Merge pull request #57 from Merck/56-release-v011

update arguments
Merck · Jul 3, 2024 · 7d9720c · 7d9720c
2 parents 62e0447 + 7bb7dae
commit 7d9720c
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Showing 9 changed files with 34 additions and 11 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,12 @@
 # forestly 0.1.1
 
+- Add button to display SOC column for subset
+- Refine the default value of `meta_forestly()`
+- Update `format_ae_listing()` to be better aligned with oncology AEs reporting
+- Enhance functionality related to drill-down listing
+- Inherit paramter_term from all parameters of a metadata by default (#20)
+- Allow user to specify treatment group (#15)
+- Add warning when using tibble as input (#17)
 - Fix bug when there is no record of a selected AE category (#9).
 - Fix bug when there are multiple plots displayed on one page (#12).
 - Update dataset `forestly_adae` since a variable was a factor

diff --git a/R/meta_forestly.R b/R/meta_forestly.R
@@ -47,8 +47,8 @@ meta_forestly <- function(
     population_term = "apat",
     observation_term = "safety",
     parameter_term = "any;rel",
-    population_subset = SAFFL == "Y",
-    observation_subset = SAFFL == "Y",
+    population_subset,
+    observation_subset,
     treatment_group = "TRTA") {
   meta <- metalite::meta_adam(
     population = as.data.frame(dataset_adsl),

diff --git a/R/prepare_ae_forestly.R b/R/prepare_ae_forestly.R
@@ -41,6 +41,7 @@ prepare_ae_forestly <- function(
     population = NULL,
     observation = NULL,
     parameter = NULL,
+    components = "par",
     reference_group = NULL,
     ae_listing_display = c(
       "USUBJID", "SITEID", "SEX", "RACE", "AGE", "ASTDY", "AESER",
@@ -101,7 +102,7 @@ prepare_ae_forestly <- function(
     metalite.ae::prepare_ae_specific(meta,
       population = population, observation = observation,
       parameter = x,
-      components = c("soc", "par"),
+      components = components,
       reference_group = reference_group
     ) |>
       metalite.ae::extend_ae_specific_inference() |>

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
@@ -18,7 +18,9 @@ forestly_adae$TRTA <- factor(forestly_adae$TRTA, levels = c("Xanomeline Low Dose
 
 meta_forestly(
   dataset_adsl = forestly_adsl,
-  dataset_adae = forestly_adae
+  dataset_adae = forestly_adae,
+  population_subset = SAFFL == "Y",
+  observation_subset = SAFFL == "Y"
 ) |>
   prepare_ae_forestly(parameter = "any;rel;ser") |>
   format_ae_forestly() |>

diff --git a/vignettes/forestly.Rmd b/vignettes/forestly.Rmd
@@ -50,7 +50,9 @@ forestly_adae$TRTA <- factor(forestly_adae$TRTA, levels = c("Xanomeline Low Dose
 meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
-  parameter_term = "any;rel;ser"
+  parameter_term = "any;rel;ser",
+  population_subset = SAFFL == "Y",
+  observation_subset = SAFFL == "Y"
 ) |>
   prepare_ae_forestly() |>
   format_ae_forestly() |>
@@ -87,7 +89,9 @@ to generate the interactive forest plot.
 meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
-  parameter_term = "any;rel;ser"
+  parameter_term = "any;rel;ser",
+  population_subset = SAFFL == "Y",
+  observation_subset = SAFFL == "Y"
 )
 ```
 

diff --git a/vignettes/layout.Rmd b/vignettes/layout.Rmd
@@ -40,7 +40,9 @@ 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,
-  parameter_term = "any;rel;ser"
+  parameter_term = "any;rel;ser",
+  population_subset = SAFFL == "Y",
+  observation_subset = SAFFL == "Y"
 )
 
 outdata <- metadata |> prepare_ae_forestly()

diff --git a/vignettes/meta-forestly.Rmd b/vignettes/meta-forestly.Rmd
@@ -72,7 +72,9 @@ If the deliverable requires a forest plot of all adverse events and serious adve
 meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
-  parameter_term = "any;ser"
+  parameter_term = "any;ser",
+  population_subset = SAFFL == "Y",
+  observation_subset = SAFFL == "Y"
 ) |>
   prepare_ae_forestly() |>
   format_ae_forestly() |>
@@ -85,7 +87,9 @@ However, if grade 3-5 adverse events need to be plotted as well, we can add `g35
 meta_forestly(
   dataset_adsl = forestly_adsl,
   dataset_adae = forestly_adae,
-  parameter_term = "any;ser;g35"
+  parameter_term = "any;ser;g35",
+  population_subset = SAFFL == "Y",
+  observation_subset = SAFFL == "Y"
 ) |>
   prepare_ae_forestly() |>
   format_ae_forestly() |>