Merge pull request #26 from Merck/parameter-default

inherit paramter_term from all parameters of a metadata by default.
Merck · Dec 31, 2023 · 947eb3b · 947eb3b
2 parents a2f36cf + d31950e
commit 947eb3b
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Showing 10 changed files with 45 additions and 29 deletions.
diff --git a/R/ae_forestly.R b/R/ae_forestly.R
@@ -34,9 +34,10 @@
 #'     dataset_adsl = adsl,
 #'     dataset_adae = adae,
 #'     population_term = "apat",
-#'     observation_term = "wk12"
+#'     observation_term = "wk12",
+#'     parameter = "any;rel"
 #'   ) |>
-#'     prepare_ae_forestly(parameter = "any;rel") |>
+#'     prepare_ae_forestly() |>
 #'     format_ae_forestly() |>
 #'     ae_forestly()
 #' }

diff --git a/R/format_ae_forestly.R b/R/format_ae_forestly.R
@@ -48,9 +48,10 @@
 #'   dataset_adsl = adsl,
 #'   dataset_adae = adae,
 #'   population_term = "apat",
-#'   observation_term = "wk12"
+#'   observation_term = "wk12",
+#'   parameter = "any;rel"
 #' ) |>
-#'   prepare_ae_forestly(parameter = "any;rel")|>
+#'   prepare_ae_forestly()|>
 #'   format_ae_forestly()
 format_ae_forestly <- function(
     outdata,

diff --git a/R/meta_forestly.R b/R/meta_forestly.R
@@ -38,17 +38,18 @@
 #'   forestly_adsl,
 #'   forestly_adae,
 #'   population_term = "apat",
-#'   observation_term = "wk12"
+#'   observation_term = "wk12",
+#'   parameter_term = "any;rel"
 #' )
 meta_forestly <- function(
     dataset_adsl,
     dataset_adae,
     population_term,
     observation_term,
+    parameter_term = "any;rel",
     population_subset = SAFFL == "Y",
     observation_subset = SAFFL == "Y",
-    treatment_group = "TRTA",
-    parameter_term = "any;rel;ser") {
+    treatment_group = "TRTA") {
   meta <- metalite::meta_adam(
     population = as.data.frame(dataset_adsl),
     observation = as.data.frame(dataset_adae)

diff --git a/R/prepare_ae_forestly.R b/R/prepare_ae_forestly.R
@@ -33,20 +33,21 @@
 #'   dataset_adsl = adsl,
 #'   dataset_adae = adae,
 #'   population_term = "apat",
-#'   observation_term = "wk12"
+#'   observation_term = "wk12",
+#'   parameter = "any;rel"
 #' ) |>
-#'   prepare_ae_forestly(parameter = "any;rel")
+#'   prepare_ae_forestly()
 prepare_ae_forestly <- function(
     meta,
     population = NULL,
     observation = NULL,
-    parameter,
+    parameter = NULL,
     reference_group = NULL,
     ae_listing_display = c(
       "SEX", "RACE", "AGE", "ASTDY", "AESEV", "AESER",
       "AEREL", "AEACN", "AEOUT", "SITEID", "ADURN", "ADURU"
     )) {
-  parameters <- unlist(strsplit(parameter, ";"))
+
 
   if (is.null(population)) {
     if (length(meta$population) == 1) {
@@ -64,6 +65,12 @@ prepare_ae_forestly <- function(
     }
   }
 
+  if( is.null(parameter)){
+    parameters <- names(meta$parameter)
+  }else{
+    parameters <- unlist(strsplit(parameter, ";"))
+  }
+
   res <- lapply(parameters, function(x) {
     # print(x)
     metalite.ae::prepare_ae_specific(meta,

diff --git a/man/ae_forestly.Rd b/man/ae_forestly.Rd
diff --git a/man/format_ae_forestly.Rd b/man/format_ae_forestly.Rd
diff --git a/man/meta_forestly.Rd b/man/meta_forestly.Rd
diff --git a/man/prepare_ae_forestly.Rd b/man/prepare_ae_forestly.Rd
diff --git a/vignettes/forestly.Rmd b/vignettes/forestly.Rmd
@@ -51,9 +51,10 @@ meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
   population_term = "apat",
-  observation_term = "wk12"
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
 ) |>
-  prepare_ae_forestly(parameter = "any;rel;ser") |>
+  prepare_ae_forestly() |>
   format_ae_forestly() |>
   ae_forestly()
 ```
@@ -89,7 +90,8 @@ meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
   population_term = "apat",
-  observation_term = "wk12"
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
 )
 ```
 

diff --git a/vignettes/layout.Rmd b/vignettes/layout.Rmd
@@ -41,10 +41,11 @@ metadata <- meta_forestly(
   dataset_adsl = forestly_adsl_3grp,
   dataset_adae = forestly_adae_3grp,
   population_term = "apat",
-  observation_term = "wk12"
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
 )
 
-outdata <- metadata |> prepare_ae_forestly(parameter = "any;rel;ser")
+outdata <- metadata |> prepare_ae_forestly()
 
 outdata
 ```
@@ -121,7 +122,6 @@ listing_var <- c(
 
 metadata |>
   prepare_ae_forestly(
-    parameter = "any;rel;ser",
     ae_listing_display = listing_var
   ) |>
   format_ae_forestly() |>