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

[Frank Harrell]

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
>

	[[alternative HTML version deleted]]