refactoring cdisc_dataset() call to return teal_data()

insightsengineering · Nov 7, 2023 · b5c3b8a · b5c3b8a
1 parent f858e5d
commit b5c3b8a
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Showing 74 changed files with 160 additions and 174 deletions.
diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -143,8 +143,8 @@ template_a_gee <- function(output_table,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADQS", adqs)
+#'     ADSL = adsl,
+#'     ADQS = adqs
 #'   ),
 #'   modules = modules(
 #'     tm_a_gee(

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -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(

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -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(

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -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(

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -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(

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -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(

diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R
@@ -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(

diff --git a/R/tm_g_km.R b/R/tm_g_km.R
@@ -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(

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -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(

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -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(

diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R
@@ -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(

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -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(

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -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(

diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R
@@ -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(

diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R
@@ -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(

diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R
@@ -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(

diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R
@@ -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(

diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R
@@ -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(
@@ -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(

diff --git a/R/tm_t_events.R b/R/tm_t_events.R
@@ -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(

diff --git a/R/tm_t_events_by_grade.R b/R/tm_t_events_by_grade.R
@@ -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(

diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R
@@ -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(

diff --git a/R/tm_t_events_summary.R b/R/tm_t_events_summary.R
@@ -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(

diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R
@@ -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(

diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R
@@ -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(

diff --git a/R/tm_t_mult_events.R b/R/tm_t_mult_events.R
@@ -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(

diff --git a/R/tm_t_pp_basic_info.R b/R/tm_t_pp_basic_info.R
@@ -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(

diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R
@@ -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(

diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R
@@ -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(

diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R
@@ -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(

diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R
@@ -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(

diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R
@@ -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(

diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R
@@ -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(

diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R
@@ -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(

diff --git a/R/tm_t_summary.R b/R/tm_t_summary.R
@@ -236,7 +236,7 @@ template_summary <- function(dataname,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl)
+#'     ADSL = adsl
 #'   ),
 #'   modules = modules(
 #'     tm_t_summary(

diff --git a/R/tm_t_summary_by.R b/R/tm_t_summary_by.R
@@ -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(