getReproductionProportion() now always correctly returns a proporti…

…on. Closing #299.
sizespectrum · Dec 8, 2024 · c2b7c50 · c2b7c50
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,7 +19,7 @@ Authors@R: c(person("Gustav", "Delius", email="[email protected]",
                     comment = c(ORCID = "0000-0002-8478-3430")),
              person("Richard", "Southwell", email="[email protected]",
                     role=c("ctb", "cph")))
-Version: 2.5.3.9000
+Version: 2.5.3.9001
 License: GPL-3
 Imports:
     assertthat,

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,15 @@
-# Development version 2.5.3.9000
+# Development version 2.5.3.9001
 
 - `species` and `gears` columns are now never factors, so no longer need to
   call `as.character()` so often.
 - `validParams()` also calls `validGearParams()`.
 - `validParams()` checks that `w_min` is valid for all species and increases it
   if necessary.
 
+## Bug fixes
+
+- `getReproductionProportion()` no longer returns incorrect proportions > 1 (#299)
+
 # mizer 2.5.3
 
 A patch update so that users who had changed `w_max` manually in their model

diff --git a/R/setReproduction.R b/R/setReproduction.R
@@ -1,68 +1,68 @@
 #' Set reproduction parameters
-#' 
+#'
 #' Sets the proportion of the total energy available for reproduction and growth
 #' that is invested into reproduction as a function of the size of the
 #' individual and sets additional density dependence.
-#' 
+#'
 #' @section Setting reproduction:
-#' 
-#' For each species and at each size, the proportion \eqn{\psi}{psi} of the 
-#' available energy 
+#'
+#' For each species and at each size, the proportion \eqn{\psi}{psi} of the
+#' available energy
 #' that is invested into reproduction is the product of two factors: the
 #' proportion `maturity` of individuals that are mature and the proportion
-#' `repro_prop` of the energy available to a mature individual that is 
+#' `repro_prop` of the energy available to a mature individual that is
 #' invested into reproduction. There is a size `w_repro_max` at which all the
 #' energy is invested into reproduction and therefore all growth stops. There
 #' can be no fish larger than `w_repro_max`. If you have not specified the
 #' `w_repro_max` column in the species parameter data frame, then the maximum size
 #' `w_max` is used instead.
-#' 
+#'
 #' \subsection{Maturity ogive}{
 #' If the the proportion of individuals that are mature is not supplied via
-#' the `maturity` argument, then it is set to a sigmoidal 
+#' the `maturity` argument, then it is set to a sigmoidal
 #' maturity ogive that changes from 0 to 1 at around the maturity size:
 #' \deqn{{\tt maturity}(w) = \left[1+\left(\frac{w}{w_{mat}}\right)^{-U}\right]^{-1}.}{
 #'   maturity(w) = [1+(w/w_mat)^(-U)]^(-1)}
 #' (To avoid clutter, we are not showing the species index in the equations,
 #' although each species has its own maturity ogive.)
-#' The maturity weights are taken from the `w_mat` column of the 
+#' The maturity weights are taken from the `w_mat` column of the
 #' species_params data frame. Any missing maturity weights are set to 1/4 of the
 #' maximum weight in the `w_max` column.
-#' 
+#'
 #' The exponent \eqn{U} determines the steepness of the maturity ogive. By
 #' default it is chosen as \eqn{U = 10}, however this can be overridden by
 #' including a column \code{w_mat25} in the species parameter dataframe that
 #' specifies the weight at which 25% of individuals are mature, which sets
 #' \eqn{U = \log(3) / \log(w_{mat} / w_{mat25}).}{U = log(3) / log(w_mat /
 #' w_mat25).}
-#' 
+#'
 #' The sigmoidal function given above would strictly reach 1 only
 #' asymptotically. Mizer instead sets the function equal to 1 already at a size
 #' taken from the `w_repro_max` column in the species parameter data frame, if it
 #' exists, or otherwise from the `w_max` column. Also, for computational
 #' simplicity, any proportion smaller than `1e-8` is set to `0`.
 #' }
-#' 
+#'
 #' \subsection{Investment into reproduction}{
-#' If the the energy available to a mature individual that is 
+#' If the the energy available to a mature individual that is
 #' invested into reproduction is not supplied via the `repro_prop` argument,
 #' it is set to the allometric form
 #' \deqn{{\tt repro\_prop}(w) = \left(\frac{w}{w_{\tt{repro\_max}}}\right)^{m-n}.}{
 #'   repro_prop(w) = (w/w_repro_max)^(m - n).}
 #' Here \eqn{n} is the scaling exponent of the energy income rate. Hence
 #' the exponent \eqn{m} determines the scaling of the investment into
-#' reproduction for mature individuals. By default it is chosen to be 
-#' \eqn{m = 1} so that the rate at which energy is invested into reproduction 
-#' scales linearly with the size. This default can be overridden by including a 
+#' reproduction for mature individuals. By default it is chosen to be
+#' \eqn{m = 1} so that the rate at which energy is invested into reproduction
+#' scales linearly with the size. This default can be overridden by including a
 #' column `m` in the species parameter dataframe. The maximum sizes are taken
 #' from the `w_repro_max` column in the species parameter data frame, if it
 #' exists, or otherwise from the `w_max` column.
-#' 
+#'
 #' The total proportion of energy invested into reproduction of an individual
 #' of size \eqn{w} is then
 #' \deqn{\psi(w) = {\tt maturity}(w){\tt repro\_prop}(w)}{psi(w) = maturity(w) * repro_prop(w)}
 #' }
-#' 
+#'
 #' \subsection{Reproductive efficiency}{
 #' The reproductive efficiency \eqn{\epsilon}, i.e., the proportion of energy allocated to
 #' reproduction that results in egg biomass, is set through the `erepro`
@@ -72,7 +72,7 @@
 #' [getRDI()]:
 #' \deqn{R_{di} = \frac{\epsilon}{2 w_{min}} \int N(w)  E_r(w) \psi(w) \, dw}{R_di = (\epsilon/(2 w_min)) \int N(w)  E_r(w) \psi(w) dw}
 #' }
-#' 
+#'
 #' \subsection{Density dependence}{
 #' The stock-recruitment relationship is an emergent phenomenon in mizer, with
 #' several sources of density dependence. Firstly, the amount of energy invested
@@ -81,7 +81,7 @@
 #' larvae that grow up to recruitment size depends on the larval mortality,
 #' which depends on the density of predators, and on larval growth rate, which
 #' depends on density of prey.
-#' 
+#'
 #' Finally, to encode all the density dependence in the stock-recruitment
 #' relationship that is not already included in the other two sources of density
 #' dependence, mizer puts the the density-independent rate of egg production
@@ -109,11 +109,11 @@
 #'   were previously overwritten with custom values. If set to FALSE (default)
 #'   then a recalculation from the species parameters will take place only if no
 #'   custom values have been set.
-#' @param RDD The name of the function calculating the density-dependent 
-#'   reproduction rate from the density-independent rate. Defaults to 
+#' @param RDD The name of the function calculating the density-dependent
+#'   reproduction rate from the density-independent rate. Defaults to
 #'   "[BevertonHoltRDD()]".
 #' @param ... Unused
-#' 
+#'
 #' @return `setReproduction()`: A MizerParams object with updated reproduction
 #'   parameters.
 #' @export
@@ -123,12 +123,12 @@
 #' # Plot maturity and reproduction ogives for Cod in North Sea model
 #' maturity <- getMaturityProportion(NS_params)["Cod", ]
 #' repro_prop <- getReproductionProportion(NS_params)["Cod", ]
-#' df <- data.frame(Size = w(NS_params), 
-#'                  Reproduction = repro_prop, 
-#'                  Maturity = maturity, 
+#' df <- data.frame(Size = w(NS_params),
+#'                  Reproduction = repro_prop,
+#'                  Maturity = maturity,
 #'                  Total = maturity * repro_prop)
-#' dff <- melt(df, id.vars = "Size", 
-#'             variable.name = "Type", 
+#' dff <- melt(df, id.vars = "Size",
+#'             variable.name = "Type",
 #'             value.name = "Proportion")
 #' library(ggplot2)
 #' ggplot(dff) + geom_line(aes(x = Size, y = Proportion, colour = Type))
@@ -144,24 +144,24 @@ setReproduction <- function(params, maturity = NULL,
                 exists(RDD),
                 is.function(get(RDD)))
     species_params <- params@species_params
-    
+
     if (reset) {
         if (!is.null(maturity)) {
-            warning("Because you set `reset = TRUE`, the value you provided ", 
+            warning("Because you set `reset = TRUE`, the value you provided ",
                     "for `maturity` will be ignored and a value will be ",
                     "calculated from the species parameters.")
             maturity <- NULL
         }
         comment(params@maturity) <- NULL
         if (!is.null(repro_prop)) {
-            warning("Because you set `reset = TRUE`, the value you provided ", 
+            warning("Because you set `reset = TRUE`, the value you provided ",
                     "for `repro_prop` will be ignored and a value will be ",
                     "calculated from the species parameters.")
             repro_prop <- NULL
         }
         comment(params@psi) <- NULL
     }
-    
+
     # Check maximum sizes
     if (!("w_max" %in% colnames(species_params))) {
         stop("The maximum sizes of the species must be specified in the w_max ",
@@ -180,12 +180,12 @@ setReproduction <- function(params, maturity = NULL,
     #     idx <- which.min(abs(species_params$w_max[i] - params@w))
     #     params@species_params$w_max[i] < params@w[idx]
     # }
-    
+
     # set maturity proportion ----
     if (!is.null(maturity)) {
         assert_that(is.array(maturity),
                     identical(dim(maturity), dim(params@psi)))
-        if (!is.null(dimnames(maturity)) && 
+        if (!is.null(dimnames(maturity)) &&
             !all(dimnames(maturity)[[1]] == species_params$species)) {
             stop("You need to use the same ordering of species as in the ",
                  "params object: ", toString(species_params$species))
@@ -213,18 +213,18 @@ setReproduction <- function(params, maturity = NULL,
         assert_that(all(species_params$w_mat > species_params$w_min))
         assert_that(all(species_params$w_mat < species_params$w_max))
         params@species_params$w_mat <- species_params$w_mat
-        
+
         # Set defaults for w_mat25
         species_params <- set_species_param_default(
-            species_params, "w_mat25",       
+            species_params, "w_mat25",
             species_params$w_mat / (3 ^ (1 / 10)))
         # Check w_mat25
         assert_that(all(species_params$w_mat25 > species_params$w_min))
         assert_that(all(species_params$w_mat25 < species_params$w_mat))
         params@species_params$w_mat25 <- species_params$w_mat25
-        
+
         maturity <- params@maturity  # To get the right dimensions
-        maturity[] <- 
+        maturity[] <-
             unlist(
                 tapply(params@w, seq_along(params@w),
                        function(wx, w_mat, w_mat25) {
@@ -235,10 +235,10 @@ setReproduction <- function(params, maturity = NULL,
                        w_mat25 = species_params$w_mat25
                 )
             )
-        
-        # For reasons of efficiency we next set all very small values to 0 
+
+        # For reasons of efficiency we next set all very small values to 0
         maturity[maturity < 1e-8] <- 0
-        
+
         # If maturity is protected by a comment, keep the old value
         if (!is.null(comment(params@maturity))) {
             if (different(params@maturity, maturity)) {
@@ -249,21 +249,21 @@ setReproduction <- function(params, maturity = NULL,
         }
     }
     assert_that(all(maturity >= 0 & maturity <= 1))
-    
+
     # Need to update psi because it contains maturity as a factor
     if (different(params@maturity, maturity)) {
         params@psi[] <- params@psi / params@maturity * maturity
         params@psi[is.nan(params@psi)] <- 0
     }
-    
+
     params@maturity[] <- maturity
     comment(params@maturity) <- comment(maturity)
-    
+
     # set reproduction proportion ----
     if (!is.null(repro_prop)) {
         assert_that(is.array(repro_prop),
                     identical(dim(repro_prop), dim(params@psi)))
-        if (!is.null(dimnames(repro_prop)) && 
+        if (!is.null(dimnames(repro_prop)) &&
             !all(dimnames(repro_prop)[[1]] == species_params$species)) {
             stop("You need to use the same ordering of species as in the ",
                  "params object: ", toString(species_params$species))
@@ -285,7 +285,7 @@ setReproduction <- function(params, maturity = NULL,
         # Set defaults for w_repro_max
         species_params <- set_species_param_default(species_params, "w_repro_max",
                                                     params@species_params$w_max)
-        
+
         repro_prop <- array(
             unlist(
                 tapply(params@w, seq_along(params@w),
@@ -296,17 +296,17 @@ setReproduction <- function(params, maturity = NULL,
             ), dim = c(nrow(species_params), length(params@w)))
         repro_prop[repro_prop > 1] <- 1
     }
-    
+
     psi <- params@maturity * repro_prop
     # psi should never be larger than 1
     psi[psi > 1] <- 1
     # Set psi for all w > w_repro_max to 1
     psi[outer(species_params$w_repro_max, params@w, "<")] <- 1
     assert_that(all(psi >= 0 & psi <= 1))
-    
+
     # if the slot is protected and the user did not supply a new repro_prop
     # then don't overwrite the slot with auto-generated values. We can
-    # detect whether repro_prop is user-supplied by checking whether it has 
+    # detect whether repro_prop is user-supplied by checking whether it has
     # a comment.
     if (!is.null(comment(params@psi)) && is.null(comment(repro_prop))) {
         if (different(params@psi, psi)) {
@@ -317,36 +317,36 @@ setReproduction <- function(params, maturity = NULL,
         params@psi[] <- psi
         comment(params@psi) <- comment(repro_prop)
     }
-    
+
     # If no erepro (reproductive efficiency), then set to 1
     params <- set_species_param_default(params, "erepro", 1)
     if (!all(params@species_params$erepro > 0)) {
         stop("Some species have negative reproductive efficiency.")
     }
-    
+
     # RDD function is currently called only with three arguments
     if (!all(names(formals(RDD)) %in%  c("rdi", "species_params", "params", "t", "..."))) {
         stop("Arguments of RDD function can only contain 'rdi', 'species_params' and `t`.")
     }
     params@rates_funcs$RDD <- RDD
     if (identical(params@rates_funcs$RDD, "BevertonHoltRDD")) {
-        
+
         # for legacy reasons (R_max used to be called r_max):
         if ("r_max" %in% names(params@species_params)) {
             params@species_params$R_max <- params@species_params$r_max
             params@species_params$r_max <- NULL
             message("The 'r_max' column has been renamed to 'R_max'.")
         }
-        
+
         params <- set_species_param_default(params, "R_max", Inf)
     }
-    
+
     params@time_modified <- lubridate::now()
     return(params)
 }
 
 #' @rdname setReproduction
-#' @return `getMaturityProportion()` or equivalently `maturity(): 
+#' @return `getMaturityProportion()` or equivalently `maturity():
 #'   An array (species x size) that holds the proportion
 #'   of individuals of each species at size that are mature.
 #' @export
@@ -379,11 +379,11 @@ getReproductionProportion <- function(params) {
     assert_that(is(params, "MizerParams"))
     repro_prop <- params@psi / params@maturity
     repro_prop[is.nan(repro_prop)] <- 0
+    repro_prop[repro_prop > 1] <- 1
     comment(repro_prop) <- comment(params@psi)
     repro_prop
 }
 
-
 #' @rdname setReproduction
 #' @export
 repro_prop <- function(params) {