ID:318021 [dv.papo] default_analysis_params not documented (#42)

* Add `default_analysis_params` argument documentation

* Fix incorrect rendering for parameter documentation auto-generation

* Improve x_axis_breaks formatting

Author: luffmark

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dv.papo
 Title: Patient Profile
-Version: 2.1.1-9001
+Version: 2.1.1-9002
 Authors@R: 
     c(person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
       person(given = "Korbinian",

NEWS.md

@@ -1,3 +1,7 @@
+# dv.papo 2.1.1-9002
+
+- Add `default_analysis_params` argument documentation (previously missed out)
+
 # dv.papo 2.1.1-9001
 
 - Fixed issue where setting analysis_indicator to NULL caused loss of plot legend.

R/dressing_room.R

@@ -139,7 +139,7 @@ T_get_use_as_text_lines <- function(elem) {
     res <- "Represents a CDISC (non-zero) Study Day"
   } else if (elem$kind == "color") {
     res <- "Contains either an HTML (#xxxxxx) or an R color"
-  } else if (elem$kind %in% c("integer", "character", "group")) {
+  } else if (elem$kind %in% c("integer", "character", "group", "or")) {
     # nothing
   } else {
     message(paste("Missing use for kind", elem$kind))

R/mod_API.R

@@ -17,8 +17,8 @@ mod_patient_profile_API_docs <- list(
   ),
   plots = list(
     "Plot section",
-    x_axis_unit = "Defines the units of the x axis in the plots",
-    x_axis_breaks = "When a single integer is passed it will use `base::pretty` to compute a set of breakpoints. If more than one value is passed it will use those breaks in the x axis",
+    x_axis_unit = 'Defines the time units of the x-axis in the plots. Expects `["weeks"/"days"]` values. Defaults to `"days"`',
+    x_axis_breaks = "Defines how many breaks will be used in the x-axis. When a single integer is passed it will use `base::pretty` to compute that number of breaks. If more than one value is passed it will use those breaks in the x-axis (e.g. if `c(1, 2, 3)` is passed it will show breaks at days/weeks 1, 2 and 3). Defaults to `5`",
     timeline_info = list(
       "Start and end study dates",
       icf_date = "Informed Consent Form signing Date",
@@ -52,10 +52,10 @@ mod_patient_profile_API_docs <- list(
         range_high_limit = "Upper limit of the reference range",
         summary_stats = "Additional value column for summary statistics"
       ),
-      tooltip = "Block of text to display as hover information over each point of the trace. The names of this list are included as literal text and honor three basic HTML formatting elements: `<b>`, `<i>`, `<br>`). The columns the values refer to are populated with the value on the dataset relevant to any given row"
-      #, default_analysis_params = "A vector of character values specifying the default analysis parameters (values from the variable specified by `analysis_param`) to display" # TODO(miguel): Add when module is ported to CM+TC # nolint
+      tooltip = "Block of text to display as hover information over each point of the trace. The names of this list are included as literal text and honor three basic HTML formatting elements: `<b>`, `<i>`, `<br>`). The columns the values refer to are populated with the value on the dataset relevant to any given row",
+      default_analysis_params = "A vector of character values specifying the default analysis parameters (values from the variable specified by `analysis_param`) to display"
     ),
-    vline_vars = "Place vertical dashed lines on days indicated by this dataset columns",
+    vline_vars = "Place vertical dashed lines on days indicated by these dataset columns",
     vline_day_numbers = "Place vertical dashed lines on days indicated by this parameter",
     palette = "If a name on this list matches the text on a plot element, the associated color will be applied to that element. This mapping takes precedence over the built-in palette"
   )
@@ -76,7 +76,7 @@ mod_patient_profile_API <- T_group(
   ) |> T_flag("optional", "zero_or_more", "named"),
   plots = T_group(
     x_axis_unit = T_character() |> T_flag("optional"),
-    x_axis_breaks = T_integer(min = 1) |> T_flag("optional", "zero_or_more", "as_array"),
+    x_axis_breaks = T_or(T_integer(), T_numeric()) |> T_flag("zero_or_more") |> T_flag("optional"),
     timeline_info = T_group(
       icf_date = T_col("subject_level_dataset_name", T_or(T_date(), T_datetime())) |> T_flag("optional"),
       trt_start_date = T_col("subject_level_dataset_name", T_or(T_date(), T_datetime())),
@@ -105,8 +105,8 @@ mod_patient_profile_API <- T_group(
         range_high_limit = T_col("dataset", T_numeric()) |> T_flag("optional"),
         summary_stats = T_col("dataset", T_numeric()) |> T_flag("optional")
       ) |> T_flag("as_array"),
-      tooltip = T_col("dataset") |> T_flag("zero_or_more", "named", "as_array")
-      #, default_analysis_params = T_choice_from_col_contents("vars/analysis_param", T_or(T_character(), T_factor())) |> T_flag("optional") # TODO(miguel): Add when module is ported to CM+TC # nolint
+      tooltip = T_col("dataset") |> T_flag("zero_or_more", "named", "as_array"),
+      default_analysis_params = T_character() |> T_flag("zero_or_more") |> T_flag("optional")
     ) |> T_flag("zero_or_more", "named"),
     vline_vars = T_col(
       "subject_level_dataset_name", T_or(T_CDISC_study_day(), T_date(), T_datetime())

R/mod_signature.R

@@ -44,18 +44,16 @@
 #'  Plot section.
 #' Composed of:
 #'  * x_axis_unit
-#' `["weeks"|"days"]`
-#' Defines the units for the time x-axis.
-# Defaults to `"days"`.
-#'
+#' `[character]` (optional)
+#'  Defines the time units of the x-axis in the plots. Expects `["weeks"/"days"]`
+#'  values. Defaults to `"days"`.
 #'  * x_axis_breaks
-#' `[integer(1)|numeric(2+)]`
-#' (optional)
-#' Defines how many breaks will be used in the time x-axis. When a single integer is passed it will use `base::pretty`
-#' to compute that number of breaks. If more than one value is passed it will use those breaks in the x-axis (e.g.
-#' if c(1,2,3) is passed it will show breaks at days/weeks 1,2 and 3).
-#' Defaults to `5`.
-#'
+#' `[integer|numeric(n)]` (optional)
+#'  Defines how many breaks will be used in the x-axis. When a single integer is
+#'  passed it will use `base::pretty` to compute that number of breaks. If more
+#'  than one value is passed it will use those breaks in the x-axis (e.g. if `c(1,
+#'  2, 3)` is passed it will show breaks at days/weeks 1, 2 and 3). Defaults to
+#'  `5`.
 #'  * timeline_info
 #' `[list]`
 #'  Start and end study dates.
@@ -164,9 +162,13 @@
 #'  formatting elements: `<b>`, `<i>`, `<br>`). The columns the values refer to are
 #'  populated with the value on the dataset relevant to any given row.
 #'  Indexes into dataset `dataset`.
+#'    * default_analysis_params
+#' `[character(n)]` (optional)
+#'  A vector of character values specifying the default analysis parameters (values
+#'  from the variable specified by `analysis_param`) to display.
 #'  * vline_vars
 #' `[character(n)]`
-#'  Place vertical dashed lines on days indicated by this dataset columns.
+#'  Place vertical dashed lines on days indicated by these dataset columns.
 #'  Indexes into dataset `subject_level_dataset_name`. Expects
 #'  `[integer|Date|POSIXt]` values.
 #'  * vline_day_numbers