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insightsengineering / tern

Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials
https://insightsengineering.github.io/tern/
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[Bug]: `var_labels` not work for ` estimate_odds_ratio` #1315

Closed lchensigma closed 1 month ago

lchensigma commented 1 month ago

What happened?

A bug happened!

nex <- 800 # Number of example rows
dta <- data.frame(
  "is_event" = sample(c(TRUE, FALSE), nex, TRUE),
  "TRT01P" = sample(c("A", "B"), nex, TRUE),
  "f1" = sample(c("a1", "a2"), nex, TRUE),
  "f2" = sample(c("x", "y", "z"), nex, TRUE),
  "BLSTRA" = factor(sample(c("C", "D"), nex, TRUE)),
  stringsAsFactors = TRUE
)

lyt_proportion <- basic_table( ) %>% 
  split_cols_by(var = "TRT01P", ref_group = "A") %>%
  estimate_proportion(
    vars = "is_event",
    table_names = "prop",
    .labels = c("Response Rate n (%)", "95% CI (Clopper-Pearson)[1]"),
    method = "clopper-pearson"
  ) |>
estimate_proportion_diff(
    var_labels = "Stratified Analysis [2]",
    vars = "is_event",
    show_labels = "visible",
    method = "cmh",
    variables = list(strata = "BLSTRA"),
    table_names = "est_prop_diff_strat"
  ) %>%
  estimate_odds_ratio(
    vars = "is_event",
    var_labels = "Stratified OR Analysis [2]",
    show_labels = "visible",
    table_names = "est_or_strata",
    variables = list(arm = "TRT01P", strata = "BLSTRA"),
    .labels = "Stratified Odds Ratio (95% CI)",
    .indent_mods = 1L
  ) 

result_proportion <- build_table(
  lyt = lyt_proportion,
  df = dta
)

result_proportion %>% tt_to_flextable()

sessionInfo()

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] optimx_2023-10.21   emmeans_1.10.4      forestploter_1.1.2  tern.mmrm_0.3.1     scda_0.1.6         
 [6] tern_0.9.5          haven_2.5.4         rtables_0.6.9       magrittr_2.0.3      formatters_0.5.9   
[11] rstan_2.32.6        StanHeaders_2.32.10 tidybayes_3.0.7     bayesplot_1.11.1    brms_2.21.0        
[16] Rcpp_1.0.13         dreamer_3.1.0       DoseFinding_1.2-1   labelled_2.13.0     gt_0.11.0          
[21] flextable_0.9.6     broom_1.0.6         readxl_1.4.3        boxr_0.3.6          pander_0.6.5       
[26] patchwork_1.3.0     ggprism_1.0.5       gtsummary_2.0.2     ggthemes_5.1.0      plyr_1.8.9         
[31] knitr_1.48          lubridate_1.9.3     forcats_1.0.0       stringr_1.5.1       dplyr_1.1.4        
[36] purrr_1.0.2         readr_2.1.5         tidyr_1.3.1         tibble_3.2.1        ggplot2_3.5.1      
[41] tidyverse_2.0.0    

loaded via a namespace (and not attached):
  [1] tensorA_0.36.2.1        rstudioapi_0.16.0       jsonlite_1.8.8          TH.data_1.1-2          
  [5] estimability_1.5.1      nloptr_2.1.1            farver_2.1.2            rmarkdown_2.28         
  [9] ragg_1.3.3              vctrs_0.6.5             askpass_1.2.0           htmltools_0.5.8.1      
 [13] distributional_0.5.0    curl_5.2.2              cellranger_1.1.0        pracma_2.4.4           
 [17] parallelly_1.38.0       sandwich_3.1-1          zoo_1.8-12              uuid_1.2-1             
 [21] lifecycle_1.0.4         pkgconfig_2.0.3         Matrix_1.6-5            R6_2.5.1               
 [25] fastmap_1.2.0           rbibutils_2.2.16        numDeriv_2016.8-1.1     digest_0.6.37          
 [29] colorspace_2.1-1        rprojroot_2.0.4         textshaping_0.4.0       fansi_1.0.6            
 [33] timechange_0.3.0        abind_1.4-8             compiler_4.3.1          here_1.0.1             
 [37] fontquiver_0.2.1        withr_3.0.1             backports_1.5.0         inline_0.3.19          
 [41] QuickJSR_1.3.1          pkgbuild_1.4.4          MASS_7.3-60.0.1         openssl_2.2.1          
 [45] equatags_0.2.1          loo_2.8.0               tools_4.3.1             zip_2.3.1              
 [49] glue_1.7.0              mmrm_0.3.12             nlme_3.1-166            grid_4.3.1             
 [53] checkmate_2.3.2         generics_0.1.3          xslt_1.4.5              gtable_0.3.5           
 [57] tzdb_0.4.0              data.table_1.16.0       hms_1.1.3               katex_1.4.1            
 [61] xml2_1.3.6              utf8_1.2.4              pillar_1.9.0            ggdist_3.3.2           
 [65] posterior_1.6.0         splines_4.3.1           lattice_0.22-6          survival_3.7-0         
 [69] tidyselect_1.2.1        fontLiberation_0.1.0    fontBitstreamVera_0.1.1 arrayhelpers_1.1-0     
 [73] gridExtra_2.3           V8_5.0.0                stats4_4.3.1            xfun_0.47              
 [77] bridgesampling_1.1-2    matrixStats_1.4.1       stringi_1.8.4           yaml_2.3.10            
 [81] evaluate_1.0.0          codetools_0.2-19        officer_0.6.6           gdtools_0.4.0          
 [85] cli_3.6.3               RcppParallel_5.1.9      xtable_1.8-4            systemfonts_1.1.0      
 [89] Rdpack_2.6.1            munsell_0.5.1           coda_0.19-4.1           svUnit_1.0.6           
 [93] parallel_4.3.1          rstantools_2.4.0        Brobdingnag_1.2-9       mvtnorm_1.3-1          
 [97] scales_1.3.0            rlang_1.1.4             cowplot_1.1.3           multcomp_1.4-26

Relevant log output

Stratified Analysis [2]

Difference in Response rate (%)

5.5

95% CI (CMH, without correction)

(-1.4, 12.4)

p-value (Cochran-Mantel-Haenszel Test)

0.1183

is_event

Stratified Odds Ratio (95% CI)

1.25 (0.95 - 1.65)

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