survminer
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kassambara
Missing at risk table using ggsurvplot_df
Expected behavior
When I use ggsurvplot(survivalobject, risk.table = TRUE) I see a nice graph with associated at risk table. In fact, one of my personal reasons for using survminer is the nicely formatted and placed at risk table.
Another option for creating the curve is to generate a summary table using surv_summary(survivalobject), and then get the graph with ggsurvplot(surv_summary(survivalobject), risk.table = TRUE). Since the output from surv_summary(survivalobject) contains the n.risk column I expected to also get the risk table. No such luck.
My underlying objective is visualize a survival curve created by another method, as suggested in the ggsurvplot_df documentation. I want the at risk table also.
Actual behavior
When I use ggsurvplot(surv_summary(survivalobject), risk.table = TRUE) I do not get the at risk table. This is true even though surv_summary(survivalobject) does contain an n.risk column.
I dug through the documentation, and in fact the risk.table is not an option for ggsurvplot_df, so perhaps the missing at risk table should not surprise me. But I really want that at risk table. I suppose I could create a phony survival object, but that seems a real hack.
Steps to reproduce the problem
I tried this on the sample data sets from both the survminer and survival packages. Always the same result. No at risk table and no error message.
session_info()
# please paste here the result of
devtools::session_info()
>
> devtools::session_info()
- Session info ---------------------------------------------------------------
setting value
version R version 3.6.0 (2019-04-26)
os Windows 10 x64
system x86_64, mingw32
ui Rgui
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Los_Angeles
date 2019-07-15
- Packages -------------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
broom 0.5.2 2019-04-07 [1] CRAN (R 3.6.0)
callr 3.2.0 2019-03-15 [1] CRAN (R 3.6.0)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
cmprsk 2.2-8 2019-05-27 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
data.table 1.12.2 2019-04-07 [1] CRAN (R 3.6.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools * 2.1.0 2019-07-06 [1] CRAN (R 3.6.1)
digest 0.6.19 2019-05-20 [1] CRAN (R 3.6.0)
dplyr 0.8.1 2019-05-14 [1] CRAN (R 3.6.0)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.0)
ggplot2 * 3.2.0 2019-06-16 [1] CRAN (R 3.6.0)
ggpubr * 0.2 2018-11-15 [1] CRAN (R 3.6.0)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
km.ci 0.5-2 2009-08-30 [1] CRAN (R 3.6.0)
KMsurv 0.1-5 2012-12-03 [1] CRAN (R 3.6.0)
knitr 1.23 2019-05-18 [1] CRAN (R 3.6.0)
labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
magrittr * 1.5 2014-11-22 [1] CRAN (R 3.6.0)
Matrix 1.2-17 2019-03-22 [2] CRAN (R 3.6.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
nlme 3.1-139 2019-04-09 [2] CRAN (R 3.6.0)
pillar 1.4.1 2019-05-28 [1] CRAN (R 3.6.0)
pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.6.1)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.3.1 2019-05-08 [1] CRAN (R 3.6.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.0)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
Rcpp 1.0.1 2019-03-17 [1] CRAN (R 3.6.0)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
rlang 0.3.4 2019-04-07 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
survival * 2.44-1.1 2019-04-01 [2] CRAN (R 3.6.0)
survminer * 0.4.4 2019-05-21 [1] CRAN (R 3.6.0)
survMisc 0.5.5 2018-07-05 [1] CRAN (R 3.6.0)
testthat 2.1.1 2019-04-23 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
tidyr 0.8.3 2019-03-01 [1] CRAN (R 3.6.0)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
xfun 0.7 2019-05-14 [1] CRAN (R 3.6.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0)
zoo 1.8-6 2019-05-28 [1] CRAN (R 3.6.0)
I never did find a solution using the package. I just worked around it, and I have now moved on to other things.
Bill
Sent from my iPad
On Jun 6, 2022, at 4:45 AM, ApexHeel @.***> wrote:
Did you ever find a solution to this? I'm having the same issue.
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