[R] Trouble getting rms::survplot(..., n.risk=TRUE) to behave properly

[Steve Lianoglou]

Ah!

Sorry ... should have dug deeper into the examples section to notice that.

Thank you for the quick reply,
-steve


On Thu, Jun 2, 2016 at 8:59 AM, Frank Harrell <f.harrell at vanderbilt.edu> wrote:
> This happens when you have not strat variables in the model.
>
>
> ------------------------------
> Frank E Harrell Jr      Professor and Chairman      School of Medicine
>
> Department of *Biostatistics*      *Vanderbilt University*
>
> On Thu, Jun 2, 2016 at 10:55 AM, Steve Lianoglou <lianoglou.steve at gene.com>
> wrote:
>
>> Hello foks,
>>
>> I'm trying to plot the number of patients at-risk by setting the
>> `n.risk` parameter to `TRUE` in the rms::survplot function, however it
>> looks as if the numbers presented in the rows for each category are
>> just summing up the total number of patients at risk in all groups for
>> each timepoint -- which is to say that the numbers are equal in each
>> category down the rows, and they don't seem to be the numbers specific
>> to each group.
>>
>> You can reproduce the observed behavior by simply running the code in
>> the Examples section of ?survplot, which I'll paste below for
>> convenience.
>>
>> Is the error between the chair and the keyboard, here, or is this perhaps
>> a bug?
>>
>> =========== code ===========
>> library(rms)
>> n <- 1000
>> set.seed(731)
>> age <- 50 + 12*rnorm(n)
>> label(age) <- "Age"
>> sex <- factor(sample(c('Male','Female'), n, rep=TRUE, prob=c(.6, .4)))
>> cens <- 15*runif(n)
>> h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
>> dt <- -log(runif(n))/h
>> label(dt) <- 'Follow-up Time'
>> e <- ifelse(dt <= cens,1,0)
>> dt <- pmin(dt, cens)
>> units(dt) <- "Year"
>> dd <- datadist(age, sex)
>> options(datadist='dd')
>> S <- Surv(dt,e)
>>
>> f <- cph(S ~ rcs(age,4) + sex, x=TRUE, y=TRUE)
>> survplot(f, sex, n.risk=TRUE)
>> ===========
>>
>> I'm using the latest version of rms (4.5-0) running on R 3.3.0-patched.
>>
>> === Output o sessionInfo() ===
>> R version 3.3.0 Patched (2016-05-26 r70671)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: OS X 10.11.4 (El Capitan)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] rms_4.5-0       SparseM_1.7     Hmisc_3.17-4    ggplot2_2.1.0
>> [5] Formula_1.2-1   survival_2.39-4 lattice_0.20-33
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.5         cluster_2.0.4       MASS_7.3-45
>>  [4] splines_3.3.0       munsell_0.4.3       colorspace_1.2-6
>>  [7] multcomp_1.4-5      plyr_1.8.3          nnet_7.3-12
>> [10] grid_3.3.0          data.table_1.9.6    gtable_0.2.0
>> [13] nlme_3.1-128        quantreg_5.24       TH.data_1.0-7
>> [16] latticeExtra_0.6-28 MatrixModels_0.4-1  polspline_1.1.12
>> [19] Matrix_1.2-6        gridExtra_2.2.1     RColorBrewer_1.1-2
>> [22] codetools_0.2-14    acepack_1.3-3.3     rpart_4.1-10
>> [25] sandwich_2.3-4      scales_0.4.0        mvtnorm_1.0-5
>> [28] foreign_0.8-66      chron_2.3-47        zoo_1.7-13
>> ===========================
>>
>>
>> Thanks,
>> -steve
>>
>>
>> --
>> Steve Lianoglou
>> Computational Biologist
>> Genentech
>>
>
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-- 
Steve Lianoglou
Computational Biologist
Genentech