Converted parameters to lower case with full stop

R/DataJoint.R

@@ -90,8 +90,8 @@ as.list.DataJoint <- function(x, ...) {
 
 #' Subsetting `DataJoint` as a `data.frame`
 #'
-#' @param x (`DataJoint`) \cr A [DataJoint][DataJoint-class] object created by [DataJoint()]
-#' @param patients (`character` or `list`)\cr the patients that you wish to subset the `data.frame`
+#' @param x (`DataJoint`) \cr object created by [DataJoint()].
+#' @param patients (`character` or `list`)\cr patients that you wish to subset the `data.frame`
 #' to contain. See details.
 #' @param ... Not used.
 #'
@@ -128,9 +128,9 @@ subset.DataJoint <- function(x, patients, ...) {
 
 #' `subset_and_add_grouping`
 #'
-#' @param dat (`data.frame`) \cr Must have a column called `patient` which corresponds to the
-#' values passed to `groupings`
-#' @param groupings (`character` or `list`)\cr the patients that you wish to subset the dataset
+#' @param dat (`data.frame`) \cr must have a column called `patient` which corresponds to the
+#' values passed to `groupings`.
+#' @param groupings (`character` or `list`)\cr patients that you wish to subset the dataset
 #' to contain. If `groupings` is a list then an additional variable `group` will be added
 #' onto the dataset specifying which group the row belongs to.
 #'
@@ -167,7 +167,7 @@ subset_and_add_grouping <- function(dat, groupings) {
 #' Extract Observed Longitudinal Values
 #'
 #' Utility function to extract the observed longitudinal values from a [`DataJoint`] object
-#' @param object ([`DataJoint`])\cr The data used to fit a [`JointModel`]
+#' @param object ([`DataJoint`])\cr data used to fit a [`JointModel`].
 #' @return A data.frame with the following columns
 #' - `subject` (`character`)\cr The subject identifier
 #' - `time` (`numeric`)\cr The time at which the observation occurred

R/LongitudinalQuantities.R

@@ -8,13 +8,13 @@ NULL
 #'
 #' Constructor function to generate a `LongitudinalQuantities` object.
 #'
-#' @param object ([`JointModelSamples`]) \cr Samples as drawn from a Joint Model
+#' @param object ([`JointModelSamples`]) \cr samples as drawn from a Joint Model.
 #'
 #' @param groups (`character`, `NULL`)\cr which patients to calculate the desired
 #' quantities for.
 #'
 #' @param time_grid (`numeric` or `NULL`)\cr a vector of time points to calculate the desired
-#' quantity at. If `NULL` will be set to `seq(0, max_longitudinal_time, length = 201)`
+#' quantity at. If `NULL` will be set to `seq(0, max_longitudinal_time, length = 201)`.
 #'
 #' @details
 #' Note that unlike [SurvivalQuantities], [LongitudinalQuantities] does not support
@@ -82,8 +82,8 @@ LongitudinalQuantities <- function(
 
 #' `as.data.frame`
 #'
-#' @param x ([`LongitudinalQuantities`]) \cr Longitudinal Quantities
-#' @param ... Not used
+#' @param x ([`LongitudinalQuantities`]) \cr longitudinal quantities.
+#' @param ... not used.
 #' @family LongitudinalQuantities
 #' @export
 as.data.frame.LongitudinalQuantities <- function(x, ...) {
@@ -105,7 +105,7 @@ as.data.frame.LongitudinalQuantities <- function(x, ...) {
 #' @description
 #' This method returns a `data.frame` of the longitudinal quantities
 #'
-#' @param object ([`LongitudinalQuantities`]) \cr Survival Quantities.
+#' @param object ([`LongitudinalQuantities`]) \cr longitudinal quantities.
 #' @param conf.level (`numeric`) \cr confidence level of the interval.
 #' @param ... Not used.
 #'
@@ -135,9 +135,9 @@ summary.LongitudinalQuantities <- function(
 #' This function predominately exists to extract core logic into its own function
 #' to enable easier unit testing.
 #'
-#' @param data (`data.frame`)\cr A `data.frame` of summary statistics for longitudinal
+#' @param data (`data.frame`)\cr summary statistics for longitudinal
 #' value estimates. See details.
-#' @param data_obs (`data.frame`)\cr A `data.frame` of real observed values to be
+#' @param data_obs (`data.frame`)\cr real observed values to be
 #' overlaid for reference.  See details.
 #' @param add_ci (`logical`)\cr Should confidence intervals be added? Default = `TRUE`.
 #' @details
@@ -185,10 +185,10 @@ longitudinal_plot <- function(
 
 #' Automatic Plotting for LongitudinalQuantities
 #'
-#' @param object ([`LongitudinalQuantities`]) \cr Longitudinal Quantities
+#' @param object ([`LongitudinalQuantities`]) \cr longitudinal quantities.
 #' @param conf.level (`numeric`) \cr confidence level of the interval. If values of `FALSE`,
-#' `NULL` or `0` are provided then confidence regions will not be added to the plot
-#' @param ... Not used.
+#' `NULL` or `0` are provided then confidence regions will not be added to the plot.
+#' @param ... not used.
 #'
 #' @family LongitudinalQuantities
 #' @family autoplot

R/Quantities.R

@@ -5,8 +5,8 @@
 #' A simple wrapper around a `list` to ensure each element complies
 #' to specific formatting rules
 #'
-#' @param x (`list`)\cr A `list` of `matrix` objects. Each matrix must have the exact
-#' same dimensions
+#' @param x (`list`)\cr a `list` of `matrix` objects. Each matrix must have the exact
+#' same dimensions.
 #'
 #' @keywords internal
 #' @name Quantities-class
@@ -47,7 +47,7 @@ setValidity(
 
 #' Dimensions of `Quantitites`
 #'
-#' @param x ([`Quantities`]) \cr Any generated model quantity
+#' @param x ([`Quantities`]) \cr generated quantities.
 #'
 #' Returns the number of rows and columns within any given
 #' element of the [Quantities] object. As each element is of the same
@@ -71,11 +71,11 @@ dim.Quantities <- function(x) {
 
 #' `Quantities` -> `data.frame`
 #'
-#' @param x ([`Quantities`]) \cr Any generated model quantity
-#' @param time_grid (`numeric`)\cr Sets the `time` variable. Must be equal in length to `ncol(x)`
-#' @param type (`character`)\cr Sets the `type` variable.
-#' @param groups (`list`)\cr Named `list`. The element names are used to set the `group` variable
-#' @param ... Not used
+#' @param x ([`Quantities`]) \cr generated quantities.
+#' @param time_grid (`numeric`)\cr sets the `time` variable. Must be equal in length to `ncol(x)`.
+#' @param type (`character`)\cr sets the `type` variable.
+#' @param groups (`list`)\cr named `list`. The element names are used to set the `group` variable.
+#' @param ... not used.
 #'
 #' @keywords internal
 #' @family Quantities
@@ -116,12 +116,13 @@ as.data.frame.Quantities <- function(x, ..., time_grid, type, groups) {
 #' is just an internal utility method in order to share common code between
 #' [LongitudinalQuantities] and [SurvivalQuantities]
 #'
-#' @param object ([`Quantities`]) \cr Any generated model quantity
-#' @param time_grid (`numeric`)\cr Sets the `time` variable. Must be equal in length to `ncol(object)`
-#' @param type (`character`)\cr Sets the `type` variable.
-#' @param groups (`list`)\cr Named `list`. The element names are used to set the `group` variable
+#' @param object ([`Quantities`]) \cr generated quantities.
+#' @param time_grid (`numeric`)\cr sets the `time` variable.
+#' Must be equal in length to `ncol(object)`.
+#' @param type (`character`)\cr sets the `type` variable.
+#' @param groups (`list`)\cr named `list`. The element names are used to set the `group` variable.
 #' @param conf.level (`numeric`) \cr confidence level of the interval.
-#' @param ... Not used.
+#' @param ... not used.
 #'
 #' @returns
 #' A `data.frame` with the following variables:
@@ -168,13 +169,13 @@ summary.Quantities <- function(object, time_grid, type, groups, conf.level = 0.9
 #' This function takes a [posterior::draws_matrix()] (matrix of cmdstanr sample draws) and extracts
 #' the specified columns and aggregates them by calculating the pointwise average.
 #'
-#' @param subject_index (`numeric`)\cr Which subject indices to extract from `quantities`.
+#' @param subject_index (`numeric`)\cr which subject indices to extract from `quantities`.
 #' See details.
 #'
-#' @param time_index (`numeric`)\cr Which time point indices to extract from `quantities`.
+#' @param time_index (`numeric`)\cr which time point indices to extract from `quantities`.
 #' See details.
 #'
-#' @param quantities ([`posterior::draws_matrix`])\cr A matrix of sample draws.
+#' @param quantities ([`posterior::draws_matrix`])\cr sample draws.
 #' See details.
 #'
 #' @details
@@ -230,8 +231,8 @@ average_samples_by_index <- function(subject_index, time_index, quantities) {
 #' Multiple quantities are generated by default so this is a convenience function to extract
 #' the desired ones and return them them as a user friendly [posterior::draws_matrix] object
 #'
-#' @param gq (`CmdStanGQ`) \cr A [cmdstanr::CmdStanGQ] object created by [generateQuantities]
-#' @param type (`character`)\cr The quantity to be generated.
+#' @param gq (`CmdStanGQ`) \cr a [cmdstanr::CmdStanGQ] object created by [generateQuantities].
+#' @param type (`character`)\cr quantity to be generated.
 #' Must be one of `surv`, `haz`, `loghaz`, `cumhaz`, `lm_identity`.
 #' @keywords internal
 extract_quantities <- function(gq, type = c("surv", "haz", "loghaz", "cumhaz", "lm_identity")) {

R/SurvivalQuantities.R

@@ -8,17 +8,17 @@ NULL
 #'
 #' Constructor function to generate a `SurvivalQuantities` object.
 #'
-#' @param object ([`JointModelSamples`]) \cr Samples as drawn from a Joint Model
+#' @param object ([`JointModelSamples`]) \cr samples as drawn from a Joint Model.
 #'
 #' @param groups (`character` or `list` or `NULL`)\cr which patients to calculate the desired
 #' quantities for.
 #' See "Group Specification" for more details.
 #'
-#' @param type (`character`)\cr The quantity to be generated.
+#' @param type (`character`)\cr quantity to be generated.
 #' Must be one of `surv`, `haz`, `loghaz`, `cumhaz`.
 #'
-#' @param time_grid (`numeric` or `NULL`)\cr a vector of time points to calculate the desired
-#' quantity at. If `NULL` will be set to `seq(0, max_survival_time, length = 201)`
+#' @param time_grid (`numeric` or `NULL`)\cr vector of time points to calculate the desired
+#' quantity at. If `NULL` will be set to `seq(0, max_survival_time, length = 201)`.
 #'
 #'
 #' @slot quantities (`Quantities`)\cr The sampled quantities. Should contain 1 element per
@@ -130,9 +130,9 @@ setValidity(
 #' @description
 #' This method returns a `data.frame` of key quantities (survival / log-hazard / etc)
 #'
-#' @param object ([`SurvivalQuantities`]) \cr Survival Quantities.
+#' @param object ([`SurvivalQuantities`]) \cr survival quantities.
 #' @param conf.level (`numeric`) \cr confidence level of the interval.
-#' @param ... Not used.
+#' @param ... not used.
 #'
 #' @family SurvivalQuantities
 #' @family summary
@@ -155,8 +155,8 @@ summary.SurvivalQuantities <- function(
 
 #' `SurvivalQuantities` -> `data.frame`
 #'
-#' @param x ([`SurvivalQuantities`]) \cr Survival Quantities
-#' @param ... Not used
+#' @param x ([`SurvivalQuantities`]) \cr survival quantities.
+#' @param ... not used.
 #' @family SurvivalQuantities
 #' @export
 as.data.frame.SurvivalQuantities <- function(x, ...) {
@@ -171,14 +171,14 @@ as.data.frame.SurvivalQuantities <- function(x, ...) {
 
 #' Automatic Plotting for LongitudinalQuantities
 #'
-#' @param object ([`SurvivalQuantities`]) \cr Survival Quantities
-#' @param add_km (`logical`) \cr If `TRUE` Kaplan-Meier curves will be added to the plot for
-#' each group/patient
-#' @param add_wrap (`logical`) \cr If `TRUE` will apply a [ggplot2::facet_wrap()] to the plot
-#' by each group/patient
+#' @param object ([`SurvivalQuantities`]) \cr survival quantities.
+#' @param add_km (`logical`) \cr if `TRUE` Kaplan-Meier curves will be added to the plot for
+#' each group/patient.
+#' @param add_wrap (`logical`) \cr if `TRUE` will apply a [ggplot2::facet_wrap()] to the plot
+#' by each group/patient.
 #' @param conf.level (`numeric`) \cr confidence level of the interval. If values of `FALSE`,
 #' `NULL` or `0` are provided then confidence regions will not be added to the plot
-#' @param ... Not Used.
+#' @param ... not used.
 #'
 #' @family SurvivalQuantities
 #' @family autoplot
@@ -225,15 +225,15 @@ autoplot.SurvivalQuantities <- function(object,
 #' This function predominately exists to extract core logic into its own function
 #' to enable easier unit testing.
 #'
-#' @param data (`data.frame`)\cr A `data.frame` of summary statistics for a survival
+#' @param data (`data.frame`)\cr summary statistics for a survival
 #' curve to be plotted. See details.
-#' @param add_ci (`logical`)\cr Should confidence intervals be added? Default = `TRUE`.
-#' @param add_wrap (`logical`)\cr Should the plots be wrapped by `data$group`? Default = `TRUE`.
-#' @param kmdf (`data.frame` or `NULL`)\cr A `data.frame` of event times and status used to plot
+#' @param add_ci (`logical`)\cr should confidence intervals be added? Default = `TRUE`.
+#' @param add_wrap (`logical`)\cr should the plots be wrapped by `data$group`? Default = `TRUE`.
+#' @param kmdf (`data.frame` or `NULL`)\cr event times and status used to plot
 #' overlaying KM curves. If `NULL` no KM curve will be plotted. See details.
-#' @param y_label (`character` or `expression`) \cr Label to display on the y-axis.
-#' Default = `expression(S(t))`
-#' @param x_label (`character` or `expression`) \cr Label to display on the x-axis.
+#' @param y_label (`character` or `expression`) \cr label to display on the y-axis.
+#' Default = `expression(S(t))`.
+#' @param x_label (`character` or `expression`) \cr label to display on the x-axis.
 #'
 #' @details
 #'