tm_t_events_by_grade - bug in grading_groups when using >= #1377
Description
What happened?
The following code (mostly taken from the example you have documented aside from me adding in the grading_groups) works fine.
library(dplyr)
data <- teal_data()
data <- within(data, {
ADSL <- tmc_ex_adsl
.lbls_adae <- col_labels(tmc_ex_adae)
ADAE <- tmc_ex_adae %>%
mutate_if(is.character, as.factor) #' be certain of having factors
col_labels(ADAE) <- .lbls_adae
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]
app <- init(
data = data,
modules = modules(
tm_t_events_by_grade(
label = "Adverse Events by Grade Table",
dataname = "ADAE",
arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
llt = choices_selected(
choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
selected = c("AEDECOD")
),
hlt = choices_selected(
choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
selected = "AEBODSYS"
),
grade = choices_selected(
choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
selected = "AETOXGR"
),
grading_groups = list(`Any Grade (%)` = c("1", "2", "3", "4", "5"),
`Grade 1 (%)` = c("1"), `Grade 2 (%)` = c("2"), `Grade 3 (%)` = c("3"), `Grade 4 (%)` = c("4"), `Grade 5 (%)` = c("5"), `Grade 3-5 (%)` = c("3", "4", "5"))
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}If you run the above code and then check the "Display grade groupings in nested columns" box, we see the desired output.
However, when i switch to use Grade >= 3 instead of Grade 3-5 and then check the "Display grade groupings in nested columns" box, the app does not run. I think it does not like the >= in some cases?
Non-working code:
library(dplyr)
data <- teal_data()
data <- within(data, {
ADSL <- tmc_ex_adsl
.lbls_adae <- col_labels(tmc_ex_adae)
ADAE <- tmc_ex_adae %>%
mutate_if(is.character, as.factor) #' be certain of having factors
col_labels(ADAE) <- .lbls_adae
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]
app <- init(
data = data,
modules = modules(
tm_t_events_by_grade(
label = "Adverse Events by Grade Table",
dataname = "ADAE",
arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
llt = choices_selected(
choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
selected = c("AEDECOD")
),
hlt = choices_selected(
choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
selected = "AEBODSYS"
),
grade = choices_selected(
choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
selected = "AETOXGR"
),
grading_groups = list(`Any Grade (%)` = c("1", "2", "3", "4", "5"),
`Grade 1 (%)` = c("1"), `Grade 2 (%)` = c("2"), `Grade 3 (%)` = c("3"), `Grade 4 (%)` = c("4"), `Grade 5 (%)` = c("5"), `Grade >=3 (%)` = c("3", "4", "5"))
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.10 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] forcats_1.0.0 teal.widgets_0.4.3 DT_0.33 openxlsx_4.2.8 fs_1.6.5
[6] stringr_1.5.1 tidyr_1.3.1 haven_2.5.4 dplyr_1.1.4 tibble_3.2.1
[11] teal.reporter_0.4.0 httr2_1.1.0 junco_0.0.1 tidytlg_0.1.5 teal.modules.clinical.jnj_0.1.3
[16] teal.modules.general_0.4.0 ggmosaic_0.3.3 ggplot2_3.5.1 teal.modules.clinical_0.10.0 tern_0.9.7
[21] rtables_0.6.11 magrittr_2.0.3 formatters_0.5.10 teal.transform_0.6.0 teal_0.16.0
[26] teal.slice_0.6.0 teal.data_0.7.0 teal.code_0.6.1 shiny_1.10.0
loaded via a namespace (and not attached):
[1] rstudioapi_0.17.1 jsonlite_1.9.0 nestcolor_0.1.3 TH.data_1.1-3 estimability_1.5.1 farver_2.1.2 rmarkdown_2.29 geepack_1.3.12
[9] vctrs_0.6.5 memoise_2.0.1 askpass_1.2.1 htmltools_0.5.8.1 broom_1.0.7 cellranger_1.1.0 gridGraphics_0.5-1 sass_0.4.9
[17] huxtable_5.5.7 bslib_0.9.0 htmlwidgets_1.6.4 fontawesome_0.5.3 sandwich_3.1-1 emmeans_1.10.7 plotly_4.10.4 zoo_1.8-13
[25] cachem_1.1.0 mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-1 R6_2.6.1 fastmap_1.2.0 rbibutils_2.3
[33] digest_0.6.37 colorspace_2.1-1 patchwork_1.3.0 shinycssloaders_1.1.0 crosstalk_1.2.1 httr_1.4.7 compiler_4.4.1 withr_3.0.2
[41] backports_1.5.0 logger_0.4.0 MASS_7.3-61 rappdirs_0.3.3 tools_4.4.1 zip_2.3.2 httpuv_1.6.15 shinyvalidate_0.1.3
[49] glue_1.8.0 nlme_3.1-166 promises_1.3.2 grid_4.4.1 checkmate_2.3.2 generics_0.1.3 gtable_0.3.6 tzdb_0.4.0
[57] data.table_1.17.0 hms_1.1.3 ggrepel_0.9.6 pillar_1.10.1 yulab.utils_0.2.0 later_1.4.1 splines_4.4.1 tern.gee_0.1.5
[65] lattice_0.22-6 renv_1.0.7 survival_3.7-0 tidyselect_1.2.1 knitr_1.49 teal.logger_0.3.2 xfun_0.51 stringi_1.8.4
[73] lazyeval_0.2.2 yaml_2.3.10 shinyWidgets_0.9.0 evaluate_1.0.3 codetools_0.2-20 ggplotify_0.1.2 cli_3.6.4 xtable_1.8-4
[81] Rdpack_2.6.2 munsell_0.5.1 jquerylib_0.1.4 Rcpp_1.0.14 readxl_1.4.3 png_0.1-8 readr_2.1.5 assertthat_0.2.1
[89] viridisLite_0.4.2 mvtnorm_1.3-3 scales_1.3.0 purrr_1.0.4 crayon_1.5.3 rlang_1.1.5 cowplot_1.1.3 multcomp_1.4-28
[97] shinyjs_2.1.0Relevant log output
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