S3 methods

DESCRIPTION

@@ -19,7 +19,7 @@ Authors@R: c(person("Gustav", "Delius", email="gustav.delius@york.ac.uk",
                     comment = c(ORCID = "0000-0002-8478-3430")),
              person("Richard", "Southwell", email="richard.southwell@york.ac.uk",
                     role=c("ctb", "cph")))
-Version: 2.5.4.9001
+Version: 2.5.4.9011
 License: GPL-3
 Imports:
     assertthat,

NAMESPACE

@@ -1,5 +1,174 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("catchability<-",MizerParams)
+S3method("diffusion<-",MizerParams)
+S3method("ext_encounter<-",MizerParams)
+S3method("ext_mort<-",MizerParams)
+S3method("gear_params<-",MizerParams)
+S3method("given_species_params<-",MizerParams)
+S3method("initialN<-",MizerParams)
+S3method("initialNResource<-",MizerParams)
+S3method("initial_effort<-",MizerParams)
+S3method("intake_max<-",MizerParams)
+S3method("interaction_matrix<-",MizerParams)
+S3method("maturity<-",MizerParams)
+S3method("metab<-",MizerParams)
+S3method("pred_kernel<-",MizerParams)
+S3method("repro_prop<-",MizerParams)
+S3method("resource_capacity<-",MizerParams)
+S3method("resource_dynamics<-",MizerParams)
+S3method("resource_level<-",MizerParams)
+S3method("resource_params<-",MizerParams)
+S3method("resource_rate<-",MizerParams)
+S3method("search_vol<-",MizerParams)
+S3method("selectivity<-",MizerParams)
+S3method("species_params<-",MizerParams)
+S3method(addSpecies,MizerParams)
+S3method(age_mat,MizerParams)
+S3method(age_mat_vB,MizerParams)
+S3method(age_mat_vB,data.frame)
+S3method(age_mat_vB,default)
+S3method(animateSpectra,MizerSim)
+S3method(calculated_species_params,MizerParams)
+S3method(calibrateBiomass,MizerParams)
+S3method(calibrateNumber,MizerParams)
+S3method(calibrateYield,MizerParams)
+S3method(catchability,MizerParams)
+S3method(compareParams,MizerParams)
+S3method(diffusion,MizerParams)
+S3method(distanceMaxRelRDI,MizerParams)
+S3method(distanceSSLogN,MizerParams)
+S3method(dw,MizerParams)
+S3method(dw_full,MizerParams)
+S3method(ext_encounter,MizerParams)
+S3method(ext_mort,MizerParams)
+S3method(gear_params,MizerParams)
+S3method(getBiomass,MizerParams)
+S3method(getBiomass,MizerSim)
+S3method(getCatchability,MizerParams)
+S3method(getColours,MizerParams)
+S3method(getCommunitySlope,MizerSim)
+S3method(getCriticalFeedingLevel,MizerParams)
+S3method(getDiet,MizerParams)
+S3method(getEGrowth,MizerParams)
+S3method(getERepro,MizerParams)
+S3method(getEReproAndGrowth,MizerParams)
+S3method(getEncounter,MizerParams)
+S3method(getExtEncounter,MizerParams)
+S3method(getExtMort,MizerParams)
+S3method(getFMort,MizerParams)
+S3method(getFMort,MizerSim)
+S3method(getFMortGear,MizerParams)
+S3method(getFMortGear,MizerSim)
+S3method(getFeedingLevel,MizerParams)
+S3method(getFeedingLevel,MizerSim)
+S3method(getGrowthCurves,MizerParams)
+S3method(getGrowthCurves,MizerSim)
+S3method(getInitialEffort,MizerParams)
+S3method(getInteraction,MizerParams)
+S3method(getLinetypes,MizerParams)
+S3method(getMaturityProportion,MizerParams)
+S3method(getMaxIntakeRate,MizerParams)
+S3method(getMeanMaxWeight,MizerSim)
+S3method(getMeanWeight,MizerSim)
+S3method(getMetabolicRate,MizerParams)
+S3method(getMetadata,MizerParams)
+S3method(getMort,MizerParams)
+S3method(getN,MizerParams)
+S3method(getN,MizerSim)
+S3method(getPredKernel,MizerParams)
+S3method(getPredMort,MizerParams)
+S3method(getPredMort,MizerSim)
+S3method(getPredRate,MizerParams)
+S3method(getProportionOfLargeFish,MizerSim)
+S3method(getRDD,MizerParams)
+S3method(getRDI,MizerParams)
+S3method(getRates,MizerParams)
+S3method(getReproductionLevel,MizerParams)
+S3method(getReproductionProportion,MizerParams)
+S3method(getRequiredRDD,MizerParams)
+S3method(getResourceMort,MizerParams)
+S3method(getSSB,MizerParams)
+S3method(getSSB,MizerSim)
+S3method(getSearchVolume,MizerParams)
+S3method(getSelectivity,MizerParams)
+S3method(getYield,MizerParams)
+S3method(getYield,MizerSim)
+S3method(getYieldGear,MizerParams)
+S3method(getYieldGear,MizerSim)
+S3method(given_species_params,MizerParams)
+S3method(initialN,MizerParams)
+S3method(initialN,MizerSim)
+S3method(initialNResource,MizerParams)
+S3method(initialNResource,MizerSim)
+S3method(initial_effort,MizerParams)
+S3method(intake_max,MizerParams)
+S3method(interaction_matrix,MizerParams)
+S3method(matchBiomasses,MizerParams)
+S3method(matchGrowth,MizerParams)
+S3method(matchNumbers,MizerParams)
+S3method(matchYields,MizerParams)
+S3method(maturity,MizerParams)
+S3method(metab,MizerParams)
+S3method(plotBiomass,MizerSim)
+S3method(plotBiomassObservedVsModel,MizerParams)
+S3method(plotBiomassObservedVsModel,MizerSim)
+S3method(plotDiet,MizerParams)
+S3method(plotDiet,MizerSim)
+S3method(plotFMort,MizerParams)
+S3method(plotFMort,MizerSim)
+S3method(plotFeedingLevel,MizerParams)
+S3method(plotFeedingLevel,MizerSim)
+S3method(plotGrowthCurves,MizerParams)
+S3method(plotGrowthCurves,MizerSim)
+S3method(plotPredMort,MizerParams)
+S3method(plotPredMort,MizerSim)
+S3method(plotSpectra,MizerParams)
+S3method(plotSpectra,MizerSim)
+S3method(plotYield,MizerSim)
+S3method(plotYieldGear,MizerSim)
+S3method(plotYieldObservedVsModel,MizerParams)
+S3method(plotYieldObservedVsModel,MizerSim)
+S3method(pred_kernel,MizerParams)
+S3method(project,MizerParams)
+S3method(project,MizerSim)
+S3method(projectToSteady,MizerParams)
+S3method(project_simple,MizerParams)
+S3method(removeSpecies,MizerParams)
+S3method(renameGear,MizerParams)
+S3method(renameSpecies,MizerParams)
+S3method(repro_prop,MizerParams)
+S3method(resource_capacity,MizerParams)
+S3method(resource_dynamics,MizerParams)
+S3method(resource_level,MizerParams)
+S3method(resource_params,MizerParams)
+S3method(resource_rate,MizerParams)
+S3method(saveParams,MizerParams)
+S3method(scaleModel,MizerParams)
+S3method(search_vol,MizerParams)
+S3method(selectivity,MizerParams)
+S3method(setBevertonHolt,MizerParams)
+S3method(setColours,MizerParams)
+S3method(setDiffusion,MizerParams)
+S3method(setExtEncounter,MizerParams)
+S3method(setExtMort,MizerParams)
+S3method(setFishing,MizerParams)
+S3method(setInitialValues,MizerParams)
+S3method(setInteraction,MizerParams)
+S3method(setLinetypes,MizerParams)
+S3method(setMaxIntakeRate,MizerParams)
+S3method(setMetabolicRate,MizerParams)
+S3method(setMetadata,MizerParams)
+S3method(setParams,MizerParams)
+S3method(setPredKernel,MizerParams)
+S3method(setReproduction,MizerParams)
+S3method(setResource,MizerParams)
+S3method(setSearchVolume,MizerParams)
+S3method(species_params,MizerParams)
+S3method(steady,MizerParams)
+S3method(steadySingleSpecies,MizerParams)
+S3method(w,MizerParams)
+S3method(w_full,MizerParams)
 export("catchability<-")
 export("diffusion<-")
 export("ext_encounter<-")

R/MizerParams-class.R

@@ -789,6 +789,10 @@ emptyParams <- function(species_params,
 #' # Summing to get total biomass
 #' sum(biomass)
 w <- function(params) {
+    UseMethod("w")
+}
+#' @export
+w.MizerParams <- function(params) {
     params@w
 }
 
@@ -798,6 +802,10 @@ w <- function(params) {
 #'   the consumer spectrum.
 #' @export
 w_full <- function(params) {
+    UseMethod("w_full")
+}
+#' @export
+w_full.MizerParams <- function(params) {    
     params@w_full
 }
 
@@ -806,6 +814,10 @@ w_full <- function(params) {
 #'   consumer spectrum.
 #' @export
 dw <- function(params) {
+    UseMethod("dw")
+}
+#' @export
+dw.MizerParams <- function(params) {
     params@dw
 }
 
@@ -814,6 +826,10 @@ dw <- function(params) {
 #'   resource spectrum.
 #' @export
 dw_full <- function(params) {
+    UseMethod("dw_full")
+}
+#' @export
+dw_full.MizerParams <- function(params) {
     params@dw_full
 }
 

R/age_mat.R

@@ -14,28 +14,42 @@
 #' missing. If `w_inf` is missing, `w_max` is used instead.
 #'
 #' @param object A MizerParams object or a species_params data frame
+#' @param ... Additional arguments
+#'
 #' @return A named vector. The names are the species names and the values are
 #'   the ages at maturity.
 #' @export
-age_mat_vB <- function(object) {
-    if (is(object, "MizerParams")) {
-        sp <- object@species_params
-    } else {
-        if (!is.data.frame(object)) {
-            stop("The first argument must be either a MizerParams object or a species_params data frame.")
-        }
-        sp <- validSpeciesParams(object)
-    }
+#' @rdname age_mat_vB
+age_mat_vB <- function(object, ...) {
+    UseMethod("age_mat_vB")
+}
+
+#' @rdname age_mat_vB
+#' @export
+age_mat_vB.MizerParams <- function(object, ...) {
+    age_mat_vB.data.frame(object@species_params)
+}
+
+#' @rdname age_mat_vB
+#' @export
+age_mat_vB.data.frame <- function(object, ...) {
+    sp <- object
     sp <- set_species_param_default(sp, "t0", 0)
     sp <- set_species_param_default(sp, "b", 3)
     sp <- set_species_param_default(sp, "k_vb", NA)
     sp <- set_species_param_default(sp, "w_inf", sp$w_max)
 
-    a_mat <- -log(1 - (sp$w_mat / sp$w_inf) ^ (1/sp$b)) / sp$k_vb + sp$t0
+    a_mat <- -log(1 - (sp$w_mat / sp$w_inf)^(1 / sp$b)) / sp$k_vb + sp$t0
     names(a_mat) <- sp$species
     a_mat
 }
 
+#' @rdname age_mat_vB
+#' @export
+age_mat_vB.default <- function(object, ...) {
+    stop("The first argument must be either a MizerParams object or a species_params data frame.")
+}
+
 #' Calculate age at maturity
 #'
 #' Uses the growth rate and the size at maturity to calculate the age at
@@ -45,14 +59,22 @@ age_mat_vB <- function(object) {
 #' \deqn{\mathrm{age_{mat}} = \int_0^{w_{mat}.}\frac{dw}{g(w)}}{age_mat = \int_0^w_mat 1/g(w) dw.}
 #'
 #' @param params A MizerParams object
+#' @param ... Additional arguments
+#'
 #' @return A named vector. The names are the species names and the values are
 #'   the ages at maturity.
 #' @export
 #' @concept helper
 #' @examples
 #' age_mat(NS_params)
-age_mat <- function(params) {
-    assert_that(is(params, "MizerParams"))
+#' @rdname age_mat
+#' @export
+age_mat <- function(params, ...) {
+    UseMethod("age_mat")
+}
+
+#' @export
+age_mat.MizerParams <- function(params, ...) {
     sp <- params@species_params
     no_sp <- nrow(sp)
 

R/animateSpectra.R

@@ -3,7 +3,7 @@
 #' `r lifecycle::badge("experimental")`
 #'
 #' @param sim A MizerSim object
-#' @param species Name or vector of names of the species to be plotted. By 
+#' @param species Name or vector of names of the species to be plotted. By
 #'   default all species are plotted.
 #' @param time_range The time range to animate over. Either a vector of values
 #'   or a vector of min and max time. Default is the entire time range of the
@@ -21,24 +21,29 @@
 #'   species in the system is plotted as well. Default is FALSE.
 #' @param resource A boolean value that determines whether resource is included.
 #'   Default is TRUE.
-#' 
+#' @param ... Additional arguments passed to the method.
+#'
 #' @return A plotly object
 #' @export
 #' @family plotting functions
 #' @examples
 #' \donttest{
 #' animateSpectra(NS_sim, power = 2, wlim = c(0.1, NA), time_range = 1997:2007)
 #' }
-animateSpectra <- function(sim,
-                           species = NULL,
-                           time_range,
-                           wlim = c(NA, NA),
-                           ylim = c(NA, NA),
-                           power = 1,
-                           total = FALSE,
-                           resource = TRUE) {
+animateSpectra <- function(sim, species, time_range,
+                           wlim,
+                           ylim,
+                           power,
+                           total,
+                           resource, ...)
+    UseMethod("animateSpectra")
+
+#' @export
+animateSpectra.MizerSim <- function(sim, species = NULL, time_range = NULL,
+                                    wlim = c(NA, NA), ylim = c(NA, NA),
+                                    power = 1, total = FALSE, resource = TRUE, ...) {
     assert_that(is.flag(total), is.flag(resource),
-                is.number(power), 
+                is.number(power),
                 length(wlim) == 2,
                 length(ylim) == 2)
 
@@ -47,7 +52,7 @@ animateSpectra <- function(sim,
         time_range  <- as.numeric(dimnames(sim@n)$time)
     }
     time_elements <- get_time_elements(sim, time_range)
-    
+
     nf <- melt(sim@n[time_elements,
                      as.character(dimnames(sim@n)$sp) %in% species,
                                , drop = FALSE])
@@ -90,7 +95,7 @@ animateSpectra <- function(sim,
                value <= ylim[2],
                w >= wlim[1],
                w <= wlim[2])
-    
+
     # Order legend to follow params@species_params$species via linecolour order ----
     # Keep only groups present in data, but preserve the order given by
     # names(sim@params@linecolour) which follows params@species_params$species.
@@ -120,3 +125,4 @@ animateSpectra <- function(sim,
                                 title = y_label),
                    legend = list(traceorder = "normal"))
 }
+