Merge branch '666-implement-the-dataordinal-class' of github.com:Roch…

…e/crmPack into 666-implement-the-dataordinal-class

R/Data-class.R

@@ -431,7 +431,7 @@ DataDA <- function(u = numeric(),
 #' @param yCategories (named `integer`)\cr the names and codes for the
 #' toxicity categories used in the data.  Category labels are taken from the
 #' names of the vector.  The names of the vector must be unique and its values
-#' must be sorted and take the values 0, 1, 2, ...'
+#' must be sorted and take the values 0, 1, 2, ...
 #' @inheritParams Data
 #' @inherit Data details note params
 #' @example examples/Data-class-DataOrdinal.R

R/Data-methods.R

@@ -51,10 +51,10 @@ setMethod(
 #'   as the active dose level in the corresponding cohort,
 #'   and DLTs are always assigned to the first subjects in a cohort.
 #' @param legend (`flag`)\cr whether the legend should be added.
-#' @param tox_labels (`named list of character`)\cr The labels of the toxicity
-#' categories
-#' @param tox_shapes (`names list of integers`)\cr The symbols used to identify
-#' the toxicity categories
+#' @param tox_labels (`named list of character`)\cr the labels of the toxicity
+#' categories.
+#' @param tox_shapes (`names list of integers`)\cr the symbols used to identify
+#' the toxicity categories.
 #' @param ... not used.
 #'
 #' @note With more than 9 toxicity categories, toxicity symbols must be
@@ -277,7 +277,12 @@ setMethod(
 #' @param new_cohort (`flag`)\cr if `TRUE` (default) the new data are assigned
 #'   to a new cohort.
 #' @param check (`flag`)\cr whether the validation of the updated object should
-#'   be conducted. Current implementation of this `update` method allows for
+#'   be conducted. See details below.
+#' @param ... not used.
+#'
+#' @return The new, updated [`Data`] object.
+#'
+#' @details The current implementation of this `update` method allows for
 #'   updating the `Data` class object by adding a single dose level `x` only.
 #'   However, there might be some use cases where the new cohort to be added
 #'   contains a placebo and active dose. Hence, such update would need to be
@@ -287,9 +292,6 @@ setMethod(
 #'   the `update` method would normally throw the error when attempting to add
 #'   a placebo in the first call. To allow for such updates, the `check`
 #'   parameter should be then set to `FALSE` for that first call.
-#' @param ... not used.
-#'
-#' @return The new, updated [`Data`] object.
 #'
 #' @aliases update-Data
 #' @export
@@ -366,7 +368,12 @@ setMethod(
 #' @param new_cohort (`flag`)\cr if `TRUE` (default) the new data are assigned
 #'   to a new cohort.
 #' @param check (`flag`)\cr whether the validation of the updated object should
-#'   be conducted. Current implementation of this `update` method allows for
+#'   be conducted. See Details below.
+#' @param ... not used.
+#'
+#' @return The new, updated [`DataOrdinal`] object.
+#'
+#' @details The current implementation of this `update` method allows for
 #'   updating the `DataOrdinal` class object by adding a single dose level `x` only.
 #'   However, there might be some use cases where the new cohort to be added
 #'   contains a placebo and active dose. Hence, such update would need to be
@@ -376,9 +383,6 @@ setMethod(
 #'   the `update` method would normally throw the error when attempting to add
 #'   a placebo in the first call. To allow for such updates, the `check`
 #'   parameter should be then set to `FALSE` for that first call.
-#' @param ... not used.
-#'
-#' @return The new, updated [`DataOrdinal`] object.
 #'
 #' @aliases update-DataOrdinal
 #' @export

R/helpers_data.R

@@ -64,9 +64,9 @@ setGeneric(
 #'   It can be e.g. an extra `column_name = value` pair based on a slot
 #'   from `x` (which in this case might be a subclass of `Data`)
 #'   which does not appear in `Data`.
-#' @return A [`data.frame`] object with columns patient, ID, cohort, dose and
+#' @return A `data.frame` object with columns patient, ID, cohort, dose and
 #' toxicity.
-#' @describeIn h_plot_data_df Class specific method for [`Data`]
+#' @describeIn h_plot_data_df method for [`Data`].
 setMethod(
   f = "h_plot_data_df",
   signature = signature(data = "Data"),