Closed Nolan-Steed closed 2 months ago
When I generate an ard for some reason it orders the adverse event grades as 1, 3, 2. shown below. This variable is a factor and the levels are in the correct order 1, 2, 3.
Here is an example
library(dplyr) library(cards) library(rmarkdown) adae <- cards::ADAE |> dplyr::mutate(TRTA = factor(TRTA), AETOXGR = factor(case_when( AESEV == 'MILD' ~ '1', AESEV == 'MODERATE' ~ '2', AESEV == 'SEVERE' ~ '3' ), levels = c('1', '2', '3')), GRD_GRP = factor(case_when( AESEV == 'MILD' | AESEV == 'MODERATE' ~ 'Grade 1-2', AESEV == 'SEVERE' ~ 'Grade 3' ), levels = c('Grade 1-2', 'Grade 3'))) |> filter( .by = c(TRTA, AEBODSYS), AEBODSYS %in% c("CARDIAC DISORDERS", "EYE DISORDERS"), AEDECOD %in% AEDECOD[1:3] ) |> select(USUBJID, TRTA, AEBODSYS, AEDECOD, AETOXGR, GRD_GRP) adae$TOTAL_VAR <- "- Any adverse events - " card_ae_grd <- adae |> # keep on AE per SOC slice(1L, .by = c(USUBJID, TRTA, AETOXGR)) |> cards::ard_hierarchical( by = TRTA, variables = AETOXGR, denominator = adsl ) |> filter(stat_name %in% c("n", "p")) # If you uncomment these 2 lines it seems to fix the issue # |> # arrange(unlist(variable_level)) card_ae_grd
When I generate an ard for some reason it orders the adverse event grades as 1, 3, 2. shown below. This variable is a factor and the levels are in the correct order 1, 2, 3.
Here is an example