Merge branch 'master' of https://github.com/sizespectrum/mizer

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mizer
 Title: Dynamic Multi-Species Size Spectrum Modelling
-Date: 2024-11-13
+Date: 2024-11-14
 Type: Package
 Description: A set of classes and methods to set up and run multi-species, trait
     based and community size spectrum ecological models, focused on the marine
@@ -19,7 +19,7 @@ Authors@R: c(person("Gustav", "Delius", email="[email protected]",
                     comment = c(ORCID = "0000-0002-8478-3430")),
              person("Richard", "Southwell", email="[email protected]",
                     role=c("ctb", "cph")))
-Version: 2.5.2
+Version: 2.5.2.1
 License: GPL-3
 Imports:
     assertthat,

NAMESPACE

@@ -246,6 +246,7 @@ export(validEffortVector)
 export(validGearParams)
 export(validGivenSpeciesParams)
 export(validParams)
+export(validSim)
 export(validSpeciesParams)
 export(valid_gears_arg)
 export(valid_species_arg)

NEWS.md

@@ -1,3 +1,9 @@
+# mizer 2.5.2.1
+
+A patch update so that users who had changed `w_max` manually in their model
+will not get unhelpful error messages when trying to use this model in the
+new version.
+
 # mizer 2.5.2
 
 - Fixed bug that had led `newCommunityParams()` to set up resource parameters

R/MizerSim-class.R

@@ -241,6 +241,28 @@ MizerSim <- function(params, t_dimnames = NA, t_max = 100, t_save = 1) {
     return(sim)
 }
 
+#' Validate MizerParams object and upgrade if necessary
+#' 
+#' Checks that the given MizerParams object is valid and upgrades it if
+#' necessary by calling [upgradeParams()].
+#' 
+#' Besides upgrading if necessary, the only change that may be made to the
+#' given MizerParams object is that the `w_min_idx` slot is recalculated.
+#' 
+#' @param params The MizerParams object to validate
+#' @return A valid MizerParams object
+#' @export
+validSim <- function(sim) {
+    assert_that(is(sim, "MizerSim"))
+    if (needs_upgrading(sim)) {
+        params <- suppressWarnings(upgradeSim(sim))
+        warning("Your MizerSim object was created with an earlier version of mizer. You can upgrade it with `sim <- upgradeSim(sim)` where you should replace `sim` by the name of the variable that holds your MizerSim object.")
+    }
+    sim@params <- validParams(sim@params)
+    validObject(sim)
+    sim
+}
+
 #' Time series of size spectra
 #' 
 #' Fetch the simulation results for the size spectra over time.

R/compareParams.R

@@ -12,8 +12,6 @@
 #' species_params(params2)$w_mat[1] <- 10
 #' compareParams(params1, params2)
 compareParams <- function(params1, params2) {
-    validObject(params1)
-    validObject(params2)
     assert_that(is(params1, "MizerParams"))
     assert_that(is(params2, "MizerParams"))
 

R/extension.R

@@ -83,8 +83,7 @@ setRateFunction <- function(params, rate, fun) {
 #'   `rate` argument.
 #' @export
 getRateFunction <- function(params, rate) {
-    assert_that(is(params, "MizerParams"))
-    validObject(params)
+    params <- validParams(params)
     if (missing(rate)) {
         return(params@rates_funcs)
     }

R/newMultispeciesParams.R

@@ -340,7 +340,6 @@ setParams <- function(params, interaction = NULL, ...) {
     params@ft_mask <- t(sapply(params@species_params$w_max, 
                                function(x) params@w_full < x))
 
-    params <- suppressWarnings(validParams(params))
     params <- setInteraction(params, interaction)
     params <- setPredKernel(params, ...)
     params <- setMaxIntakeRate(params, ...)

R/upgrade.R

@@ -15,7 +15,7 @@ needs_upgrading <- function(object) {
         stop("The object you supplied is neither a MizerParams nor a MizerSim object.")
     }
     !.hasSlot(params, "mizer_version") ||
-        params@mizer_version < "2.4.1.9002"
+        params@mizer_version < "2.5.2"
 }
 
 #' Upgrade MizerParams object from earlier mizer versions
@@ -360,6 +360,18 @@ upgradeParams <- function(params) {
             params@species_params$w_mat / (3 ^ (1 / 10)))
     }
 
+    # Before 2.5.2 ----
+    if (version < "2.5.2") {
+        # setParams() will update the ft_mask if necessary
+        # It will also warn if `w_max` is not valid
+        ft_mask <- params@ft_mask
+        params <- setParams(params)
+        if (!identical(as.vector(params@ft_mask), 
+                       as.vector(ft_mask))) {
+            warning("The ft_mask slot has been updated.")
+        }
+    }
+
     params@mizer_version <- packageVersion("mizer")
     params@time_modified <- lubridate::now()
     validObject(params)

R/validSpeciesParams.R

@@ -146,7 +146,7 @@ validGivenSpeciesParams <- function(species_params) {
         if (any(wrong)) {
             warning("For the species ", 
                     paste(sp$species[wrong], collapse = ", "),
-                    " the value for `w_max` is smaller than that of `w_repro_max`.",
+                    " the value for `w_max` is larger than that of `w_repro_max`.",
                     " I have corrected that by setting `w_max` equal to `w_repro_max`.")
             sp$w_max[wrong] <- sp$w_repro_max[wrong]
         }