The package maintainer may be able to give help. However, I don't get the
same output as you (3.1.2). Perhaps you can update and solve your problem.
> require(survMisc)
Loading required package: survMisc
Loading required package: survival
Loading required package: splines
Loading required package: ggplot2
Attaching package: ?survMisc?
The following object is masked from ?package:ggplot2?:
autoplot
The following objects are masked from ?package:stats?:
AIC, BIC, median, quantile
> 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: 0.5 119 6 76 6 43 0
2: 1.5 103 1 60 0 43 1
3: 2.5 98 2 56 2 42 0
4: 3.5 89 2 49 1 40 1
5: 4.5 79 2 43 0 36 2
6: 5.5 73 1 40 0 33 1
7: 6.5 66 1 35 1 31 0
8: 8.5 55 2 30 0 25 2
9: 9.5 49 1 27 0 22 1
10: 10.5 45 1 25 0 20 1
11: 11.5 40 1 22 0 18 1
12: 15.5 25 2 14 1 11 1
13: 16.5 23 1 13 0 10 1
14: 18.5 20 1 11 0 9 1
15: 23.5 9 1 5 0 4 1
16: 26.5 5 1 3 0 2 1
$tests
$tests$lrTests
ChiSq df p
Log-rank 2.529506318 1 0.11174
Gehan-Breslow (mod~ Wilcoxon) 0.002084309 1 0.96359
Tarone-Ware 0.402738202 1 0.52568
Peto-Peto 1.399160019 1 0.23686
Mod~ Peto-Peto (Andersen) 1.275908836 1 0.25866
Flem~-Harr~ with p=1, q=1 9.834062861 1 0.00171
$tests$supTests
Q p
Log-rank 1.590442 0.22347
Gehan-Breslow (mod~ Wilcoxon) 1.430499 0.30511
Tarone-Ware 1.260498 0.41467
Peto-Peto 1.166979 0.48551
Mod~ Peto-Peto (Andersen) 1.185549 0.47085
Renyi Flem~-Harr~ with p=1, q=1 7.460348 0.00000
-----Original Message-----
From: Endy BlackEndy [mailto:pertsou at gmail.com]
Sent: Sunday, March 08, 2015 12:44 PM
To: r-help
Subject: [R] "survMisc" package
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: survival
Loading required package: splines
Loading required package: km.ci
Loading required package: ggplot2
Loading required package: data.table
data.table 1.9.4 For help type: ?data.table
*** NB: by=.EACHI is now explicit. See README to restore previous behaviour.
Loading required package: gridExtra
Loading required package: grid
Loading 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 2
10: 16.5 26 2 13 1
13 1
11: 18.5 22 2 11 1
11 1
12: 23.5 8 2 4 1
4 1
13: 26.5 6 2 3 1
3 1
$tests
$tests$lrTests
ChiSq df p
Log-rank 0 1 1
Gehan-Breslow (mod~ Wilcoxon) 0 1 1
Tarone-Ware 0 1 1
Peto-Peto 0 1 1
Mod~ Peto-Peto (Andersen) 0 1 1
Flem~-Harr~ with p=1, q=1 0 1 1
$tests$supTests
Q p
Log-rank 0 1
Gehan-Breslow (mod~ Wilcoxon) 0 1
Tarone-Ware 0 1
Peto-Peto 0 1
Mod~ Peto-Peto (Andersen) 0 1
Renyi 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 04/17/1991
When I run the function proc() I am getting the answer
> proc()
Error in Surv(d[, 2], d[, 5]) : object 'd' not found
In contrast when I run the same routine command-by-command I am getting the
following output
$lrTests
ChiSq df p
Log-rank 0 1 1
Gehan-Breslow (mod~ Wilcoxon) 0 1 1
Tarone-Ware 0 1 1
Peto-Peto 0 1 1
Mod~ Peto-Peto (Andersen) 0 1 1
Flem~-Harr~ with p=1, q=1 0 1 1
$supTests
Q p
Log-rank 0 1
Gehan-Breslow (mod~ Wilcoxon) 0 1
Tarone-Ware 0 1
Peto-Peto 0 1
Mod~ Peto-Peto (Andersen) 0 1
Renyi Flem~-Harr~ with p=1, q=1 0 1
Any assistance will greatly appreciated.
Cheers
Endy
I am using the
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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