[R] [R-pkgs] rms 4.1-0

[David Winsemius]

On Nov 20, 2014, at 7:56 AM, Dewi VERNEREY wrote:

> 
> Hi Franck,
> 
> I am using the calibrate function from the package rms (4.2-1) with R (3.1.2) in a Mac OS 10.10.1 environment .

That's the Yosemite platform. I'm running R 3.1.2 with the current CRAN binaries (which were recently updated) and I get no error with the example in the help page for `calibrate`. At the moment you example is not reproducible since we do not have your data. Do you get an error with the code on `?calibrate`  (and are you using the most up-to-date versions of everything?
> 
> With my previous configuration (other computer) the function calibrate worked very well.
> 
> Unfortunately, now the calibrate function doesn’t work. Do you have an idea to help me in order to solve this problem. The validate function works.
> 
> Thank you very much for your help
> 
> Kind regards,
> 
> Dewi
> 
> 
> Please find bellow my code :
> 
> 
> W =read.table("export_R_model_proba.txt",sep="\t",header=TRUE)
> 
> W= as.data.frame(W)
> 
> ls()
> 
> summary(W)
> 
> library(survival)
> 
> library(survplot)
> 
> library(rms)
> 
> library(SvyNom)
> 
> library(SvyNom)
> 
> library(survey)
> 
> 
> f <- cph(Surv(OS_time_months, OS_event) ~ CT + VE + Nratio_rcd + log_LYPREOP + log_LYPO , dist='lognormal',data=W,surv=T,dxy = TRUE,time.inc =48,x=TRUE, y=TRUE)
> 
> f
> 
> Cox Proportional Hazards Model
> 
> cph(formula = Surv(OS_time_months, OS_event) ~ CT + VE + Nratio_rcd +
> 
>    log_LYPREOP + log_LYPO, data = W, x = TRUE, y = TRUE, surv = T,
> 
>    time.inc = 48, dist = "lognormal", dxy = TRUE)
> 
> 
>                     Model Tests       Discrimination
> 
>                                          Indexes
> 
> Obs        241    LR chi2     42.15    R2       0.161
> 
> Events     179    d.f.            5    Dxy     -0.283
> 
> Center -5.6749    Pr(> chi2) 0.0000    g        0.608
> 
>                  Score chi2  46.25    gr       1.837
> 
>                  Pr(> chi2) 0.0000
> 
> 
>            Coef    S.E.   Wald Z Pr(>|Z|)
> 
> CT          -0.6056 0.1891 -3.20  0.0014
> 
> VE           0.4153 0.1640  2.53  0.0114
> 
> Nratio_rcd   0.6746 0.1778  3.79  0.0001
> 
> etc etc
> 
> plot(calibrate(f,u=48,method="boot",cmethod="KM",xlim=c(0,1),ylim=c(0,1),surv=T,m=33),xlim=c(0,1),ylim=c(0,1))
> 
> Erreur dans UseMethod("calibrate") :
> 
>  pas de méthode pour 'calibrate' applicable pour un objet de classe "c('cph', 'rms', 'coxph')"
> 
> 
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> 
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David Winsemius
Alameda, CA, USA