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Refactor default parameter calculators get_gamma/f0/ks_default into S3 generics #429

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Refactor default parameter calculators get_gamma/f0/ks_default into S3 generics #429

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f18a123
Refactor get_gamma_default, get_f0_default, and get_ks_default to S3 …
gustavdelius Jun 30, 2026
c5fa1dd
Update roxygen param doc for get_gamma_default to match signature
gustavdelius Jun 30, 2026
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3 changes: 3 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -136,9 +136,12 @@ S3method(getYield,MizerParams)
S3method(getYield,MizerSim)
S3method(getYieldGear,MizerParams)
S3method(getYieldGear,MizerSim)
S3method(get_f0_default,MizerParams)
S3method(get_gamma_default,MizerParams)
S3method(get_h_default,MizerParams)
S3method(get_h_default,data.frame)
S3method(get_h_default,species_params)
S3method(get_ks_default,MizerParams)
S3method(given_species_params,MizerParams)
S3method(given_species_params,MizerSim)
S3method(given_species_params,data.frame)
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43 changes: 33 additions & 10 deletions R/species_params.R
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Expand Up @@ -632,13 +632,20 @@ get_h_default.data.frame <- function(object) {
#' spectrum described by the power law \eqn{\kappa w^{-\lambda}} achieve a
#' feeding level \eqn{f_0}. Only for internal use.
#'
#' @param params A MizerParams object
#' @param object A MizerParams object
#' @return A vector with the values of gamma for all species
#' @export
#' @concept helper
#' @family functions calculating defaults
get_gamma_default <- function(params) {
assert_that(is(params, "MizerParams"))
get_gamma_default <- function(object) {
UseMethod("get_gamma_default")
}

#' @rdname get_gamma_default
#' @usage NULL
#' @export
get_gamma_default.MizerParams <- function(object) {
params <- object
species_params <- params@species_params %>%
set_species_param_default("f0", 0.6)
if (!("gamma" %in% colnames(species_params))) {
Expand Down Expand Up @@ -683,6 +690,7 @@ get_gamma_default <- function(params) {
return(species_params$gamma)
}


#' Get default value for f0
#'
#' Fills in any missing values for f0 so that if the prey abundance was
Expand All @@ -695,13 +703,20 @@ get_gamma_default <- function(params) {
#' parameter data frame, the `f0` values is kept as provided in the species
#' parameter data frame or it is set to 0.6 if it is not provided.
#'
#' @param params A MizerParams object
#' @param object A MizerParams object
#' @return A vector with the values of f0 for all species
#' @export
#' @concept helper
#' @family functions calculating defaults
get_f0_default <- function(params) {
assert_that(is(params, "MizerParams"))
get_f0_default <- function(object) {
UseMethod("get_f0_default")
}

#' @rdname get_f0_default
#' @usage NULL
#' @export
get_f0_default.MizerParams <- function(object) {
params <- object
species_params <- params@species_params %>%
set_species_param_default("f0", 0.6)
if (!("gamma" %in% colnames(species_params))) {
Expand Down Expand Up @@ -736,21 +751,29 @@ get_f0_default <- function(params) {
return(species_params$f0)
}


#' Get default value for `ks`
#'
#' Fills in any missing values for `ks` so that the critical feeding level needed
#' to sustain the species is as specified in the `fc` column in the species
#' parameter data frame. If that column is not provided the default critical
#' feeding level \eqn{f_c = 0.2} is used.
#'
#' @param params A MizerParams object
#' @param object A MizerParams object
#' @return A vector with the values of ks for all species
#' @export
#' @concept helper
#' @family functions calculating defaults
get_ks_default <- function(params) {
assert_that(is(params, "MizerParams"),
"n" %in% names(params@species_params),
get_ks_default <- function(object) {
UseMethod("get_ks_default")
}

#' @rdname get_ks_default
#' @usage NULL
#' @export
get_ks_default.MizerParams <- function(object) {
params <- object
assert_that("n" %in% names(params@species_params),
"p" %in% names(params@species_params))
if (!"h" %in% names(params@species_params) ||
any(is.na(params@species_params[["h"]]))) {
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5 changes: 3 additions & 2 deletions man/get_f0_default.Rd
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5 changes: 3 additions & 2 deletions man/get_gamma_default.Rd
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5 changes: 3 additions & 2 deletions man/get_ks_default.Rd
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5 changes: 5 additions & 0 deletions tests/testthat/test-species_params.R
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Expand Up @@ -334,4 +334,9 @@ test_that("get_h_default S3 methods work", {

expect_equal(h_params, h_sp)
expect_equal(h_params, h_df)

# Test other default S3 generics
expect_equal(get_gamma_default(params), get_gamma_default.MizerParams(params))
expect_equal(get_f0_default(params), get_f0_default.MizerParams(params))
expect_equal(get_ks_default(params), get_ks_default.MizerParams(params))
})