type="lp") Under R 2.7.1 this produces the following output: > totalut [,1] 1 0.01534582 2 -0.07628528 3 -0.88085189 4 -1.19458045 5 -1.03579684 6 0.40065672 7 0.15922492 8 -0.49233524 9 -0.65483441 10 -1.07739920 11 0.27589201 12 0.48055065 13 0.33638585 14 -0.28416678 15 -0.48762319 16 1.06071986 17 0.69041596 18 0.67479476 19 0.36360168 20 -0.09492167 21 0.66554276 22 0.55748465 23 0.37596413 24 0.01612020 25 -0.03567735 > The problem is that under R 2.8.1 and R 2.9.1 the previous line fails with the following error: > totalut<-predict(mod1,newdata=newdata,type="lp") Error in model.frame.default(Terms2, newdata, xlev = object$xlevels) : variable lengths differ (found for 'Price') In addition: Warning message: 'newdata' had 25 rows but variable(s) found have 43350 rows Does anyone have an idea what is going on? Best regards, Michael Conklin W. Michael Conklin Chief Methodologist MarketTools, Inc. | www.markettools.com<http://www.markettools.com> 6465 Wayzata Blvd | Suite 170 | St. Louis Park, MN 55426. PHONE: 952.417.4719 | CELL: 612.201.8978 This email and attachment(s) may contain confidential and/or proprietary information and is intended only for the intended addressee(s) or its authorized agent(s). Any disclosure, printing, copying or use of such information is strictly prohibited. If this email and/or attachment(s) were received in error, please immediately notify the sender and delete all copies [[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-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.