addSpecies() no longer requires new species to grow to maximum size…

…, only maturity size is required.

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: 2.5.1.9004
+Version: 2.5.1.9005
 License: GPL-3
 Imports:
     assertthat,

NEWS.md

@@ -1,7 +1,9 @@
-# mizer 2.5.1.9004
+# mizer 2.5.1.9005
 
 - `addSpecies()` now correctly preserves all `species_params` of the existing
   model.
+- `addSpecies()` no longer requires new species to grow to maximum size, only
+  maturity size is required.
 - 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

R/manipulate_species.R

@@ -267,24 +267,12 @@ addSpecies <- function(params, species_params,
     # Turn off self-interaction among the new species, so we can determine the
     # growth rates, and death rates induced upon them by the pre-existing species
     p@interaction[new_sp, new_sp] <- 0
-    mumu <- getMort(p)
-    gg <- getEGrowth(p)
 
     # Compute solution for new species
+    p <- steadySingleSpecies(p, species = new_sp)
+
+    # set low abundance ----
     for (i in new_sp) {
-        g <- gg[i, ]
-        mu <- mumu[i, ]
-        w_max_idx <- sum(p@w < p@species_params$w_max[i])
-        idx <- p@w_min_idx[i]:(w_max_idx - 1)
-        if (any(g[idx] == 0)) {
-            stop("Can not compute steady state due to zero growth rates for ",
-                 p@species_params$species[i])
-        }
-        p@initial_n[i, ] <- 0
-        p@initial_n[i, p@w_min_idx[i]:w_max_idx] <-
-            c(1, cumprod(g[idx] / ((g + mu * p@dw)[idx + 1])))
-
-        # set low abundance ----
         # Normalise solution so that it is never more than 1/100th of the
         # Sheldon spectrum.
         # We look at the maximum of abundance times w^lambda

tests/testthat/test-manipulate_species.R

@@ -83,7 +83,7 @@ test_that("addSpecies handles interaction matrix correctly", {
     interaction <- matrix(1:16/16, ncol = 4)
     (pa <- addSpecies(p, sp, interaction = interaction)) |>
         expect_message() |>
-        expect_warning("The following species require an unrealistic reproductive efficiency greater than 1: new2")
+        expect_warning("The following species require an unrealistic value greater than 1 for `erepro`: new2")
     expect_equal(pa@interaction, interaction, ignore_attr = TRUE)
 
     addSpecies(p, sp, interaction = matrix(1:9, ncol = 3)) |>