R help - May 2009 - Changelog for the survival package

>  Several changes in print.survfit, plot.survfit and seemingly in the
structure
> of ratetabels effect some of my syntax files.
> Is there somewhere a documentation of these changes, besides the code
itself?
 I agree, the Changelog.09 file is not as comprehensive as one would like.  
Specific comments:

 1. The ratetables were recently changed to accomodate a new option.  I thought 
that I had made them completely backwards compatable with the old -- please let 
me know specifics if I overlooked something.
  The routines that make use of the rate tables can now use multiple date types,
but they still support the older 'date' class.
  
  2. My local code and the R code had gotton badly out of sync, I spent a 
substantial fraction of my evenings re-merging them for over a year.  2/3 of the
changes were disjoint improvments in the two trees, these were easy to merge.  
The hardest were survfit and its print/plot methods and some summary methods, 
where both of us had worked towards the same goal but in not quite the same way.
  I had made 3x as many updates to survfit as the R tree, so used my (Mayo) code
as the base, almost all the others stayed closer to the R side.
  Feel free to ask me direct questions about any feature or change.  I can't
necessarily promise fast resolution, but will try.
  
  3. I don't understand putting legend or title options into a plot method, 
since a separate call after the plot is so much more flexible.  They got pushed 
to the bottom of my change list, and then completely forgotton. 
  
  4. In the last few weeks issues with anova.coxph, and 
predict.coxph/factors/newdata were raised.  The fixes were added to Rforge last 
night, and include 2 new test cases to avoid future mishaps.
  
   Terry T.

Dear Terry,

first of all, thank you for your immense work. At the moment, I don't 
have a small reproducible example for the ratetable difficulty I 
have. I will work on it. Maybe the error message I get is of some 
information to you.

Error in match.ratetable(m[, rate], ratetable) :
   Data has a date type variable, but the reference ratetable is not 
a date for variable year

If I want to make str(survexp.ode) that is my ratetable, I get:
str(survexp.ode)
Error in `[.ratetable`(object, seq_len(iv.len)) : Invalid subscript
The same, however, is possible in version 2.34-1^

Try:
str(survexp.us)
Error in `[.ratetable`(object, seq_len(iv.len)) : Invalid subscript

But with unclass() it works
str(unclass(survexp.us))
  num [1:113, 1:2, 1:65] 1.58e-02 1.87e-03 3.01e-04 6.05e-05 1.52e-05 ...
  - attr(*, "dimnames")=List of 3
   ..$ : chr [1:113] "0-1d" "1-7d" "7-28d"
"28-365d" ...
   ..$ : chr [1:2] "male" "female"
   ..$ : chr [1:65] "1940" "1941" "1942"
"1943" ...
  - attr(*, "dimid")= chr [1:3] "age" "sex"
"year"
  - attr(*, "type")= num [1:3] 2 1 4
  - attr(*, "cutpoints")=List of 3
   ..$ : num [1:113] 0 1 7 28 365 ...
   ..$ : NULL
   ..$ : int [1:65] -7305 -6939 -6574 -6209 -5844 -5478 -5113 -4748 
-4383 -4017 ...
  - attr(*, "summary")=function (R)
 >

Concerning the legend, I fully aggree with you. It's just that I have 
several syntax files, where I made use of the legend parameters and 
so I noted the change. For these files I rebuilt your old plot.survfit().

Further I appreciate your new function survmean(). At the moment it 
seems to be intended as internal, and not documented in the help. 
Still, I use it to get the old form of the output and to get the 
output as an object. I think, with only right censored data, n.max 
and n.start are not informative.

To underline, I appreciate your changes, it's only a little difficult 
to recognize them correctly by trial and error.

Thanks,
Heinz

At 18:57 21.05.2009, Terry Therneau wrote:
> >  Several changes in print.survfit, plot.survfit and seemingly in 
> the structure
> > of ratetabels effect some of my syntax files.
> > Is there somewhere a documentation of these changes, besides the 
> code itself?
>
>  I agree, the Changelog.09 file is not as comprehensive as one would like.
>Specific comments:
>
>  1. The ratetables were recently changed to accomodate a new 
> option.  I thought
>that I had made them completely backwards compatable with the old -- 
>please let
>me know specifics if I overlooked something.
>   The routines that make use of the rate tables can now use 
> multiple date types,
>but they still support the older 'date' class.
>
>   2. My local code and the R code had gotton badly out of sync, I spent a
>substantial fraction of my evenings re-merging them for over a 
>year.  2/3 of the
>changes were disjoint improvments in the two trees, these were easy 
>to merge.
>The hardest were survfit and its print/plot methods and some summary
methods,
>where both of us had worked towards the same goal but in not quite 
>the same way.
>   I had made 3x as many updates to survfit as the R tree, so used 
> my (Mayo) code
>as the base, almost all the others stayed closer to the R side.
>   Feel free to ask me direct questions about any feature or change.  I
can't
>necessarily promise fast resolution, but will try.
>
>   3. I don't understand putting legend or title options into a plot
method,
>since a separate call after the plot is so much more flexible.  They 
>got pushed
>to the bottom of my change list, and then completely forgotton.
>
>   4. In the last few weeks issues with anova.coxph, and
>predict.coxph/factors/newdata were raised.  The fixes were added to 
>Rforge last
>night, and include 2 new test cases to avoid future mishaps.
>
>    Terry T.
>
>