Re: [R] I can't programe routine comp()

[PIKAL Petr]

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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