Merge pull request #17 from dom-muston/main

Update documentation and site

Author: dom-muston

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(class_dynpv)
 export(dynpv)
 export(futurepv)
 export(get_dynfields)

R/dynamic.R

@@ -48,7 +48,7 @@ trim_vec <- function(vec){
 #' @param dpv_name Name to be given to Dynamic Present Value object created by this function call
 #' @returns A list containing `inputs` and `results`.
 #' The `inputs` list contains a list of the following parameters called with the function: `uptakes, payoffs, horizon, tzero, prices`, and `discrate`. 
-#' The `results` output is a `class_dynpv` S7 object that contains the following elements:
+#' The `results` output is a [class_dynpv()] S7 object that contains the following elements:
 #' - `name`: Name given to the object
 #' - `df`: Tibble of calculation results
 #' - `ncoh`: Number of cohorts of uptaking patients

R/future.R

@@ -28,7 +28,7 @@
 #' @seealso [dynpv()]
 #' @returns A list `inputs`, `results` and `pv`.
 #' The `inputs` list contains a list of the following parameters called with the function: `uptakes, payoffs, horizon, tzero, prices`, and `discrate`. 
-#' The `results` output is a `class_dynpv` S7 object that contains the following elements:
+#' The `results` output is a [class_dynpv()] S7 object that contains the following elements:
 #' - `name`: Name given to the object
 #' - `df`: Tibble of calculation results
 #' - `ncoh`: Number of cohorts of uptaking patients (always 1)

R/oop.R

@@ -11,17 +11,18 @@
 # https://rconsortium.github.io/S7/articles/packages.html#:~:text=Documentation%20and%20exports,/S7/issues/315
 # and my documentation of the class_dynpv S7 class just results in a codoc error on calling check()
 
-# @title S7 Class Representing a Dynamic Present Value object
-# @description A Dynamic Present Value object has a name and a proscribed dataset.
-# @param name Name of object (character string)
-# @param df Dataframe of proscribed format, such as generated by `dynamicpv::dynpv()` and `dynamicpv::futurepv()`.
-# @return An object of class `class_dynpv`, with additional properties:
-# - `ncoh` Number of cohorts of uptaking patients
-# - `uptake` Total number of uptaking patients
-# - `sum_by_coh` Tibble of summarized calculation results for each uptake cohort
-# - `total` Total present value
-# - `mean` Average present value per uptaking patient (=total/uptake)
-# @export
+#' @title S7 Class Representing a Dynamic Present Value object
+#' @description A Dynamic Present Value object has a name and a proscribed dataset.
+#' @param name Name of object (character string)
+#' @param df Dataframe of proscribed format, such as generated by [dynamicpv::dynpv()] and [dynamicpv::futurepv()].
+#' @return An object of class [class_dynpv()], with additional properties:
+#' - `ncoh` Number of cohorts of uptaking patients
+#' - `uptake` Total number of uptaking patients
+#' - `sum_by_coh` Tibble of summarized calculation results for each uptake cohort
+#' - `total` Total present value
+#' - `mean` Average present value per uptaking patient (=total/uptake)
+#' @export
+#' @name class_dynpv
 class_dynpv <- S7::new_class(
   name = "class_dynpv",
   properties = list(
@@ -106,15 +107,16 @@ class_dynpv <- S7::new_class(
 #`-` <- S7::new_generic("-", c("e1", "e2"))
 addprod <- S7::new_generic("addprod", c("e1", "e2"))
 
-# @title Method to add two class_dynpv S7 objects together
-# @description Add together two objects each of S7 class `class_dynpv`: e1 + mult * e2
-# @param e1 First `class_dynpv` object
-# @param e2 Second `class_dynpv` object
-# @param mult Numeric
-# Present value is present value from `e1` plus `mult` times the present value from `e2`.
-# Total uptake is the uptake from `e1` plus `mult` times the uptake from `e2`. Take care of this when using `@mean` of the summed object.
-# @returns S7 object of class `class_dynpv`
-# @export
+#' @title Method to add two class_dynpv S7 objects together
+#' @description Add together two objects each of S7 class [class_dynpv()]: e1 + mult * e2
+#' @param e1 First [class_dynpv()] object
+#' @param e2 Second [class_dynpv()]  object
+#' @param mult Numeric
+#' Present value is present value from `e1` plus `mult` times the present value from `e2`.
+#' Total uptake is the uptake from `e1` plus `mult` times the uptake from `e2`. Take care of this when using `@mean` of the summed object.
+#' @returns S7 object of class [class_dynpv()]
+#' @noRd
+#' @name addprod.class_dynpv
 S7::method(addprod, signature = list(e1 = class_dynpv, e2 = class_dynpv)) <- function(e1, e2, mult) {
   # Pull out xdata and subset of ydata; add dpvno=1 or 2 depending on source
   xdata <- e1@df |>
@@ -148,30 +150,36 @@ S7::method(addprod, signature = list(e1 = class_dynpv, e2 = class_dynpv)) <- fun
   )
 }
 
-# @title Method to add two class_dynpv S7 objects together
-# @description Add together two objects each of S7 class `class_dynpv`
-# @param e1 First `class_dynpv` object
-# @param e2 Second `class_dynpv` object
-# Present value of `e1+e2` is sum of present values from `e1` and `e2`.
-# Total uptake of `e1+e2` is sum of uptake from `e1` and `e2`. Take care of this when using `@mean` of the summed object.
-# @returns S7 object of class `class_dynpv`
-# @export
+#' @title Method to add two class_dynpv S7 objects together
+#' @description Add together two objects each of S7 class [class_dynpv()]
+#' @param e1 First [class_dynpv()] object
+#' @param e2 Second [class_dynpv()] object
+#' Present value of `e1+e2` is sum of present values from `e1` and `e2`.
+#' Total uptake of `e1+e2` is sum of uptake from `e1` and `e2`. Take care of this when using `@mean` of the summed object.
+#' @returns S7 object of class [class_dynpv()]
+#' @noRd
+#' @name `+`.class_dynpv
 S7::method(`+`, signature = list(e1 = class_dynpv, e2 = class_dynpv)) <- function(e1, e2) {
   addprod(e1, e2, mult=1)
 }
 
-# Method to subtract one class_dynpv S7 object from another
-# @description Subtract one object of S7 class `class_dynpv` from another
-# @param e1 First `class_dynpv` object
-# @param e2 Second `class_dynpv` object
-# Present value of `e1-e2` is the present values from `e1` less that from `e2`.
-# Total uptake of `e1-e2` is the uptake from `e1` less that from `e2`. Take care of this when using `@mean` of the summed object.
-# @returns S7 object of class `class_dynpv`
+#' @title Method to subtract one class_dynpv S7 object from another
+#' @description Subtract one object of S7 class [class_dynpv()] from another
+#' @param e1 First [class_dynpv()] object
+#' @param e2 Second [class_dynpv()] object
+#' Present value of `e1-e2` is the present values from `e1` less that from `e2`.
+#' Total uptake of `e1-e2` is the uptake from `e1` less that from `e2`. Take care of this when using `@mean` of the summed object.
+#' @returns S7 object of class [class_dynpv()]
+#' @noRd
+#' @name `-`.class_dynpv
 S7::method(`-`, signature = list(e1 = class_dynpv, e2 = class_dynpv)) <- function(e1, e2) {
   addprod(e1, e2, mult=-1)
 }
 
-# Define a print method for the class_dynpv class
+#' @title Print method for the class_dynpv class
+#' @description Print [class_dynpv()] objects
+#' @name print.class_dynpv
+#' @noRd
 S7::method(print, class_dynpv) <- function(x, ...) {
   cat("This is a dynamicpv::class_dynpv S7 object, named", x@name, ". \n")
   cat("     Number of cohorts:            ", x@ncoh, "\n")