Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

pariwise_survdiff throws unusual error when a model with strata is used #648

Open
dryals opened this issue Mar 14, 2024 · 0 comments
Open

Comments

@dryals
Copy link

dryals commented Mar 14, 2024

Expected behavior

I'm attempting to analyse a survival model with strata using pariwise_survdiff

Actual behavior

pairwise_survdiff(Surv(time, status) ~ effect1 + strata(strata1), data = data)

produces the error

Error in '[.data.frame'(data, , group_var, drop = FALSE) : undefined columns selected

for reference, the same model without strata:

pairwise_survdiff(Surv(time, status) ~ effect1, data = data)

works as expected. Also, using a different function with strata

survdiff(Surv(time, status) ~ effect1 + strata(strata1), data = data)

works as expected.

Steps to reproduce the problem

attempting to fit a model using strata

pairwise_survdiff(Surv(time, status) ~ effect1 + strata(strata1), data = data)

session_info()

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.2 (2023-10-31)
 os       Manjaro Linux
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Indiana/Indianapolis
 date     2024-03-14
 rstudio  2023.12.1+402 Ocean Storm (desktop)
 pandoc   3.1.8 @ /usr/bin/pandoc

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 abind          1.4-5   2016-07-21 [1] CRAN (R 4.3.0)
 backports      1.4.1   2021-12-13 [1] CRAN (R 4.3.0)
 broom          1.0.5   2023-06-09 [1] CRAN (R 4.3.2)
 cachem         1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
 car            3.1-2   2023-03-30 [1] CRAN (R 4.3.0)
 carData        3.0-5   2022-01-06 [1] CRAN (R 4.3.0)
 cellranger     1.1.0   2016-07-27 [1] CRAN (R 4.3.0)
 cli            3.6.2   2023-12-11 [1] CRAN (R 4.3.2)
 colorspace     2.1-0   2023-01-23 [1] CRAN (R 4.3.0)
 data.table     1.14.10 2023-12-08 [1] CRAN (R 4.3.2)
 devtools       2.4.5   2022-10-11 [1] CRAN (R 4.3.2)
 digest         0.6.33  2023-07-07 [2] CRAN (R 4.3.1)
 dplyr        * 1.1.4   2023-11-17 [1] CRAN (R 4.3.2)
 ellipsis       0.3.2   2021-04-29 [2] CRAN (R 4.3.1)
 fansi          1.0.6   2023-12-08 [1] CRAN (R 4.3.2)
 farver         2.1.1   2022-07-06 [1] CRAN (R 4.3.0)
 fastmap        1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
 forcats      * 1.0.0   2023-01-29 [1] CRAN (R 4.3.0)
 fs             1.6.3   2023-07-20 [2] CRAN (R 4.3.1)
 generics       0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
 ggplot2      * 3.4.4   2023-10-12 [1] CRAN (R 4.3.2)
 ggpubr       * 0.6.0   2023-02-10 [1] CRAN (R 4.3.0)
 ggrepel      * 0.9.4   2023-10-13 [1] CRAN (R 4.3.2)
 ggsignif       0.6.4   2022-10-13 [1] CRAN (R 4.3.1)
 glue           1.6.2   2022-02-24 [2] CRAN (R 4.3.1)
 gridExtra      2.3     2017-09-09 [1] CRAN (R 4.3.0)
 gtable         0.3.4   2023-08-21 [1] CRAN (R 4.3.2)
 hms            1.1.3   2023-03-21 [1] CRAN (R 4.3.0)
 htmltools      0.5.7   2023-11-03 [1] CRAN (R 4.3.2)
 htmlwidgets    1.6.4   2023-12-06 [1] CRAN (R 4.3.2)
 httpuv         1.6.13  2023-12-06 [1] CRAN (R 4.3.2)
 km.ci          0.5-6   2022-04-06 [1] CRAN (R 4.3.0)
 KMsurv         0.1-5   2012-12-03 [1] CRAN (R 4.3.0)
 knitr          1.45    2023-10-30 [2] CRAN (R 4.3.2)
 labeling       0.4.3   2023-08-29 [1] CRAN (R 4.3.2)
 later          1.3.2   2023-12-06 [1] CRAN (R 4.3.2)
 lattice        0.22-5  2023-10-24 [1] CRAN (R 4.3.2)
 lifecycle      1.0.4   2023-11-07 [2] CRAN (R 4.3.2)
 lubridate    * 1.9.3   2023-09-27 [1] CRAN (R 4.3.2)
 magrittr       2.0.3   2022-03-30 [2] CRAN (R 4.3.0)
 Matrix         1.6-5   2024-01-11 [1] CRAN (R 4.3.2)
 memoise        2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
 mime           0.12    2021-09-28 [1] CRAN (R 4.3.0)
 miniUI         0.1.1.1 2018-05-18 [1] CRAN (R 4.3.2)
 munsell        0.5.0   2018-06-12 [1] CRAN (R 4.3.0)
 pillar         1.9.0   2023-03-22 [2] CRAN (R 4.3.0)
 pkgbuild       1.4.3   2023-12-10 [1] CRAN (R 4.3.2)
 pkgconfig      2.0.3   2019-09-22 [2] CRAN (R 4.3.1)
 pkgload        1.3.3   2023-09-22 [2] CRAN (R 4.3.1)
 profvis        0.3.8   2023-05-02 [1] CRAN (R 4.3.2)
 promises       1.2.1   2023-08-10 [1] CRAN (R 4.3.2)
 purrr        * 1.0.2   2023-08-10 [1] CRAN (R 4.3.2)
 R6             2.5.1   2021-08-19 [2] CRAN (R 4.3.0)
 RColorBrewer   1.1-3   2022-04-03 [1] CRAN (R 4.3.0)
 Rcpp           1.0.11  2023-07-06 [1] CRAN (R 4.3.2)
 readr        * 2.1.4   2023-02-10 [1] CRAN (R 4.3.0)
 readxl       * 1.4.3   2023-07-06 [1] CRAN (R 4.3.2)
 remotes        2.4.2.1 2023-07-18 [1] CRAN (R 4.3.2)
 rlang          1.1.2   2023-11-04 [2] CRAN (R 4.3.2)
 rstatix        0.7.2   2023-02-01 [1] CRAN (R 4.3.0)
 rstudioapi     0.15.0  2023-07-07 [2] CRAN (R 4.3.2)
 scales         1.3.0   2023-11-28 [1] CRAN (R 4.3.2)
 sessioninfo    1.2.2   2021-12-06 [1] CRAN (R 4.3.2)
 shiny          1.8.0   2023-11-17 [1] CRAN (R 4.3.2)
 stringi        1.8.3   2023-12-11 [1] CRAN (R 4.3.2)
 stringr      * 1.5.1   2023-11-14 [1] CRAN (R 4.3.2)
 survival     * 3.5-8   2024-02-14 [1] CRAN (R 4.3.2)
 survminer    * 0.4.9   2021-03-09 [1] CRAN (R 4.3.0)
 survMisc       0.5.6   2022-04-07 [1] CRAN (R 4.3.0)
 tibble       * 3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
 tidyr        * 1.3.0   2023-01-24 [1] CRAN (R 4.3.0)
 tidyselect     1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
 tidyverse    * 2.0.0   2023-02-22 [1] CRAN (R 4.3.0)
 timechange     0.2.0   2023-01-11 [1] CRAN (R 4.3.0)
 tzdb           0.4.0   2023-05-12 [1] CRAN (R 4.3.0)
 urlchecker     1.0.1   2021-11-30 [1] CRAN (R 4.3.2)
 usethis        2.2.3   2024-02-19 [1] CRAN (R 4.3.2)
 utf8           1.2.4   2023-10-22 [2] CRAN (R 4.3.2)
 vctrs          0.6.5   2023-12-01 [1] CRAN (R 4.3.2)
 withr          2.5.2   2023-10-30 [2] CRAN (R 4.3.2)
 xfun           0.41    2023-11-01 [2] CRAN (R 4.3.2)
 xtable         1.8-4   2019-04-21 [1] CRAN (R 4.3.0)
 zoo            1.8-12  2023-04-13 [1] CRAN (R 4.3.0)

 [1] /home/dylan/R/x86_64-pc-linux-gnu-library/4.3
 [2] /usr/lib/R/library
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant