fix code reproducibility using within

insightsengineering · Nov 8, 2023 · 98f00c7 · 98f00c7
1 parent 671f8be
commit 98f00c7
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Showing 6 changed files with 72 additions and 78 deletions.
diff --git a/R/adtteSpec.R b/R/adtteSpec.R
@@ -208,16 +208,15 @@ adtteSpecInput <- function(inputId, # nolint
 #' }
 #'
 #' my_app <- function() {
-#'   adtte <- teal.modules.hermes::rADTTE %>%
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADTTE = teal.modules.hermes::rADTTE %>%
 #'     dplyr::mutate(is_event = .data$CNSR == 0)
-#'
-#'   data <- teal_data(
-#'     ADTTE = adtte,
-#'     MAE = hermes::multi_assay_experiment,
-#'     code =
-#'        "adtte <- teal.modules.hermes::rADTTE %>%
-#'         dplyr::mutate(is_event = .data$CNSR == 0)"
-#'   )
+#'   MAE = hermes::multi_assay_experiment
+#' })
+#' datanames <- c("ADTTE", "MAE")
+#' datanames(data) <- datanames
+#' data@join_keys <- cdisc_join_keys(!!!datanames)
 #'
 #'   app <- init(
 #'     data = data,

diff --git a/R/forestplot.R b/R/forestplot.R
@@ -11,16 +11,16 @@
 #' @export
 #'
 #' @examples
-#' adtte <- teal.modules.hermes::rADTTE %>%
-#'   dplyr::mutate(is_event = (.data$CNSR == 0))
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADTTE = teal.modules.hermes::rADTTE %>%
+#'     dplyr::mutate(is_event = .data$CNSR == 0)
+#'   MAE = hermes::multi_assay_experiment
+#' })
+#' datanames <- c("ADTTE", "MAE")
+#' datanames(data) <- datanames
+#' data@join_keys <- cdisc_join_keys(!!!datanames)
 #'
-#' data <- teal_data(
-#'   ADTTE = adtte,
-#'   MAE = hermes::multi_assay_experiment,
-#'   code =
-#'      "adtte <- teal.modules.hermes::rADTTE %>%
-#'       dplyr::mutate(is_event = (.data$CNSR == 0))"
-#' )
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -283,17 +283,15 @@ srv_g_forest_tte <- function(id,
 #'   sample_tm_g_forest_tte()
 #' }
 sample_tm_g_forest_tte <- function() { # nolint
-
-  adtte <- teal.modules.hermes::rADTTE %>%
-    dplyr::mutate(is_event = (.data$CNSR == 0))
-
-  data <- teal_data(
-    ADTTE = adtte,
-    MAE = hermes::multi_assay_experiment,
-    code =
-       "adtte <- teal.modules.hermes::rADTTE %>%
-        dplyr::mutate(is_event = (.data$CNSR == 0))"
-  )
+  data <- teal_data()
+  data <- within(data, {
+    ADTTE = teal.modules.hermes::rADTTE %>%
+      dplyr::mutate(is_event = .data$CNSR == 0)
+    MAE = hermes::multi_assay_experiment
+  })
+  datanames <- c("ADTTE", "MAE")
+  datanames(data) <- datanames
+  data@join_keys <- cdisc_join_keys(!!!datanames)
 
   app <- teal::init(
     data = data,

diff --git a/R/km.R b/R/km.R
@@ -12,16 +12,16 @@
 #' @export
 #'
 #' @examples
-#' adtte <- teal.modules.hermes::rADTTE %>%
-#'   dplyr::mutate(is_event = (.data$CNSR == 0))
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADTTE = teal.modules.hermes::rADTTE %>%
+#'     dplyr::mutate(is_event = .data$CNSR == 0)
+#'   MAE = hermes::multi_assay_experiment
+#' })
+#' datanames <- c("ADTTE", "MAE")
+#' datanames(data) <- datanames
+#' data@join_keys <- cdisc_join_keys(!!!datanames)
 #'
-#' data <- teal_data(
-#'   ADTTE = adtte,
-#'   MAE = hermes::multi_assay_experiment,
-#'   code =
-#'      "adtte <- teal.modules.hermes::rADTTE %>%
-#'       dplyr::mutate(is_event = (.data$CNSR == 0))"
-#' )
 #'
 #' modules <- modules(
 #'   tm_g_km(
@@ -275,17 +275,15 @@ srv_g_km <- function(id,
 #'   sample_tm_g_km()
 #' }
 sample_tm_g_km <- function() { # nolint
-
-  adtte <- teal.modules.hermes::rADTTE %>%
-    dplyr::mutate(is_event = (.data$CNSR == 0))
-
-  data <- teal_data(
-    ADTTE = adtte,
-    MAE = hermes::multi_assay_experiment,
-    code =
-       "adtte <- teal.modules.hermes::rADTTE %>%
-        dplyr::mutate(is_event = (.data$CNSR == 0))"
-  )
+  data <- teal_data()
+  data <- within(data, {
+    ADTTE = teal.modules.hermes::rADTTE %>%
+      dplyr::mutate(is_event = .data$CNSR == 0)
+    MAE = hermes::multi_assay_experiment
+  })
+  datanames <- c("ADTTE", "MAE")
+  datanames(data) <- datanames
+  data@join_keys <- cdisc_join_keys(!!!datanames)
 
   modules <- teal::modules(
     tm_g_km(

diff --git a/man/adtteSpecServer.Rd b/man/adtteSpecServer.Rd
diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd
diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd