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?$supTests???????????????????????????????
??????????????????????????????Q pLog-rank??????????????????????
???????????????????????? ??0 1Gehan-Breslow (mod~ Wilcoxon)? ? ? ? ? ? ? ?0
1Tarone-Ware???????????????????? ? ? ? ? ? ? ? ? ? ? ? ?0
1Peto-Peto?????????????????????? ? ? ? ? ? ? ? ? ? ? ? ? ?0 1Mod~ Peto-Peto
(Andersen)?????? ? ? ? ? ? ? ? ?0 1Renyi Flem~-Harr~ with p=1, q=1 ? ? ? ? ?
???0 1Any assistance will greatly appreciated.CheersEndyI am using theR version
3.1.1 (2014-07-10) -- "Sock it to Me"Copyright (C) 2014 The R
Foundation for Statistical ComputingPlatform: i386-w64-mingw32/i386 (32-bit)?
[[alternative HTML version deleted]]
> On 08-03-2015, at 19:29, Endy <pertsou at yahoo.gr> wrote: > > Hi R users. I have some problems with the package ?survMisc?. When I am loading it I am getting the following > library(survMisc)Loading required package: survivalLoading required package: splinesLoading required package: km.ciLoading required package: ggplot2Loading required package: data.tabledata.table 1.9.4 For help type: ?data.table*** NB: by=.EACHI is now explicit. See README to restore previous behaviour.Loading required package: gridExtraLoading required package: gridLoading required package: rpart Attaching package: ?survMisc? The following objects are masked from ?package:stats?: AIC, BIC, median, quantile In the above output I noticed the line with the three stars (*). In order to restore the data.table in its previous behavior I tried to locate the README file but I couldn?t. I ignored that NB in the previous output and I continue to run the example given in the above mentioned package for the routine comp(). The commands and the output are given below.> ### 2 curves> data(kidney,package="KMsurv")> s1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney )> comp(s1)$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) > > [[alternative HTML version deleted]]Do not post twice in a space of 10 minutes. Your mail is completely mangled and unreadable. Please follow the posting guide and DO NOT post in html. Berend