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

[Steve Lianoglou]

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