Updated documentation

R/Grid.R

@@ -1,9 +1,114 @@
 
-# TODO - Docs
+#' Quantity Grid Specification
+#'
+#' @param subjects (`character` or `NULL`)\cr vector of subjects to extract quantities for.
+#' If `NULL` will default to all subjects within the dataset.
+#' @param times (`numeric` or `NULL`)\cr vector of time points to extract quantities at.
+#' If `NULL` will default to 201 evenly spaced timepoints between 0 and either the max
+#' observation time (for [`LongitudinalQuantities`]) or max event time (for [`SurvivalQuantities`]).
+#' @param groups (`list`)\cr named list of subjects to extract quantities for. See Group Specification.
+#'
+#' @description
+#' These functions are used to specify which subjects and timepoints should be generated
+#' when calculating quantities via [`SurvivalQuantities`] and [`LongitudinalQuantities`].
+#'
+#' @section Group Specification:
+#' For `GridGrouped()`, `groups` must be a named list of character vectors. Each element of the list
+#' must be a character vector of the subjects that will form the group where the element name
+#' is the corresponding name of the group. For example if the goal was to create two groups
+#' named `Group-1` and `Group-2` which are composed of the subjects `pt-1`, `pt-2` and
+#' `pt-3`, `pt-4` respectively then this would be specified as:
+#' ```
+#' GridGrouped(
+#'     groups = list(
+#'         "Group-1" = c("pt-1", "pt-2"),
+#'         "Group-2" = c("pt-3", "pt-4")
+#'     )
+#' )
+#' ```
+#' @seealso [`SurvivalQuantities`], [`LongitudinalQuantities`]
+#' @name Grid-Functions
+NULL
 
+
+
+
+
+
+#' Grid Developer Notes
+#'
+#' @description
+#' Developer details for implementing / extending `Grid` objects for defining
+#' generated quantities for [`SurvivalQuantities`] and [`LongitudinalQuantities`].
+#'
+#' @slot subjects (`character` or `NULL`)\cr vector of subjects to extract quantities for.
+#' If `NULL` will default to all subjects within the dataset.
+#' @slot times (`numeric` or `NULL`)\cr vector of time points to extract quantities at.
+#' If `NULL` will default to 201 evenly spaced timepoints between 0 and either the max
+#' @slot groups (`list`)\cr named list of subjects to extract quantities for. See details.
+#'
+#' @details
+#' All grid classes must inherit from the abstract `Grid` class.
+#' All grid classes must provide `as.QuantityGenerator(object, data)` and
+#' `as.QuantityCollapser(object, data)` methods where `data` is a [`DataJoint`] object.
+#' These methods must return a `QuantityGenerator` and `QuantityCollapser` object respectively.
+#' The `QuantityGenerator` object specifies unique subject/timepoint combinations that samples
+#' should be generated at.
+#' The `QuantityCollapser` object specifies how to combine these generated samples
+#' to form the desired quantities.
+#' As an example say we want to generate grouped samples for the groups `Group-1` and `Group-2`
+#' which consist of the subjects `pt-1`, `pt-2` and `pt-3`, `pt-4` respectively at two time points
+#' `10` and `20`. We can achieve this as follows:
+#' ```
+#' .QuantityGenerator(
+#'     times = c(10, 10, 10, 10, 20, 20, 20, 20),
+#'     subjects = c("pt-1" "pt-2", "pt-3", "pt-4", "pt-1" "pt-2", "pt-3", "pt-4")
+#' )
+#' .QuantityCollapser(
+#'     times = c(10, 20, 10 , 20),
+#'     groups = c("Group-1", "Group-1", "Group-2", "Group-2"),
+#'     indexes = list(c(1, 2), c(5, 6), c(3, 4), c(7, 8))
+#' )
+#' ```
+#'
+#' @inheritSection Grid-Functions Group Specification
+#'
+#' @keywords internal
+#' @seealso Quant-Dev
+#' @name Grid-Dev
+NULL
+
+
+
+#' Quantity Developer Notes
+#'
+#' @description
+#' Developer details for `QuantityX` objects/methods. This page just outlines the arguements
+#' and slots of these objects/methods. For the full implementation details please see [Grid-Dev]
+#'
+#' @slot times (`numeric`)\cr vector of time points to extract quantities at.
+#' @slot subjects (`character`)\cr vector of subjects to extract quantities for.
+#' @slot groups (`character`)\cr vector of labels to apply to the generated quantities.
+#' @slot indexes (`list`)\cr list of indexes that specify which observations from a
+#' `QuantityGenerator` should be combined to form the desired quantities.
+#'
+#' @param object (`Grid`)\cr object to convert to a `QuantityGenerator` or `QuantityCollapser`.
+#' @param data (`DataJoint`)\cr Survival and Longitudinal Data.
+#' @param ... Not currently used.
+#'
+#' @details
+#' The `as.QuantityGenerator` must return a `QuantityGenerator` object.
+#' The `as.QuantityCollapser` must return a `QuantityCollapser` object.
+#' @keywords internal
+#' @name Quant-Dev
+NULL
+
+
+#' @rdname Grid-Dev
 .Grid <- setClass("Grid")
 
 
+#' @rdname Quant-Dev
 .QuantityGenerator <- setClass(
     "QuantityGenerator",
     slots = c(
@@ -12,7 +117,7 @@
     )
 )
 
-
+#' @rdname Quant-Dev
 .QuantityCollapser <- setClass(
     "QuantityCollapser",
     slots = c(

R/GridFixed.R

@@ -2,6 +2,8 @@
 #' @include generics.R
 NULL
 
+
+#' @rdname Grid-Dev
 .GridFixed <- setClass(
     "GridFixed",
     contains = "Grid",
@@ -11,6 +13,7 @@ NULL
     )
 )
 
+#' @rdname Grid-Functions
 #' @export
 GridFixed <- function(subjects = NULL, times = NULL) {
     .GridFixed(
@@ -19,8 +22,9 @@ GridFixed <- function(subjects = NULL, times = NULL) {
     )
 }
 
+#' @rdname Quant-Dev
 #' @export
-as.QuantityGenerator.GridFixed <- function(object, data) {
+as.QuantityGenerator.GridFixed <- function(object, data, ...) {
     assert_class(data, "DataJoint")
     data_list <- as.list(data)
     subjects <- unlist(as.list(object, data = data), use.names = FALSE)
@@ -38,8 +42,9 @@ as.QuantityGenerator.GridFixed <- function(object, data) {
     )
 }
 
+#' @rdname Quant-Dev
 #' @export
-as.QuantityCollapser.GridFixed <- function(object, data) {
+as.QuantityCollapser.GridFixed <- function(object, data, ...) {
     generator <- as.QuantityGenerator(object, data)
     .QuantityCollapser(
         times = generator@times,
@@ -50,7 +55,7 @@ as.QuantityCollapser.GridFixed <- function(object, data) {
 
 
 #' @export
-as.list.GridFixed <- function(x, data) {
+as.list.GridFixed <- function(x, data, ...) {
     data_list <- as.list(data)
     subjects <- if (is.null(x@subjects)) {
         subs <- as.list(names(data_list$pt_to_ind))

R/GridGrouped.R

@@ -3,6 +3,7 @@
 #' @include generics.R
 NULL
 
+#' @rdname Grid-Dev
 .GridGrouped <- setClass(
     "GridGrouped",
     contains = "Grid",
@@ -12,6 +13,7 @@ NULL
     )
 )
 
+#' @rdname Grid-Functions
 #' @export
 GridGrouped <- function(groups, times = NULL) {
     .GridGrouped(
@@ -37,9 +39,9 @@ setValidity(
 )
 
 
-
+#' @rdname Quant-Dev
 #' @export
-as.QuantityGenerator.GridGrouped <- function(object, data) {
+as.QuantityGenerator.GridGrouped <- function(object, data, ...) {
     assert_class(data, "DataJoint")
     data_list <- as.list(data)
     patients_unique <- unique(unlist(object@groups))
@@ -56,8 +58,9 @@ as.QuantityGenerator.GridGrouped <- function(object, data) {
 }
 
 
+#' @rdname Quant-Dev
 #' @export
-as.QuantityCollapser.GridGrouped <- function(object, data) {
+as.QuantityCollapser.GridGrouped <- function(object, data, ...) {
     assert_class(data, "DataJoint")
     data_list <- as.list(data)
     assert_that(

R/GridObserved.R

@@ -2,6 +2,7 @@
 #' @include generics.R
 NULL
 
+#' @rdname Grid-Dev
 .GridObserved <- setClass(
     "GridObserved",
     contains = "Grid",
@@ -10,15 +11,18 @@ NULL
     )
 )
 
+
+#' @rdname Grid-Functions
 #' @export
 GridObserved <- function(subjects = NULL) {
     .GridObserved(
         subjects = subjects
     )
 }
 
+#' @rdname Quant-Dev
 #' @export
-as.QuantityGenerator.GridObserved <- function(object, data) {
+as.QuantityGenerator.GridObserved <- function(object, data, ...) {
     assert_class(data, "DataJoint")
     data_list <- as.list(data)
     subjects <- unlist(as.list(object, data = data), use.names = FALSE)
@@ -31,9 +35,9 @@ as.QuantityGenerator.GridObserved <- function(object, data) {
     )
 }
 
-
+#' @rdname Quant-Dev
 #' @export
-as.QuantityCollapser.GridObserved <- function(object, data) {
+as.QuantityCollapser.GridObserved <- function(object, data, ...) {
     generator <- as.QuantityGenerator(object, data)
 
     .QuantityCollapser(
@@ -44,7 +48,7 @@ as.QuantityCollapser.GridObserved <- function(object, data) {
 }
 
 #' @export
-as.list.GridObserved <- function(x, data) {
+as.list.GridObserved <- function(x, data, ...) {
     data_list <- as.list(data)
     subjects <- if (is.null(x@subjects)) {
         subs <- as.list(names(data_list$pt_to_ind))

R/JointModelSamples.R

@@ -27,11 +27,10 @@ setOldClass("CmdStanMCMC")
 
 
 #' @rdname generateQuantities
-#' @param patients (`character`)\cr explicit vector of patient IDs for whom the
-#' generated quantities should be extracted
-#' @param type (`character`)\cr type of quantities to be generated, must be either "survial" or
+#' @param generator ([`QuantityGenerator`])\cr object that specifies which subjects and time points
+#' to calculate the quantities at
+#' @param type (`character`)\cr type of quantities to be generated, must be either "survival" or
 #' "longitudinal".
-#' @param times TODO
 #' @export
 generateQuantities.JointModelSamples <- function(object, generator, type, ...) {
 

R/LongitudinalQuantities.R

@@ -15,7 +15,6 @@ NULL
 NULL
 
 
-# TODO - Update docs
 #' `LongitudinalQuantities` Object & Constructor Function
 #'
 #' Constructor function to generate a `LongitudinalQuantities` object.
@@ -27,6 +26,7 @@ NULL
 #' @slot quantities (`Quantities`)\cr The sampled quantities. Should contain 1 element per
 #' element of `group`
 #'
+#' @slot data (`DataJoint`)\cr Survival and Longitudinal Data.
 #'
 #' @family LongitudinalQuantities
 #' @name LongitudinalQuantities-class
@@ -41,11 +41,8 @@ NULL
 
 #' @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)`.
+#' @param grid (`Grid`) \cr object that specifies which subjects and time points to calculate the
+#' quantities for. See [Grid-Functions].
 #' @rdname LongitudinalQuantities-class
 LongitudinalQuantities <- function(
     object,