Changed parameter name to w_repro_max

NEWS.md

@@ -1,5 +1,7 @@
 # Development version
 
+- New species parameter `w_repro_max` giving the size at which a species 
+  invests 100% of its energy into reproduction. Set to `w_max` by default.
 - `getDiet()` now also includes the contribution of the external encounter rate
   to the diet.
 - Improved scaling of the y-axis in `plotGrowthCurves()`.

R/setReproduction.R

@@ -11,10 +11,10 @@
 #' 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 
-#' invested into reproduction. There is a size `w_mat_max` at which all the
+#' 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_mat_max`. If you have not specified the
-#' `w_mat_max` column in the species parameter data frame, then the maximum size
+#' 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}{
@@ -38,7 +38,7 @@
 #' 
 #' 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_mat_max` column in the species parameter data frame, if it
+#' 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`.
 #' }
@@ -48,14 +48,14 @@
 #' 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_{mat_max}}\right)^{m-n}.}{
-#'   repro_prop(w) = (w/w_mat_max)^(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 
 #' column `m` in the species parameter dataframe. The maximum sizes are taken
-#' from the `w_mat_max` column in the species parameter data frame, if it
+#' 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
@@ -281,15 +281,15 @@ setReproduction <- function(params, maturity = NULL,
         if (any(species_params$m < species_params[["n"]])) {
             stop("The exponent `m` must not be smaller than the exponent `n`.")
         }
-        # Set defaults for w_mat_max
-        species_params <- set_species_param_default(species_params, "w_mat_max",
+        # Set defaults for w_repro_max
+        species_params <- set_species_param_default(species_params, "w_repro_max",
                                                     params@species_params$w_max)
 
         repro_prop <- array(
             unlist(
                 tapply(params@w, seq_along(params@w),
-                       function(wx, w_mat_max, mn) (wx / w_mat_max)^(mn),
-                       w_mat_max = species_params$w_mat_max,
+                       function(wx, w_repro_max, mn) (wx / w_repro_max)^(mn),
+                       w_repro_max = species_params$w_repro_max,
                        mn = species_params[["m"]] - species_params[["n"]]
                 )
             ), dim = c(nrow(species_params), length(params@w)))
@@ -299,8 +299,8 @@ setReproduction <- function(params, maturity = NULL,
     psi <- params@maturity * repro_prop
     # psi should never be larger than 1
     psi[psi > 1] <- 1
-    # Set psi for all w > w_mat_max to 1
-    psi[outer(species_params$w_mat_max, params@w, "<")] <- 1
+    # Set psi for all w > w_repro_max to 1
+    psi[outer(species_params$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

R/species_params.R

@@ -33,7 +33,7 @@
 #' * `k`, `ks` and `p` are used to set activity and basic metabolic rate, 
 #'   see [setMetabolicRate()].
 #' * `z0` is used to set the external mortality rate, see [setExtMort()].
-#' * `w_mat`, `w_mat25`, `w_mat_max` and `m` are used to set the allocation to
+#' * `w_mat`, `w_mat25`, `w_repro_max` and `m` are used to set the allocation to
 #'   reproduction, see [setReproduction()].
 #' * `pred_kernel_type` specifies the shape of the predation kernel. The default
 #'   is a "lognormal", for other options see the "Setting predation kernel"
@@ -72,7 +72,7 @@
 #'   relationship \eqn{w = a l ^ b}.
 #'   
 #' If you have supplied the `a` and `b` parameters, then you can replace weight
-#' parameters like `w_max`, `w_mat`, `w_mat25`, w_mat_max and `w_min` by their
+#' parameters like `w_max`, `w_mat`, `w_mat25`, w_repro_max and `w_min` by their
 #' corresponding length parameters `l_max`, `l_mat`, `l_mat25`, `l_mat_max` and
 #' `l_min`.
 #'   
@@ -579,7 +579,7 @@ validSpeciesParams <- function(species_params) {
         sp <- sp %>%
             set_species_param_from_length("w_mat", "l_mat") %>%
             set_species_param_from_length("w_mat25", "l_mat25") %>%
-            set_species_param_from_length("w_mat_max", "l_mat_max") %>%
+            set_species_param_from_length("w_repro_max", "l_mat_max") %>%
             set_species_param_from_length("w_max", "l_max") %>%
             set_species_param_from_length("w_min", "l_min")
     }