Skip snapshot tests on CI (#218)

Closes #217
insightsengineering · Feb 23, 2024 · 180f125 · 180f125
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Showing 66 changed files with 253 additions and 251 deletions.
diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd
@@ -225,20 +225,20 @@ app <- init(
     tm_g_forest_rsp(
       label = "Forest Response",
       dataname = "ADRS",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         variable_choices(ADSL, c("ARM", "ARMCD")),
         "ARMCD"
       ),
       arm_ref_comp = arm_ref_comp,
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         value_choices(ADRS, "PARAMCD", "PARAM"),
         "BESRSPI"
       ),
-      subgroup_var = choices_selected(
+      subgroup_var = teal.transform::choices_selected(
         variable_choices(ADSL, names(ADSL)),
         c("BMRKR2", "SEX")
       ),
-      strata_var = choices_selected(
+      strata_var = teal.transform::choices_selected(
         variable_choices(ADSL, c("STRATA1", "STRATA2")),
         "STRATA2"
       ),

diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd
@@ -227,10 +227,10 @@ app <- init(
     tm_g_forest_tte(
       label = "Forest Survival",
       dataname = "ADTTE",
-      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
-      subgroup_var = choices_selected(names(ADSL), c("SEX", "BMRKR2")),
-      paramcd = choices_selected(value_choices(ADTTE, "PARAMCD", "PARAM"), "OS"),
-      strata_var = choices_selected(c("STRATA1", "STRATA2"), "STRATA2"),
+      arm_var = teal.transform::choices_selected(c("ARM", "ARMCD"), "ARM"),
+      subgroup_var = teal.transform::choices_selected(names(ADSL), c("SEX", "BMRKR2")),
+      paramcd = teal.transform::choices_selected(value_choices(ADTTE, "PARAMCD", "PARAM"), "OS"),
+      strata_var = teal.transform::choices_selected(c("STRATA1", "STRATA2"), "STRATA2"),
       plot_height = c(600, 200, 2000),
       plot_width = c(1500, 200, 5000)
     )

diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd
@@ -154,17 +154,17 @@ app <- init(
     tm_a_mmrm(
       label = "MMRM",
       dataname = "ADQS",
-      aval_var = choices_selected(c("AVAL", "CHG"), "AVAL"),
-      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
-      arm_var = choices_selected(c("ARM", "ARMCD"), "ARMCD"),
-      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
+      aval_var = teal.transform::choices_selected(c("AVAL", "CHG"), "AVAL"),
+      id_var = teal.transform::choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
+      arm_var = teal.transform::choices_selected(c("ARM", "ARMCD"), "ARMCD"),
+      visit_var = teal.transform::choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
       arm_ref_comp = arm_ref_comp,
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         choices = value_choices(ADQS, "PARAMCD", "PARAM"),
         selected = "FKSI-FWB"
       ),
-      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
-      conf_level = choices_selected(c(0.95, 0.9, 0.8), 0.95)
+      cov_var = teal.transform::choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
+      conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95)
     )
   )
 )

diff --git a/book/graphs/other/ippg01.qmd b/book/graphs/other/ippg01.qmd
@@ -120,33 +120,33 @@ app <- init(
     tm_g_ipp(
       label = "Individual Patient Plot",
       dataname = "ADLB",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         value_choices(ADLB, c("ARMCD")),
         "ARM A"
       ),
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         value_choices(ADLB, "PARAMCD"),
         "ALT"
       ),
-      aval_var = choices_selected(
+      aval_var = teal.transform::choices_selected(
         variable_choices(ADLB, c("AVAL")),
         "AVAL"
       ),
-      avalu_var = choices_selected(
+      avalu_var = teal.transform::choices_selected(
         variable_choices(ADLB, c("AVALU")),
         "AVALU",
         fixed = TRUE
       ),
-      id_var = choices_selected(
+      id_var = teal.transform::choices_selected(
         variable_choices(ADLB, c("USUBJID")),
         "USUBJID",
         fixed = TRUE
       ),
-      visit_var = choices_selected(
+      visit_var = teal.transform::choices_selected(
         variable_choices(ADLB, c("AVISIT")),
         "AVISIT"
       ),
-      baseline_var = choices_selected(
+      baseline_var = teal.transform::choices_selected(
         variable_choices(ADLB, c("BASE")),
         "BASE",
         fixed = TRUE

diff --git a/book/graphs/other/kmg01.qmd b/book/graphs/other/kmg01.qmd
@@ -159,20 +159,20 @@ app <- init(
       label = "KM PLOT",
       plot_height = c(600, 100, 2000),
       dataname = "ADTTE",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
         "ARM"
       ),
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         value_choices(ADTTE, "PARAMCD", "PARAM"),
         "OS"
       ),
       arm_ref_comp = arm_ref_comp,
-      strata_var = choices_selected(
+      strata_var = teal.transform::choices_selected(
         variable_choices(ADSL, c("SEX", "BMRKR2")),
         "SEX"
       ),
-      facet_var = choices_selected(
+      facet_var = teal.transform::choices_selected(
         variable_choices(ADSL, c("SEX", "BMRKR2")),
         NULL
       )

diff --git a/book/graphs/other/mng01.qmd b/book/graphs/other/mng01.qmd
@@ -174,15 +174,15 @@ app <- init(
     tm_g_lineplot(
       label = "LINE PLOT",
       dataname = "ADLB",
-      strata = choices_selected(
+      strata = teal.transform::choices_selected(
         variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
         "ARM"
       ),
-      y = choices_selected(
+      y = teal.transform::choices_selected(
         variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
         "AVAL"
       ),
-      param = choices_selected(
+      param = teal.transform::choices_selected(
         value_choices(ADLB, "PARAMCD", "PARAM"),
         "ALT"
       )

diff --git a/book/tables/ECG/egt01.qmd b/book/tables/ECG/egt01.qmd
@@ -113,20 +113,20 @@ app <- init(
     tm_t_summary_by(
       label = "ECG Results and Change from Baseline by Visit",
       dataname = "ADEG",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         choices = variable_choices(ADSL, c("ARM", "ARMCD")),
         selected = "ARM"
       ),
-      by_vars = choices_selected(
+      by_vars = teal.transform::choices_selected(
         choices = variable_choices(ADEG, c("PARAM", "AVISIT")),
         selected = c("AVISIT")
       ),
-      summarize_vars = choices_selected(
+      summarize_vars = teal.transform::choices_selected(
         choices = variable_choices(ADEG, c("AVAL", "CHG")),
         selected = c("AVAL")
       ),
       useNA = "ifany",
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         choices = value_choices(ADEG, "PARAMCD", "PARAM"),
         selected = "HR"
       ),

diff --git a/book/tables/ECG/egt02.qmd b/book/tables/ECG/egt02.qmd
@@ -104,16 +104,16 @@ app <- init(
     tm_t_abnormality(
       label = "Abnormality Table",
       dataname = "ADEG",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
         selected = "ARM"
       ),
-      by_vars = choices_selected(
+      by_vars = teal.transform::choices_selected(
         choices = variable_choices(ADEG, subset = c("EGCAT", "PARAM", "AVISIT")),
         selected = c("PARAM"),
         keep_order = TRUE
       ),
-      grade = choices_selected(
+      grade = teal.transform::choices_selected(
         choices = variable_choices(ADEG, subset = "ANRIND"),
         selected = "ANRIND",
         fixed = TRUE

diff --git a/book/tables/ECG/egt03.qmd b/book/tables/ECG/egt03.qmd
@@ -169,31 +169,31 @@ app <- init(
     tm_t_shift_by_arm(
       label = "Shift by Arm Table",
       dataname = "ADEG",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         variable_choices(ADSL, subset = c("ARM", "ARMCD")),
         selected = "ARM"
       ),
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         value_choices(ADEG, "PARAMCD"),
         selected = "HR"
       ),
-      visit_var = choices_selected(
+      visit_var = teal.transform::choices_selected(
         value_choices(ADEG, "AVISIT"),
         selected = "POST-BASELINE MINIMUM"
       ),
-      aval_var = choices_selected(
+      aval_var = teal.transform::choices_selected(
         variable_choices(ADEG, subset = "ANRIND"),
         selected = "ANRIND", fixed = TRUE
       ),
-      baseline_var = choices_selected(
+      baseline_var = teal.transform::choices_selected(
         variable_choices(ADEG, subset = "BNRIND"),
         selected = "BNRIND", fixed = TRUE
       ),
-      treatment_flag_var = choices_selected(
+      treatment_flag_var = teal.transform::choices_selected(
         variable_choices(ADEG, subset = "ONTRTFL"),
         selected = "ONTRTFL", fixed = TRUE
       ),
-      treatment_flag = choices_selected(
+      treatment_flag = teal.transform::choices_selected(
         value_choices(ADEG, "ONTRTFL"),
         selected = "Y", fixed = TRUE
       )

diff --git a/book/tables/ECG/egt05_qtcat.qmd b/book/tables/ECG/egt05_qtcat.qmd
@@ -185,20 +185,20 @@ app <- init(
     tm_t_summary_by(
       label = "ECG Actual Values and Changes from Baseline by Visit",
       dataname = "ADEG",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         choices = variable_choices(ADSL, c("ARM", "ARMCD")),
         selected = "ARM"
       ),
-      by_vars = choices_selected(
+      by_vars = teal.transform::choices_selected(
         choices = variable_choices(ADEG, c("PARAM", "AVISIT")),
         selected = c("AVISIT")
       ),
-      summarize_vars = choices_selected(
+      summarize_vars = teal.transform::choices_selected(
         choices = variable_choices(ADEG, c("AVALCAT1", "CHGCAT1")),
         selected = c("AVALCAT1", "CHGCAT1")
       ),
       useNA = "ifany",
-      paramcd = choices_selected(
+      paramcd = teal.transform::choices_selected(
         choices = value_choices(ADEG, "PARAMCD", "PARAM"),
         selected = "QT"
       )

diff --git a/book/tables/adverse-events/aet01.qmd b/book/tables/adverse-events/aet01.qmd
@@ -389,17 +389,17 @@ app <- init(
     tm_t_events_summary(
       label = "Adverse Events Summary",
       dataname = "ADAE",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         choices = variable_choices("ADSL", c("ARM", "ARMCD")),
         selected = "ARM"
       ),
-      flag_var_anl = choices_selected(
+      flag_var_anl = teal.transform::choices_selected(
         choices = variable_choices("ADAE", ae_anl_vars),
         selected = ae_anl_vars[1],
         keep_order = TRUE,
         fixed = FALSE
       ),
-      flag_var_aesi = choices_selected(
+      flag_var_aesi = teal.transform::choices_selected(
         choices = variable_choices("ADAE", aesi_vars),
         selected = aesi_vars[1],
         keep_order = TRUE,

diff --git a/book/tables/adverse-events/aet01_aesi.qmd b/book/tables/adverse-events/aet01_aesi.qmd
@@ -563,11 +563,11 @@ app <- init(
     tm_t_events_summary(
       label = "Adverse Events Summary",
       dataname = "ADAE",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         choices = variable_choices("ADSL", c("ARM", "ARMCD")),
         selected = "ARM"
       ),
-      flag_var_anl = choices_selected(
+      flag_var_anl = teal.transform::choices_selected(
         choices = variable_choices("ADAE", aesi_vars),
         selected = aesi_vars[1],
         keep_order = TRUE,

diff --git a/book/tables/adverse-events/aet02.qmd b/book/tables/adverse-events/aet02.qmd
@@ -668,12 +668,12 @@ app <- init(
     tm_t_events(
       label = "Adverse Event Table",
       dataname = "ADAE",
-      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
-      llt = choices_selected(
+      arm_var = teal.transform::choices_selected(c("ARM", "ARMCD"), "ARM"),
+      llt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
         selected = c("AEDECOD")
       ),
-      hlt = choices_selected(
+      hlt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
         selected = "AEBODSYS"
       ),

diff --git a/book/tables/adverse-events/aet02_smq.qmd b/book/tables/adverse-events/aet02_smq.qmd
@@ -193,11 +193,11 @@ ADAE <- data[["ADAE"]]
 names_baskets <- grep("^(SMQ|CQ).*NAM$", names(ADAE), value = TRUE)
 names_scopes <- grep("^SMQ.*SC$", names(ADAE), value = TRUE)
 
-cs_baskets <- choices_selected(
+cs_baskets <- teal.transform::choices_selected(
   choices = variable_choices(ADAE, subset = names_baskets),
   selected = names_baskets
 )
-cs_scopes <- choices_selected(
+cs_scopes <- teal.transform::choices_selected(
   choices = variable_choices(ADAE, subset = names_scopes),
   selected = names_scopes,
   fixed = TRUE
@@ -210,14 +210,14 @@ app <- init(
     tm_t_smq(
       label = "Adverse events by `SMQ` Table",
       dataname = "ADAE",
-      arm_var = choices_selected(
+      arm_var = teal.transform::choices_selected(
         choices = variable_choices(ADSL, subset = c("ARM", "SEX")),
         selected = "ARM"
       ),
       add_total = FALSE,
       baskets = cs_baskets,
       scopes = cs_scopes,
-      llt = choices_selected(
+      llt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, subset = c("AEDECOD")),
         selected = "AEDECOD"
       )

diff --git a/book/tables/adverse-events/aet03.qmd b/book/tables/adverse-events/aet03.qmd
@@ -130,16 +130,16 @@ app <- init(
     tm_t_events_by_grade(
       label = "Adverse Events by Grade Table",
       dataname = "ADAE",
-      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
-      llt = choices_selected(
+      arm_var = teal.transform::choices_selected(c("ARM", "ARMCD"), "ARM"),
+      llt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
         selected = c("AEDECOD")
       ),
-      hlt = choices_selected(
+      hlt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
         selected = "AEBODSYS"
       ),
-      grade = choices_selected(
+      grade = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
         selected = "AESEV"
       )

diff --git a/book/tables/adverse-events/aet04.qmd b/book/tables/adverse-events/aet04.qmd
@@ -585,16 +585,16 @@ app <- init(
     tm_t_events_by_grade(
       label = "Adverse Events by Grade Table",
       dataname = "ADAE",
-      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
-      llt = choices_selected(
+      arm_var = teal.transform::choices_selected(c("ARM", "ARMCD"), "ARM"),
+      llt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AETERM", "AEDECOD")),
         selected = c("AEDECOD")
       ),
-      hlt = choices_selected(
+      hlt = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AEBODSYS", "AESOC")),
         selected = "AEBODSYS"
       ),
-      grade = choices_selected(
+      grade = teal.transform::choices_selected(
         choices = variable_choices(ADAE, c("AETOXGR", "AESEV")),
         selected = "AETOXGR"
       )