Merge pull request #48 from Merck/meta-forest-default

add default values for `meta_forestly`.
Merck · May 12, 2024 · e47ea57 · e47ea57
2 parents 7bb0f22 + b348240
commit e47ea57
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Showing 12 changed files with 12 additions and 40 deletions.
diff --git a/R/ae_forestly.R b/R/ae_forestly.R
@@ -33,9 +33,6 @@
 #'   meta_forestly(
 #'     dataset_adsl = adsl,
 #'     dataset_adae = adae,
-#'     population_term = "apat",
-#'     observation_term = "wk12",
-#'     parameter = "any;rel"
 #'   ) |>
 #'     prepare_ae_forestly() |>
 #'     format_ae_forestly() |>

diff --git a/R/format_ae_forestly.R b/R/format_ae_forestly.R
@@ -46,10 +46,7 @@
 #' adae <- forestly_adae[1:100,]
 #' meta_forestly(
 #'   dataset_adsl = adsl,
-#'   dataset_adae = adae,
-#'   population_term = "apat",
-#'   observation_term = "wk12",
-#'   parameter = "any;rel"
+#'   dataset_adae = adae
 #' ) |>
 #'   prepare_ae_forestly()|>
 #'   format_ae_forestly()

diff --git a/R/meta_forestly.R b/R/meta_forestly.R
@@ -38,14 +38,14 @@
 #'   forestly_adsl,
 #'   forestly_adae,
 #'   population_term = "apat",
-#'   observation_term = "wk12",
+#'   observation_term = "safety",
 #'   parameter_term = "any;rel"
 #' )
 meta_forestly <- function(
     dataset_adsl,
     dataset_adae,
-    population_term,
-    observation_term,
+    population_term = "apat",
+    observation_term = "safety",
     parameter_term = "any;rel",
     population_subset = SAFFL == "Y",
     observation_subset = SAFFL == "Y",

diff --git a/R/prepare_ae_forestly.R b/R/prepare_ae_forestly.R
@@ -33,10 +33,7 @@
 #' adae <- forestly_adae[1:100,]
 #' meta_forestly(
 #'   dataset_adsl = adsl,
-#'   dataset_adae = adae,
-#'   population_term = "apat",
-#'   observation_term = "wk12",
-#'   parameter = "any;rel"
+#'   dataset_adae = adae
 #' ) |>
 #'   prepare_ae_forestly()
 prepare_ae_forestly <- function(

diff --git a/README.md b/README.md
@@ -56,9 +56,7 @@ library("forestly")
 
 meta_forestly(
   forestly_adsl,
-  forestly_adae,
-  population_term = "apat",
-  observation_term = "wk12"
+  forestly_adae
 ) |>
   prepare_ae_forestly(parameter = "any;rel;ser") |>
   format_ae_forestly() |>

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-cran.Rmd b/vignettes/forestly-cran.Rmd
@@ -18,9 +18,7 @@ forestly_adae$TRTA <- factor(forestly_adae$TRTA, levels = c("Xanomeline Low Dose
 
 meta_forestly(
   dataset_adsl = forestly_adsl,
-  dataset_adae = forestly_adae,
-  population_term = "apat",
-  observation_term = "wk12"
+  dataset_adae = forestly_adae
 ) |>
   prepare_ae_forestly(parameter = "any;rel;ser") |>
   format_ae_forestly() |>

diff --git a/vignettes/forestly.Rmd b/vignettes/forestly.Rmd
@@ -50,8 +50,6 @@ forestly_adae$TRTA <- factor(forestly_adae$TRTA, levels = c("Xanomeline Low Dose
 meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
-  population_term = "apat",
-  observation_term = "wk12",
   parameter_term = "any;rel;ser"
 ) |>
   prepare_ae_forestly() |>
@@ -89,8 +87,6 @@ to generate the interactive forest plot.
 meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
-  population_term = "apat",
-  observation_term = "wk12",
   parameter_term = "any;rel;ser"
 )
 ```

diff --git a/vignettes/layout.Rmd b/vignettes/layout.Rmd
@@ -40,8 +40,6 @@ The `outdata` contains all the parameters required to generate the interactive f
 metadata <- meta_forestly(
   dataset_adsl = forestly_adsl_3grp,
   dataset_adae = forestly_adae_3grp,
-  population_term = "apat",
-  observation_term = "wk12",
   parameter_term = "any;rel;ser"
 )