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Replace TealData with teal_data in the docs #845

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Replace TealData with teal_data in the docs #845

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b5c3b8a
refactoring cdisc_dataset() call to return teal_data()
kartikeyakirar Nov 7, 2023
d79eff1
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 7, 2023
2bfb054
adding code for reproducibility and updated news
kartikeyakirar Nov 8, 2023
3a11031
Merge branch '842_replace_tealdata@main' of https://github.com/insigh…
kartikeyakirar Nov 8, 2023
07fd195
fixing join_key issues.
kartikeyakirar Nov 8, 2023
f3d6296
included code vignettes and fixing notes
kartikeyakirar Nov 8, 2023
a5643f4
addressing comment.
kartikeyakirar Nov 8, 2023
bbbee71
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 8, 2023
cb4bccc
fixing styling and rd files
kartikeyakirar Nov 8, 2023
00ecbf5
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 8, 2023
b560850
'Empty-Commit'
kartikeyakirar Nov 9, 2023
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4 changes: 2 additions & 2 deletions R/tm_a_gee.R
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Expand Up @@ -143,8 +143,8 @@ template_a_gee <- function(output_table,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADQS", adqs)
Comment on lines -146 to -147
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I know this was not the case before, But I think we should make the teal_data object reproducible so that the code in the Show R code works. Right now it won't work because the data creation code is not specified.

@kartikeyakirar what do you think about adding it for all the examples so they are improved?

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I think its good idea. However, considering that these are for example for TMC modules and the preprocessing code be lengthy in some cases, which in turn might elongate the 'cdisc_data' call, I would lean towards not including it in for all the examples.
@gogonzo @donyunardi WDYT?

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@vedhav vedhav Nov 7, 2023 •
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I think there is no need to specify the code anymore, we have the new within() function. I think we need to document it as I believe it's the best practice.

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There are very few examples like that, and it's included in most of the tmg examples. I will make the update.

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@vedhav I think this qualifies to another issue. @kartikeyakirar feel free to make code reproducible or keep as reproducible as it was before. We need this soon on @main so I advise to make this branch ready as quick as possible.

#' ADSL = adsl,
#' ADQS = adqs
#' ),
#' modules = modules(
#' tm_a_gee(
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4 changes: 2 additions & 2 deletions R/tm_a_mmrm.R
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Expand Up @@ -473,8 +473,8 @@ template_mmrm_plots <- function(fit_name,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADQS", adqs)
#' ADSL = adsl,
#' ADQS = adqs
#' ),
#' modules = modules(
#' tm_a_mmrm(
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4 changes: 2 additions & 2 deletions R/tm_g_barchart_simple.R
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Expand Up @@ -22,8 +22,8 @@
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = adsl,
#' ADAE = adae
#' ),
#' modules = modules(
#' tm_g_barchart_simple(
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4 changes: 2 additions & 2 deletions R/tm_g_ci.R
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Expand Up @@ -197,8 +197,8 @@ template_g_ci <- function(dataname, # nolint
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_g_ci(
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4 changes: 2 additions & 2 deletions R/tm_g_forest_rsp.R
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Expand Up @@ -236,8 +236,8 @@ template_forest_rsp <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADRS", adrs)
#' ADSL = adsl,
#' ADRS = adrs
#' ),
#' modules = modules(
#' tm_g_forest_rsp(
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4 changes: 2 additions & 2 deletions R/tm_g_forest_tte.R
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Expand Up @@ -243,8 +243,8 @@ template_forest_tte <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADTTE", adtte)
#' ADSL = adsl,
#' ADTTE = adtte
#' ),
#' modules = modules(
#' tm_g_forest_tte(
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4 changes: 2 additions & 2 deletions R/tm_g_ipp.R
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Expand Up @@ -196,8 +196,8 @@ template_g_ipp <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_g_ipp(
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4 changes: 2 additions & 2 deletions R/tm_g_km.R
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Expand Up @@ -263,8 +263,8 @@ template_g_km <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADTTE", adtte)
#' ADSL = adsl,
#' ADTTE = adtte
#' ),
#' modules = modules(
#' tm_g_km(
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4 changes: 2 additions & 2 deletions R/tm_g_lineplot.R
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Expand Up @@ -223,8 +223,8 @@ template_g_lineplot <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_g_lineplot(
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4 changes: 2 additions & 2 deletions R/tm_g_pp_adverse_events.R
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Expand Up @@ -196,8 +196,8 @@ template_adverse_events <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = adsl,
#' ADAE = adae
#' ),
#' modules = modules(
#' tm_g_pp_adverse_events(
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6 changes: 3 additions & 3 deletions R/tm_g_pp_patient_timeline.R
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Expand Up @@ -372,9 +372,9 @@ template_patient_timeline <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae),
#' cdisc_dataset("ADCM", adcm, keys = adcm_keys)
#' ADSL = adsl,
#' ADAE = adae,
#' ADCM = adcm # TODO use adcm_keys
#' ),
#' modules = modules(
#' tm_g_pp_patient_timeline(
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4 changes: 2 additions & 2 deletions R/tm_g_pp_therapy.R
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Expand Up @@ -271,8 +271,8 @@ template_therapy <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADCM", adcm, keys = adcm_keys)
#' ADSL = adsl,
#' ADCM = adcm # TODO use adcm_keys
#' ),
#' modules = modules(
#' tm_g_pp_therapy(
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4 changes: 2 additions & 2 deletions R/tm_g_pp_vitals.R
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Expand Up @@ -196,8 +196,8 @@ template_vitals <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADVS", advs)
#' ADSL = adsl,
#' ADVS = advs
#' ),
#' modules = modules(
#' tm_g_pp_vitals(
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4 changes: 2 additions & 2 deletions R/tm_t_abnormality.R
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Expand Up @@ -249,8 +249,8 @@ template_abnormality <- function(parentname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_t_abnormality(
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4 changes: 2 additions & 2 deletions R/tm_t_abnormality_by_worst_grade.R
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Expand Up @@ -251,8 +251,8 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_t_abnormality_by_worst_grade(
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4 changes: 2 additions & 2 deletions R/tm_t_ancova.R
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Expand Up @@ -445,8 +445,8 @@ template_ancova <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADQS", adqs)
#' ADSL = adsl,
#' ADQS = adqs
#' ),
#' modules = modules(
#' tm_t_ancova(
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4 changes: 2 additions & 2 deletions R/tm_t_binary_outcome.R
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Expand Up @@ -407,8 +407,8 @@ template_binary_outcome <- function(dataname,
#' )
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADRS", adrs)
#' ADSL = adsl,
#' ADRS = adrs
#' ),
#' modules = modules(
#' tm_t_binary_outcome(
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13 changes: 4 additions & 9 deletions R/tm_t_coxreg.R
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Expand Up @@ -368,8 +368,8 @@ template_coxreg_m <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADTTE", adtte)
#' ADSL = adsl,
#' ADTTE = adtte
#' ),
#' modules = modules(
#' tm_t_coxreg(
Expand Down Expand Up @@ -439,13 +439,8 @@ template_coxreg_m <- function(dataname,
#' arm_ref_comp <- list(ARMCD = list(ref = "ARM A", comp = c("ARM B")))
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset(
#' dataname = "ADSL",
#' x = adsl
#' ),
#' cdisc_dataset(
#' dataname = "ADTTE",
#' x = adtte
#' ADSL = adsl,
#' ADTTE = adtte
#' )
#' ),
#' modules = modules(
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4 changes: 2 additions & 2 deletions R/tm_t_events.R
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Expand Up @@ -452,8 +452,8 @@ template_events <- function(dataname,
#'
#' app <- teal::init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = adsl,
#' ADAE = adae
#' ),
#' modules = modules(
#' tm_t_events(
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4 changes: 2 additions & 2 deletions R/tm_t_events_by_grade.R
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Expand Up @@ -791,8 +791,8 @@ template_events_col_by_grade <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = adsl,
#' ADAE = adae
#' ),
#' modules = modules(
#' tm_t_events_by_grade(
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4 changes: 2 additions & 2 deletions R/tm_t_events_patyear.R
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Expand Up @@ -160,8 +160,8 @@ template_events_patyear <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAETTE", adaette)
#' ADSL = adsl,
#' ADAETTE = adaette
#' ),
#' modules = modules(
#' tm_t_events_patyear(
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4 changes: 2 additions & 2 deletions R/tm_t_events_summary.R
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Expand Up @@ -535,8 +535,8 @@ template_events_summary <- function(anl_name,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = adsl,
#' ADAE = adae
#' ),
#' modules = modules(
#' tm_t_events_summary(
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4 changes: 2 additions & 2 deletions R/tm_t_exposure.R
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Expand Up @@ -243,8 +243,8 @@ template_exposure <- function(parentname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADEX", adex)
#' ADSL = adsl,
#' ADEX = adex
#' ),
#' modules = modules(
#' tm_t_exposure(
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4 changes: 2 additions & 2 deletions R/tm_t_logistic.R
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Expand Up @@ -245,8 +245,8 @@ template_logistic <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADRS", adrs)
#' ADSL = adsl,
#' ADRS = adrs
#' ),
#' modules = modules(
#' tm_t_logistic(
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4 changes: 2 additions & 2 deletions R/tm_t_mult_events.R
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Expand Up @@ -286,8 +286,8 @@ template_mult_events <- function(dataname,
#'
#' app <- teal::init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADCM", adcm, keys = adcm_keys)
#' ADSL = adsl,
#' ADCM = adcm # TODO use adcm_keys
#' ),
#' modules = modules(
#' tm_t_mult_events(
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2 changes: 1 addition & 1 deletion R/tm_t_pp_basic_info.R
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Expand Up @@ -69,7 +69,7 @@ template_basic_info <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl)
#' ADSL = adsl
#' ),
#' modules = modules(
#' tm_t_pp_basic_info(
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4 changes: 2 additions & 2 deletions R/tm_t_pp_laboratory.R
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Expand Up @@ -123,8 +123,8 @@ template_laboratory <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_t_pp_laboratory(
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4 changes: 2 additions & 2 deletions R/tm_t_pp_medical_history.R
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Expand Up @@ -94,8 +94,8 @@ template_medical_history <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADMH", admh)
#' ADSL = adsl,
#' ADMH = admh
#' ),
#' modules = modules(
#' tm_t_pp_medical_history(
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4 changes: 2 additions & 2 deletions R/tm_t_pp_prior_medication.R
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Expand Up @@ -80,8 +80,8 @@ template_prior_medication <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADCM", adcm, keys = adcm_keys)
#' ADSL = adsl,
#' ADCM = adcm
#' ),
#' modules = modules(
#' tm_t_pp_prior_medication(
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4 changes: 2 additions & 2 deletions R/tm_t_shift_by_arm.R
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Expand Up @@ -173,8 +173,8 @@ template_shift_by_arm <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADEG", adeg)
#' ADSL = adsl,
#' ADEG = adeg
#' ),
#' modules = modules(
#' tm_t_shift_by_arm(
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4 changes: 2 additions & 2 deletions R/tm_t_shift_by_arm_by_worst.R
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Expand Up @@ -181,8 +181,8 @@ template_shift_by_arm_by_worst <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADEG", adeg)
#' ADSL = adsl,
#' ADEG = adeg
#' ),
#' modules = modules(
#' tm_t_shift_by_arm_by_worst(
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4 changes: 2 additions & 2 deletions R/tm_t_shift_by_grade.R
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Expand Up @@ -483,8 +483,8 @@ template_shift_by_grade <- function(parentname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_t_shift_by_grade(
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4 changes: 2 additions & 2 deletions R/tm_t_smq.R
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Expand Up @@ -337,8 +337,8 @@ template_smq <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = adsl,
#' ADAE = adae
#' ),
#' modules = modules(
#' tm_t_smq(
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2 changes: 1 addition & 1 deletion R/tm_t_summary.R
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Expand Up @@ -236,7 +236,7 @@ template_summary <- function(dataname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl)
#' ADSL = adsl
#' ),
#' modules = modules(
#' tm_t_summary(
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4 changes: 2 additions & 2 deletions R/tm_t_summary_by.R
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Expand Up @@ -336,8 +336,8 @@ template_summary_by <- function(parentname,
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = adsl,
#' ADLB = adlb
#' ),
#' modules = modules(
#' tm_t_summary_by(
Expand Down
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