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

[Dewi VERNEREY]

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 .

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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