> On 08-03-2015, at 19:29, Endy <pert...@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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