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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