setExtEncounter() no longer resets the external encounter rate to z…

…ero when called without the `ext_encounter` argument.

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: 2.5.1.9001
+Version: 2.5.1.9002
 License: GPL-3
 Imports:
     assertthat,
@@ -103,7 +103,7 @@ Collate:
     'matchGrowth.R'
     'steadySingleSpecies.R'
     'defaults_edition.R'
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 LazyData: true

NEWS.md

@@ -1,6 +1,9 @@
-## Updating default values for plotBiomassObservedVsModel
+# Development version
 
-The function `plotBiomassObservedVsModel` now plots the ratio of modelled
+- `setExtEncounter()` no longer resets the external encounter rate to zero when
+  called without the `ext_encounter` argument.
+
+- The function `plotBiomassObservedVsModel()` now plots the ratio of modelled
 to observed biomass as default (`ratio = T`), as this is more useful visually to 
 see how far off modelled biomass is from observed biomass.
 

R/newMultispeciesParams.R

@@ -236,6 +236,7 @@ newMultispeciesParams <- function(
 #' \item [setMaxIntakeRate()]
 #' \item [setMetabolicRate()]
 #' \item [setExtMort()]
+#' \item [setExtEncounter()]
 #' \item [setReproduction()]
 #' \item [setFishing()]
 #' \item [setResource()]

R/setExtEncounter.R

@@ -10,7 +10,8 @@
 #' 
 #' @param params MizerParams
 #' @param ext_encounter Optional. An array (species x size) holding the external
-#'   encounter rate.  If not supplied, a default of 0 is used.
+#'   encounter rate.  If not supplied, the external encounter rate is left
+#'   unchanged. Initially is is set to 0.
 #' @param ... Unused
 #' 
 #' @return `setExtEncounter()`: A MizerParams object with updated external encounter
@@ -36,7 +37,6 @@ setExtEncounter <- function(params, ext_encounter = NULL, ...) {
 
     if (is.null(ext_encounter)) {
         ext_encounter <- params@ext_encounter
-        ext_encounter[] <- 0
     }
 
     assert_that(is.array(ext_encounter),