Incorrect denom counts when creating combined treatment group

snehagaddam commented 4 years ago

Description

[Description of the bug or feature]

Steps to Reproduce (Bug Report Only)

I executed the following code:

adae_table <- tplyr_table(adae, TRTA) %>%
  add_treat_grps("Treated" = c("Xanomeline High Dose", "Xanomeline Low Dose")) %>%
  add_layer(
    group_count(AEDECOD) %>%
      set_distinct_by(USUBJID) %>% 
      set_nest_count(TRUE)
  )

adae_build <- adae_table %>%
  build()

Expected behavior: The creation of a combined treatment group named "Treated", and accurately calculated summary statistics for all treatment groups.

Actual behavior: While a new treatment group named "Treated" was created, and denominator counts and percentages were correctly calculated, this is not the case for the original two treatment groups. "Xanomeline High Dose" and "Xanomeline Low Dose" denominator counts are not being correctly calculated, causing the percentages to be rendered as "(Inf%)".

Versions

R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] huxtable_5.0.0 magrittr_1.5 Tplyr_0.1.1 forcats_0.5.0 stringr_1.4.0 [6] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0 tibble_3.0.3 [11] ggplot2_3.3.2 tidyverse_1.3.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.5 cellranger_1.1.0 pillar_1.4.6 compiler_4.0.2 dbplyr_1.4.4 [6] odbc_1.2.3 tools_4.0.2 bit_1.1-15.2 lubridate_1.7.9 jsonlite_1.7.0 [11] lifecycle_0.2.0 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.7 reprex_0.3.0 [16] cli_2.0.2 DBI_1.1.0 rstudioapi_0.11 yaml_2.2.1 haven_2.3.1 [21] xfun_0.15 withr_2.2.0 xml2_1.3.2 httr_1.4.2 knitr_1.29 [26] fs_1.4.2 hms_0.5.3 generics_0.0.2 vctrs_0.3.2 bit64_0.9-7.1 [31] grid_4.0.2 tidyselect_1.1.0 glue_1.4.1 R6_2.4.1 fansi_0.4.1 [36] readxl_1.3.1 modelr_0.1.8 blob_1.2.1 backports_1.1.8 scales_1.1.1 [41] ellipsis_0.3.1 rvest_0.3.5 assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.6 [46] munsell_0.5.0 broom_0.7.0 crayon_1.3.4

elimillera commented 4 years ago

@snehagaddam thanks for the issue! The dplyr::distinct() function didn't include !!treat_var in count.R which would cause it to remove the rows of the grouped treatments. See PR 370: Fix bug for pcts when there is a distinct_by and a custom group for the fix.

This has been resolved on GitHub and CRAN with the release of 0.1.2.

mstackhouse commented 4 years ago

Just writing to note that this update is up and posted to CRAN.

snehagaddam commented 4 years ago

Thanks for the update!

atorus-research / Tplyr