- removeSpecies() now also removes species parameters that are not …

…set for any of the remaining species.

NEWS.md

@@ -6,6 +6,8 @@
   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.
+- `removeSpecies()` now also removes species parameters that are not set for
+  any of the remaining species.
 - `compareParams()` now also spells out differences in given species parameters.
 - `getDiet()` now also includes the contribution of the external encounter rate
   to the diet.

R/manipulate_species.R

@@ -382,6 +382,12 @@ removeSpecies <- function(params, species) {
                                        p@species_params$species, ]
     p@gear_params <- validGearParams(p@gear_params, p@species_params)
 
+    # Drop species parameters with all values NA
+    keep <- colSums(is.na(p@species_params)) < nrow(p@species_params)
+    p@species_params <- p@species_params[, keep]
+    keep <- colSums(is.na(p@given_species_params)) < nrow(p@given_species_params)
+    p@given_species_params <- p@given_species_params[, keep]
+
     # Preserve comments
     for (slot in (slotNames(p))) {
         comment(slot(p, slot)) <- comment(slot(params, slot))

tests/testthat/test-manipulate_species.R

@@ -226,6 +226,7 @@ test_that("adding and then removing species leaves params unaltered", {
     sp <- data.frame(species = c("new1", "new2"),
                      w_max = c(10, 100),
                      k_vb = c(4, 2),
+                     test = "test",
                      stringsAsFactors = FALSE)
     # add comments to test that they will be preserved as well
     comment(params) <- "test"