From 5fb6f2ab6bc76c809761ad11ae9e6a27403f1dfc Mon Sep 17 00:00:00 2001
From: Gustav Delius <gustav.delius@gmail.com>
Date: Fri, 2 Aug 2024 21:43:56 +0100
Subject: [PATCH] `setExtEncounter()` no longer resets the external encounter
 rate to zero when called without the `ext_encounter` argument.

---
 DESCRIPTION                  | 4 ++--
 NEWS.md                      | 7 +++++--
 R/newMultispeciesParams.R    | 1 +
 R/setExtEncounter.R          | 4 ++--
 man/newMultispeciesParams.Rd | 3 ++-
 man/setExtEncounter.Rd       | 3 ++-
 man/setParams.Rd             | 1 +
 7 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 789e77ad..a3bbbe0a 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/NEWS.md b/NEWS.md
index 616459be..1c4f0c88 100644
--- a/NEWS.md
+++ b/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.
 
diff --git a/R/newMultispeciesParams.R b/R/newMultispeciesParams.R
index 9fed3a6e..cdb0d0e6 100644
--- a/R/newMultispeciesParams.R
+++ b/R/newMultispeciesParams.R
@@ -236,6 +236,7 @@ newMultispeciesParams <- function(
 #' \item [setMaxIntakeRate()]
 #' \item [setMetabolicRate()]
 #' \item [setExtMort()]
+#' \item [setExtEncounter()]
 #' \item [setReproduction()]
 #' \item [setFishing()]
 #' \item [setResource()]
diff --git a/R/setExtEncounter.R b/R/setExtEncounter.R
index f872c7f1..e3e49f9f 100644
--- a/R/setExtEncounter.R
+++ b/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),
diff --git a/man/newMultispeciesParams.Rd b/man/newMultispeciesParams.Rd
index 0992c95f..070e7455 100644
--- a/man/newMultispeciesParams.Rd
+++ b/man/newMultispeciesParams.Rd
@@ -92,7 +92,8 @@ the species data frame, it is calculated as \code{z0pre * w_max ^ z0exp}.
 Default value is \code{n-1}.}
 
 \item{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.}
 
 \item{maturity}{Optional. An array (species x size) that holds the proportion
 of individuals of each species at size that are mature. If not supplied, a
diff --git a/man/setExtEncounter.Rd b/man/setExtEncounter.Rd
index 3aee9376..38c36610 100644
--- a/man/setExtEncounter.Rd
+++ b/man/setExtEncounter.Rd
@@ -19,7 +19,8 @@ ext_encounter(params) <- value
 \item{params}{MizerParams}
 
 \item{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.}
 
 \item{...}{Unused}
 
diff --git a/man/setParams.Rd b/man/setParams.Rd
index c184d6a7..a7322b9f 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -75,6 +75,7 @@ functions
 \item \code{\link[=setMaxIntakeRate]{setMaxIntakeRate()}}
 \item \code{\link[=setMetabolicRate]{setMetabolicRate()}}
 \item \code{\link[=setExtMort]{setExtMort()}}
+\item \code{\link[=setExtEncounter]{setExtEncounter()}}
 \item \code{\link[=setReproduction]{setReproduction()}}
 \item \code{\link[=setFishing]{setFishing()}}
 \item \code{\link[=setResource]{setResource()}}