Ensure that all man pages state the return value, as required by CRAN.

Author: gustavdelius

R/compareParams.R

@@ -4,6 +4,7 @@
 #'
 #' @param params1 First MizerParams object
 #' @param params2 Second MizerParams object
+#' @return String describing the differences
 #' @export
 #' @examples
 #' params1 <- NS_params

R/customFunction.R

@@ -34,6 +34,7 @@
 #'
 #' @param name Name of mizer function to replace
 #' @param fun The custom function to use as replacement
+#' @return No return value, called for side effects
 #' @export
 #' @examples
 #' \dontrun{
@@ -54,4 +55,5 @@ customFunction <- function(name, fun) {
     }
     environment(fun) <- asNamespace("mizer")
     utils::assignInNamespace(name, fun, ns = "mizer")
+    invisible()
 }

R/deprecated.R

@@ -10,6 +10,7 @@
 #' @inheritParams newTraitParams
 #' @param q Allometric exponent of search volume
 #' @param ... Unused
+#' @return A MizerParams object
 #' @export
 #' @concept deprecated
 set_multispecies_model <- 

R/extension.R

@@ -255,6 +255,8 @@ getComponent <- function(params, component) {
 
 #' @param object An object of class MizerParams or MizerSim
 #' @rdname initialNOther-set
+#' @return A named list with the initial values of other ecosystem
+#'   components
 #' @export
 initialNOther <- function(object) {
     if (is(object, "MizerParams")) {

R/plots.R

@@ -115,6 +115,7 @@ utils::globalVariables(c("time", "value", "Species", "w", "gear", "Age",
 #' @param ytrans Transformation for the y-axis.
 #' @param y_ticks The approximate number of ticks desired on the y axis
 #' @param highlight Name or vector of names of the species to be highlighted.
+#' @return A ggplot2 object
 #' @keywords internal
 #' @export
 plotDataFrame <- function(frame, params, style = "line", xlab = waiver(),

R/project_methods.R

@@ -41,6 +41,7 @@
 #' @param rates_fns Named list of the functions to call to calculate the rates.
 #'   Note that this list holds the functions themselves, not their names.
 #' @param ... Unused
+#' @return List of rates.
 #' @export
 #' @family mizer rate functions
 mizerRates <- function(params, n, n_pp, n_other,

R/reproduction.R

@@ -67,7 +67,7 @@ mizerRDI <- function(params, n, n_pp, n_other, t,
 #' @param mort A two dimensional array (species x size) holding the mortality
 #'   rate as calculated by [mizerMort()].
 #' @param ... Unused
-#'
+#' @return Vector with the value for each species
 #' @export
 #' @family functions calculating density-dependent reproduction rate
 #' @examples

R/resource_dynamics.R

@@ -53,6 +53,7 @@ resource_constant <- function(params, n_pp, ...) {
 #' sizes.
 #' 
 #' @param params A MizerParams object
+#' @return A named list of resource parameters.
 #' @export
 resource_params <- function(params) {
     params@resource_params
@@ -86,6 +87,7 @@ resource_params <- function(params) {
 #' [resource_level()], [resource_rate()] and [resource_capacity()] instead.
 #' 
 #' @param params A MizerParams object
+#' @return Name of the function that determines the resource dynamics
 #' @keywords internal
 #' @export
 getResourceDynamics <- function(params) {

R/saveParams.R

@@ -11,6 +11,7 @@
 #' @param params A MizerParams object
 #' @param file The name of the file or a connection where the MizerParams object
 #'   is saved to or read from.
+#' @return NULL invisibly
 #' @export
 saveParams <- function(params, file) {
     params <- validParams(params)

R/selectivity_funcs.R

@@ -13,12 +13,13 @@
 #' selectivity function is length based, it uses the
 #' length-weight parameters `a` and `b` to convert between length and weight.
 #'
-#' @param w the size of the individual.
+#' @param w Vector of sizes.
 #' @param l25 the length which gives a selectivity of 25%.
 #' @param l50 the length which gives a selectivity of 50%.
 #' @param species_params A list with the species params for the current species.
-#'   Used to get at the length-weight parameters `a` and `b`
+#'   Used to get at the length-weight parameters `a` and `b`.
 #' @param ... Unused
+#' @return Vector of selectivities at the given sizes.
 #' @export
 #' @family selectivity functions
 sigmoid_length <- function(w, l25, l50, species_params, ...) {
@@ -56,14 +57,15 @@ sigmoid_length <- function(w, l25, l50, species_params, ...) {
 #' selectivity function is length based, it uses the
 #' length-weight parameters `a` and `b` to convert between length and weight.
 #'
-#' @param w the size of the individual.
+#' @param w Vector of sizes.
 #' @param l25 the length which gives a selectivity of 25%.
 #' @param l50 the length which gives a selectivity of 50%.
 #' @param l50_right the length which gives a selectivity of 50%.
 #' @param l25_right the length which gives a selectivity of 25%.
 #' @param species_params A list with the species params for the current species.
 #'   Used to get at the length-weight parameters `a` and `b`
 #' @param ... Unused
+#' @return Vector of selectivities at the given sizes.
 #' @export
 #' @family selectivity functions
 double_sigmoid_length <- function(w, l25, l50, l50_right, l25_right,
@@ -98,9 +100,10 @@ double_sigmoid_length <- function(w, l25, l50, l50_right, l25_right,
 #' A knife-edge selectivity function where weights greater or equal to
 #' `knife_edge_size` are selected.
 #'
-#' @param w The size of the individual.
+#' @param w Vector of sizes.
 #' @param knife_edge_size The weight at which the knife-edge operates.
 #' @param ... Unused
+#' @return Vector of selectivities at the given sizes.
 #' @export
 #' @family selectivity functions
 knife_edge <- function(w, knife_edge_size, ...) {
@@ -114,10 +117,11 @@ knife_edge <- function(w, knife_edge_size, ...) {
 #' A sigmoidal selectivity function with 50% selectivity at
 #' weight `sigmoidal_weight` and width `sigmoidal_sigma`.
 #'
-#' @param w The size of the individual.
+#' @param w Vector of sizes.
 #' @param sigmoidal_weight The weight at which the knife-edge operates.
-#' @param sigmoidal_sigma The width of the selection function
+#' @param sigmoidal_sigma The width of the selection function.
 #' @param ... Unused
+#' @return Vector of selectivities at the given sizes.
 #' @export
 #' @family selectivity functions
 sigmoid_weight <- function(w, sigmoidal_weight, sigmoidal_sigma, ...) {

R/setFishing.R

@@ -322,6 +322,7 @@ setFishing <- function(params, selectivity = NULL, catchability = NULL,
 #' illustrates how this facilitates changing an individual gear parameter.
 #' 
 #' @param params A MizerParams object
+#' @return Data frame with gear parameters
 #' @export
 #' @family functions for setting parameters
 #' @examples 
@@ -427,6 +428,7 @@ getInitialEffort <- function(params) {
 #' specify a time-varying effort.
 #' 
 #' @param params A MizerParams object
+#' @return Effort vector
 #' @export
 initial_effort <- function(params) {
     params@initial_effort

R/setInitialValues.R

@@ -132,6 +132,8 @@ setInitialValues <- function(params, sim, time_range, geometric_mean = FALSE) {
 
 #' @rdname initialN-set
 #' @param object An object of class MizerParams or MizerSim
+#' @return A matrix with dimensions species x size holding the initial number
+#'   densities for the fish spectra.
 #' @export
 #' @examples 
 #' # Doubling abundance of Cod in the initial state of the North Sea model
@@ -184,6 +186,8 @@ initialN <- function(object) {
 
 #' @rdname initialNResource-set
 #' @param object An object of class MizerParams or MizerSim
+#' @return A vector with the initial number densities for the resource
+#'   spectrum
 #' @export
 initialNResource <- function(object) {
     if (is(object, "MizerParams")) {

R/species_params.R

@@ -114,6 +114,7 @@
 #' MizerParams object, in case your own code makes use of them.
 #' 
 #' @param params A MizerParams object
+#' @return Data frame of species parameters
 #' @export
 #' @seealso [validSpeciesParams()]
 #' @family functions for setting parameters

R/steady.R

@@ -68,6 +68,8 @@ distanceSSLogN <- function(params, current, previous) {
 #'   this uses the function [distanceSSLogN()] that you can use as a model for your
 #'   own distance function.
 #' @param ... Further arguments will be passed on to your distance function.
+#' 
+#' @return A MizerParams or a MizerSim object
 #' @seealso [distanceSSLogN()], [distanceMaxRelRDI()]
 #' @export
 projectToSteady <- function(params,
@@ -216,6 +218,7 @@ projectToSteady <- function(params,
 #'   of the `reproduction_level`.
 #' @param progress_bar A shiny progress object to implement a progress bar in a
 #'   shiny app. Default FALSE.
+#' @return A MizerParams or a MizerSim object
 #' @export
 #' @examples
 #' \dontrun{
@@ -301,6 +304,7 @@ steady <- function(params, t_max = 100, t_per = 1.5, dt = 0.1,
 #' @param n_other Abundances of other components
 #' @param component Name of the component that is being updated
 #' @param ... Unused
+#' @return The current value of the component
 #' @export
 #' @concept helper
 constant_other <- function(params, n_other, component, ...) {