Fix bug that appeared when some species had no associated gear.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mizerExperimental
 Type: Package
 Title: Extends the mizer package with experimental features
-Version: 2.4.0.9007
+Version: 2.4.0.9008
 Author: Various contributors
 Maintainer: Gustav Delius <[email protected]>
 Description: This mizer extension package collects contributions from the mizer

R/tuneParams_helpers.R

@@ -7,6 +7,22 @@ prepare_params <- function(p) {
     p <- set_species_param_default(p, "t0", 0)
     p <- set_species_param_default(p, "w_mat25",
                                    p@species_params$w_mat/(3^(1/10)))
+    # Make sure every species has a gear by adding a "no gear" gear
+    # This will be removed again at the end
+    sp <- species_params(p)
+    gp <- gear_params(p)
+    missing_species <- setdiff(sp$species, gp$species)
+    if (length(missing_species) > 0) {
+        gp_missing <- data.frame(species = missing_species,
+                                 gear = "no gear",
+                                 catchability = 0,
+                                 sel_func = "sigmoid_length",
+                                 l25 = 10,
+                                 l50 = 15)
+        gp_missing <- validGearParams(gp_missing, sp)
+        gear_params(p) <- dplyr::bind_rows(gp, gp_missing)
+    }
+
     return(p)
 }
 
@@ -16,6 +32,11 @@ finalise_params <- function(p) {
     # Clear attribute that was only needed for the undo functionality
     attr(p, "changes") <- NULL
 
+    # Remove the "no gear" gear that was added at the beginning
+    gp <- gear_params(p)
+    gp <- gp[gp$gear != "no gear", ]
+    gear_params(p) <- gp
+
     # Set reproduction
     if ("tuneParams_old_repro_level" %in% names(p@species_params)) {
         p <- setBevertonHolt(p, reproduction_level =