If an effort vector or effort array contains NA's, these are now repl…

…aced by the default effort value. Closes #230

NEWS.md

@@ -1,11 +1,13 @@
 # mizer (development version)
 
 * Improved defaults can now be implemented while keeping backwards compatibility
-  via `defaults_edition()`.
+  via `defaults_edition()`. #186
 * New defaults edition 2: catchability = 0.3 instead of 1, initial effort = 1
-  instead of 0.
+  instead of 0. #243
 * In defaults edition 2, `get_gamma_default()` ensures a feeding level of `f0`
-  for larvae also if `interaction_resource` is not equal to 1.
+  for larvae also if `interaction_resource` is not equal to 1. #238
+* If an effort vector or effort array contains NA's, these are now replaced by
+  the default effort value. #230
 * The entries of the interaction matrix and of interaction_resource are not
   longer restricted to be less or equal to 1. #232
 * If user supplies no row names in the interaction matrix but give column names

R/project.R

@@ -418,6 +418,11 @@ validEffortArray <- function(effort, params) {
     if (is.unsorted(time_effort)) {
         stop("The time dimname of the effort argument should be increasing.")
     }
+
+    # Replace any NA's with default value
+    effort_default <- ifelse(defaults_edition() < 2, 0, 1)
+    effort[is.na(effort)] <- effort_default
+
     names(dimnames(effort)) <- c("time", "gear")
     effort
 }

R/setFishing.R

@@ -650,6 +650,9 @@ validEffortVector <- function(effort, params) {
     names(new) <- missing
     effort <- c(effort, new)
 
+    # Set any NAs to default
+    effort[is.na(effort)] <- effort_default
+
     # Sort vector
     effort <- effort[gear_names]
 

tests/testthat/test-setFishing.R

@@ -58,6 +58,11 @@ test_that("validEffort works", {
     # A scrambled vector is put in the right order
     ies <- ie[c(2,3,1,4)]
     expect_identical(validEffortVector(ies, params), ie)
+    # NA's are replaced by default
+    ie[2] <- 0
+    iesn <- ie
+    iesn[2] <- NA
+    expect_identical(validEffortVector(iesn, params), ie)
     # A single number is converted into a constant vector
     ie[] <- 2
     expect_identical(validEffortVector(2, params), ie)