Hi
see in line.
From: Endy BlackEndy [mailto:pert...@gmail.com]
Sent: Tuesday, April 15, 2014 5:38 PM
To: PIKAL Petr
Subject: Re: [R] I can't programe routine comp()
Dear Pert,
thank you for your advise. Unfortunately it does not work as you can see from
the commands below.
>d=read.table("C:\\Program
>Files\\R\\Data\\Survival\\Sasdata.txt",fill=TRUE,header=TRUE)
Ah I see, you got an error when reading data as I did.
> d=read.table("C:\\Program
> Files\\R\\Data\\Survival\\Sasdata.txt",fill=TRUE,header=TRUE)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:\Program Files\R\Data\Survival\Sasdata.txt': No such file
or directory
>
You need to have Sasdata.txt in your Survival directory.
Do you get the same error?
How does your nn looks like.
Mind reading function is not developped yet. Sorry.
> nn<-names(d)
> s=survfit(Surv(get(nn[2]), get(nn[3]))~get(nn[1]), data=d)
> comp(s)
Error in get(t1, loc1) : object 'get(nn[2])' not found
> a=dput(d, "foo")
>
Also, I do not know how to use the command 'dput'. I used the command
'a=dput(d,"foo")'. I hope it shall work.
I would greatly appreciate any other suggestion.
What dit you find from ?dput help page?
Please try to do some homework and read docs.
I do not know anything about survival and just reading help pages and about 10
minutes trial and error I could do following:
library(survival)
?survfit
head(heart)
start stop event age year surgery transplant id
1 0 50 1 -17.155373 0.1232033 0 0 1
2 0 6 1 3.835729 0.2546201 0 0 2
3 0 1 0 6.297057 0.2655715 0 0 3
4 1 16 1 6.297057 0.2655715 0 1 3
5 0 36 0 -7.737166 0.4900753 0 0 4
6 36 39 1 -7.737166 0.4900753 0 1 4
nn<-names(heart)
survfit(with(heart, (Surv(get(nn[1]), get(nn[2]), get(nn[3]))))~1)
Call: survfit(formula = with(heart, (Surv(get(nn[1]), get(nn[2]), get(nn[3]))))
~
1)
records n.max n.start events median 0.95LCL 0.95UCL
172 103 0 75 100 72 263
plot(survfit(with(heart, (Surv(get(nn[1]), get(nn[2]), get(nn[3]))))~1))
So my suggestion actually works with right data and a bit of effort to get the
right code.
Regards
Petr
Many thanks
Endy
2014-04-15 12:26 GMT+03:00 PIKAL Petr
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>>:
Hi
better to use dput for presenting data as it is directly usable by anybody. So
I did not test it.
Try to get names for appropriate columns
nn<-names(d)
and use get
s=survfit(Surv(get(nn[2]), get(nn[3]))~get(nn[1]), data=d)
It works with lm and shall work with survit too.
Regards
Petr
> -----Original Message-----
> From: r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>
> [mailto:r-help-bounces@r-<mailto:r-help-bounces@r->
> project.org<http://project.org>] On Behalf Of Endy
> Sent: Monday, April 14, 2014 12:56 PM
> To: r-help@r-project.org<mailto:r-help@r-project.org>
> Subject: [R] I can't programe routine comp()
>
> Dear R users.
> I am trying to program the comp() routine in package survMisc. I am
> reading the data below with d=read.table( "C:\\. .
> .",fill=TRUE,header=TRUE) Then I load the packages 'survival' and
> 'survMisc', library(survival), library(survMisc)
> and I run the commands
> s=survfit(Surv(d[,2],
> d[,3])~d[,1], data=d)
> comp(s)
> and I am getting the error
> Error in get(t1, loc1) : object
> 'd[, 2]' not found If instead I use the commands
> s=survfit(Surv(T,
> Status)~Group, data=d)
> comp(s) routine comp() runs
> perfectly. However when I am programing I can't see a way to know in
> advance the variable names in order to use them.
> Can anybody give me a suggestion?
>
> Thanks in advance
> Endy
>
> NB. The data must be stacked in three (3) columns before red.
> They are repeated in nine (9) columns for space saving.
>
> GroupTStatusGroupTStatusGroupTStatus
>
> 120810155124141
> 116020111222041
> 11496011071210631
> 1146201110124811
> 1143301332121051
> 11377022569026411
> 11330022506023901
> 1996022409022881
> 1226022218024211
> 1119902185702791
> 11111021829027481
> 1530021562024861
> 1118202147002481
> 11167021363022721
> 14181210300210741
> 138312860023811
> 127612125802101
> 110412224602531
> 160912187002801
> 117212179902351
> 1487121709022481
> 1662121674027041
> 1194121568022111
> 1230121527022191
> 1526121324026061
> 1122129570
> 1129129320
> 174128470
> 1122128480
> 1861218500
> 14661218430
> 11921215350
> 11091214470
> 1551213840
> [[alternative HTML version deleted]]
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