On 08-03-2015, at 19:29, Endy <pertsou at yahoo.gr> wrote:
Hi R users. I have some problems with the package ?survMisc?. When I am loading it I am getting the following > library(survMisc)Loading required package: survivalLoading required package: splinesLoading required package: km.ciLoading required package: ggplot2Loading required package: data.tabledata.table 1.9.4 For help type: ?data.table*** NB: by=.EACHI is now explicit. See README to restore previous behaviour.Loading required package: gridExtraLoading required package: gridLoading required package: rpart Attaching package: ?survMisc? The following objects are masked from ?package:stats?: AIC, BIC, median, quantile In the above output I noticed the line with the three stars (*). In order to restore the data.table in its previous behavior I tried to locate the README file but I couldn?t. I ignored that NB in the previous output and I continue to run the example given in the above mentioned package for the routine comp(). The commands and the output are given below.> ### 2 curves> data(kidney,package="KMsurv")> s1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney )> comp(s1)$tne t n e n_type=1 e_type=1 n_type=2 e_type=2 1: 1.5 86 2 43 1 43 1 2: 3.5 80 2 40 1 40 1 3: 4.5 72 4 36 2 36 2 4: 5.5 66 2 33 1 33 1 5: 8.5 60 4 30 2 30 2 6: 9.5 54 2 27 1 27 1 7: 10.5 50 2 25 1 25 1 8: 11.5 44 2 22 1 22 1 9: 15.5 28 4 14 2 14 210: 16.5 26 2 13 1 13 111: 18.5 22 2 11 1 11 112: 23.5 8 2 4 1 4 113: 26.5 6 2 3 1 3 1 $tests$tests$lrTests ChiSq df pLog-rank 0 1 1Gehan-Breslow (mod~ Wilcoxon) 0 1 1Tarone-Ware 0 1 1Peto-Peto 0 1 1Mod~ Peto-Peto (Andersen) 0 1 1Flem~-Harr~ with p=1, q=1 0 1 1 $tests$supTests Q pLog-rank 0 1Gehan-Breslow (mod~ Wilcoxon) 0 1Tarone-Ware 0 1Peto-Peto 0 1Mod~ Peto-Peto (Andersen) 0 1Renyi Flem~-Harr~ with p=1, q=1 0 1 Notice the zeros (0) that corresponds to the test statistics. (To my opinion those zeros are strongly related to the NB above). Next I noticed the following strange, to my opinion, thing. More precisely I have written the following routine proc<-function(){ rm(list=ls()) library(survMisc) d<-read.table("C:\\Program Files\\R\\Data\\Survival\\HosmLem.txt",fill=TRUE,header=TRUE) d4<-as.factor(d[,4]) s<-survfit(Surv(d[,2], d[,5])~d4) ctest<-comp(s)$tests print(ctest)}The data used are those of Hosmer and Lemeshow book on Applied Survival Analysis. The first rows of this data set follow.id Time Age Drug Censor entdate enddate 1 5 46 0 1 05/15/1990 10/14/1990 2 6 35 1 0 09/19/1989 03/20/1990 3 8 30 1 1 04/21/1991 12/20/1991 4 3 30 1 1 01/03/1991 04/04/1991 5 22 36 0 1 09/18/1989 07/19/1991 6 1 32 1 0 03/18/1991 04/17/1991When I run the function proc() I am getting the answer> proc()Error in Surv(d[, 2], d[, 5]) : object 'd' not foundIn contrast when I run the same routine command-by-command I am getting the following output$lrTests ChiSq df pLog-rank 0 1 1Gehan-Breslow (mod~ Wilcoxon) 0 1 1Tarone-Ware 0 1 1Peto-Peto 0 1 1Mod~ Peto-Peto (Andersen) 0 1 1Flem~-Harr~ with p=1, q=1 0 1 1 $supTests Q pLog-rank 0 1Gehan-Breslow (mod~ Wilcoxon) 0 1Tarone-Ware 0 1Peto-Peto 0 1Mod~ Peto-Peto (Andersen) 0 1Renyi Flem~-Harr~ with p=1, q=1 0 1Any assistance will greatly appreciated.CheersEndyI am using theR version 3.1.1 (2014-07-10) -- "Sock it to Me"Copyright (C) 2014 The R Foundation for Statistical ComputingPlatform: i386-w64-mingw32/i386 (32-bit)
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