[R] command in survival package

[Marc Schwartz]

> On Mon, 2006-01-23 at 10:52 -0800, Thomas Lumley wrote:
> > On Mon, 23 Jan 2006, Linda Lei wrote:
> > 
> > > Thank you guys.
> > > But I tried the commands and I still get:
> > >
> > >> aml1<-aml[aml$group==1,]
> > >> aml1
> > > [1] time   status x
> > > <0 rows> (or 0-length row.names)
> > >> esf.fit <- survfit(Surv(aml1$weeks,status) ~ 1)
> > > Error in Surv(aml1$weeks, status) : Time variable is not numeric
> > > In addition: Warning message:
> > > is.na() applied to non-(list or vector) in: is.na(time)
> > >
> > > which still looks confusing. Or are they should be applied in
> s-plus
> > > instead of R?
> > 
> > You *still* haven't said where the aml dataset comes from, but as I
> said 
> > before, it isn't the same as the one built in to R, so you need to
> load it 
> > somehow.  The one in R has columns called "time", "status" and "x";
> you 
> > appear to want one with columns "weeks","status", and "group", and
> with 
> > "group" being numeric rather than factor.
> > 
> > 
> >  	-thomas
> 
> 
> I don't have the book with me (it's at home), but I suspect that the
> problem here is that the 'aml' dataset provided at the aforementioned
> web site: 
> 
> 
> http://www.crcpress.com/e_products/downloads/download.asp?cat_no=C4088
> 
> which is to be used with the code under discussion, was more than
> likely
> not imported into an R session by Linda.
> 
> Since one needs to do a:
> 
>   > library(survival) 
> 
> to utilize the R code examples, that loads that package's 'aml'
> dataset,
> resulting in:
> 
>   > aml[aml$group==1,]
> [1] time   status x     
> <0 rows> (or 0-length row.names)
> 
> since there is no 'group' column in the built in 'aml' dataset as
> Thomas
> points out.
> 
> There is such a structure to the authors' version of the dataset:
> 
> > str(read.table("aml.txt", header = TRUE))
> `data.frame':	23 obs. of  3 variables:
>  $ weeks : num  9 13 13 18 23 28 31 34 45 48 ...
>  $ group : num  1 1 1 1 1 1 1 1 1 1 ...
>  $ status: num  1 1 0 1 1 0 1 1 0 1 ...
> 
> 
> Thus:
> 
> >  aml <- read.table("aml.txt", header = TRUE)
> 
> > (aml1 <- aml[aml$group==1,])
>    weeks group status
> 1      9     1      1
> 2     13     1      1
> 3     13     1      0
> 4     18     1      1
> 5     23     1      1
> 6     28     1      0
> 7     31     1      1
> 8     34     1      1
> 9     45     1      0
> 10    48     1      1
> 11   161     1      0
> 
> 
> This bring us to the still remaining error in the authors' survival
> code, which is not fully corrected in the authors' online errata:
> 
> > esf.fit <- survfit(Surv(aml1$weeks,status) ~ 1)
> Error in Surv(aml1$weeks, status) : object "status" not found
> 
> 
> Thus, something like one of the following should be used instead:
> 
> > esf.fit <- survfit(Surv(aml1$weeks, aml1$status) ~ 1)
> 
> > esf.fit <- with(aml1, survfit(Surv(weeks, status) ~ 1))

Hi all,

A quick follow up here. Prof. Kim, one of the authors for the book in
question, replied to my e-mail of earlier today.

There are two issues here:

1. The confounding of the two versions of the 'aml' data set, which has
been identified above. Linda needs to be sure to import the authors'
version of the data set to be able to follow along with the code
examples and exercises in the book. 



2. In the code that Linda posted above, in combination with my not
having the book at hand earlier today, there is a single critical line
of code missing that impacts my reply with respect to the final couple
of statements.

The three full lines of code should be:

  aml1 <- aml[aml$group==1,]

  status <- rep(1, 11)

  esf.fit <- survfit(Surv(aml1$weeks,status) ~ 1)


The middle line, creating the local vector 'status', is why the code
that appears corrected in the errata does in fact work and why my
corrections above are not required. 

Hope those clarifications help.

Marc Schwartz