On Sep 12, 2013, at 8:38 PM, Marine Regis wrote: > Hello everybody, > > Thank you David for your answer. Sorry I am beginner with cox model and R > software. Is it possible to do predictions from newdata which has a size > equal to the vector hour <- seq(0,23.99,0.1) ? In fact, I don't know how to > define parameters "cluster" and "strata" in the newdata knowing that I would > like to have one prediction value for each vector value "hour <- > seq(0,23.99,0.1)" and to have a prediction curve for each category "anthro", > "cor", "for" (these covariates are dichotomic) ?
I'm sorry. Did you think that we would understand this question without a data example and reference to specific features of results developed with code applied to that example? -- David. > > Thank you very much for your help. > Have a good day > Marine > >> CC: r-help@r-project.org >> From: dwinsem...@comcast.net >> To: marine.re...@hotmail.fr >> Subject: Re: [R] predict() from conditional logit model? >> Date: Thu, 12 Sep 2013 17:52:33 -0500 >> >> >> On Sep 12, 2013, at 3:31 PM, Marine Regis wrote: >>> >>> Hello everybody, >>> >>> I used the function clogit() (package survival) to build a >>> conditional logit >>> model. This is the R output of my model : >>> coef exp(coef) se(coef) robust se z >>> Pr(>|z|) >>> anthro 2.14776 8.56565 0.09352 0.53989 3.978 6.94e-05 *** >>> cor 0.92365 2.51846 0.07757 0.41944 2.202 0.027659 * >>> for 1.55191 4.72047 0.07513 0.41488 3.741 0.000184 >>> *** >>> --- >>> Signif. codes: 0 Œ***‚ 0.001 Œ**‚ 0.01 Œ*‚ 0.05 Œ.‚ 0.1 Œ ‚ 1 >>> >>> The covariates anthro, cor and for are dichotomic covariates (0/1). >>> Then, I used the function predict() to calculate predicted values as >>> follows >>> : >>> >>> modpred <- predict(ML,type="lp") >> >> You do understand that is on a log-relative-probability scale, right? >> And that it is relative to the mean values for the entire dataset? >> >>> >>> and I obtained the following values for the first line of my >>> original data : >>> >>> anthro cor for predited >>> 1 0 1 0 0.0839679 >>> >>> With modpred <- predict(ML,type="expected"), I obtained : >>> anthro cor for predited >>> 1 0 1 0 0.09618096 >> >>> >>> My question is : from coefficients of clogit model, how can I find the >>> predicted values 0.0839679 and 0.09618096 ? >> >> You need to understand that those are really very different >> "predictions". >> >>> In addition, how can I obtain predicted values ranged from 0 to 1 ? >>> >>> Thank you very much for your help. >> >> (Reading the help pages.) There does not appear to be a >> `predict.clogit` function but clogit objects inherit from coxph >> objects so reading the Details section from `predict.coxph`: >> >> "The Cox model is a relative risk model; predictions of type "linear >> predictor", "risk", and "terms" are all relative to the sample from >> which they came. By default, the reference value for each of these is >> the mean covariate within strata. The primary underlying reason is >> statistical: a Cox model only predicts relative risks between pairs of >> subjects within the same strata, and hence the addition of a constant >> to any covariate, either overall or only within a particular stratum, >> has no effect on the fitted results. Using the reference="strata" >> option causes this to be true for predictions as well." >> >> The predict.coxph function is fairly long: >> >> getAnywhere(predict.coxph) >> >> -- >> David Winsemius, MD >> Alameda, CA, USA >> > > [[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. David Winsemius Alameda, CA, USA ______________________________________________ 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.
