Merge pull request #288 from SamikDatta/master

Using ratio by default for plotBiomassObservedVsModel...
sizespectrum · Apr 10, 2024 · 18860c5 · 18860c5
2 parents e350640 + 49dea1b
commit 18860c5
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diff --git 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
+Version: 2.5.1.9000
 License: GPL-3
 Imports:
     assertthat,
@@ -41,7 +41,7 @@ LinkingTo: Rcpp
 Depends:
     R (>= 3.1)
 Suggests:
-    testthat (>= 2.1.0),
+    testthat (>= 3.0.0),
     vdiffr,
     roxygen2,
     knitr,
@@ -112,3 +112,4 @@ BugReports: https://github.com/sizespectrum/mizer/issues
 Language: en-GB
 RdMacros: lifecycle
 VignetteBuilder: knitr
+Config/testthat/edition: 3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+## Updating default values for plotBiomassObservedVsModel
+
+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.
+
+
 # mizer 2.5.1
 
 This is a patch release made necessary by a change in CRAN's requirement

diff --git a/R/MizerParams-class.R b/R/MizerParams-class.R
@@ -823,7 +823,7 @@ validParams <- function(params) {
     assert_that(is(params, "MizerParams"))
 
     if (needs_upgrading(params)) {
-        params <- upgradeParams(params)
+        params <- suppressWarnings(upgradeParams(params))
         warning("Your MizerParams object was created with an earlier version of mizer. You can upgrade it with `params <- upgradeParams(params)` where you should replace `params` by the name of the variable that holds your MizerParams object.")
     }
 

diff --git a/R/plotBiomassObservedVsModel.R b/R/plotBiomassObservedVsModel.R
@@ -29,7 +29,7 @@
 #'   with the species indices, or a logical vector indicating for each species
 #'   whether it is to be included (TRUE) or not.
 #' @param ratio Whether to plot model biomass vs. observed biomass (FALSE) or
-#'   the ratio of model : observed biomass (TRUE). Default is FALSE.
+#'   the ratio of model : observed biomass (TRUE). Default is TRUE.
 #' @param log_scale Whether to plot on the log10 scale (TRUE) or not (FALSE).
 #'   For the non-ratio plot this applies for both axes, for the ratio plot only
 #'   the x-axis is on the log10 scale. Default is TRUE.
@@ -62,7 +62,7 @@
 #'
 #' # Show the ratio instead
 #' plotBiomassObservedVsModel(params, ratio = TRUE)
-plotBiomassObservedVsModel <- function(object, species = NULL, ratio = FALSE,
+plotBiomassObservedVsModel <- function(object, species = NULL, ratio = TRUE,
                                       log_scale = TRUE, return_data = FALSE, 
                                       labels = TRUE, show_unobserved = FALSE) {
 

diff --git a/man/animateSpectra.Rd b/man/animateSpectra.Rd
diff --git a/man/figures/Beverton-Holt-plot-1.png b/man/figures/Beverton-Holt-plot-1.png
diff --git a/man/getBiomass.Rd b/man/getBiomass.Rd
diff --git a/man/getDiet.Rd b/man/getDiet.Rd
diff --git a/man/getEGrowth.Rd b/man/getEGrowth.Rd
diff --git a/man/getERepro.Rd b/man/getERepro.Rd
diff --git a/man/getEReproAndGrowth.Rd b/man/getEReproAndGrowth.Rd
diff --git a/man/getESpawning.Rd b/man/getESpawning.Rd
diff --git a/man/getEncounter.Rd b/man/getEncounter.Rd
diff --git a/man/getFMort.Rd b/man/getFMort.Rd
diff --git a/man/getFMortGear.Rd b/man/getFMortGear.Rd
diff --git a/man/getFeedingLevel.Rd b/man/getFeedingLevel.Rd
diff --git a/man/getGrowthCurves.Rd b/man/getGrowthCurves.Rd
diff --git a/man/getM2.Rd b/man/getM2.Rd
diff --git a/man/getM2Background.Rd b/man/getM2Background.Rd
diff --git a/man/getMort.Rd b/man/getMort.Rd
diff --git a/man/getN.Rd b/man/getN.Rd
diff --git a/man/getPredMort.Rd b/man/getPredMort.Rd
diff --git a/man/getPredRate.Rd b/man/getPredRate.Rd
diff --git a/man/getRDD.Rd b/man/getRDD.Rd
diff --git a/man/getRDI.Rd b/man/getRDI.Rd
diff --git a/man/getRates.Rd b/man/getRates.Rd
diff --git a/man/getResourceMort.Rd b/man/getResourceMort.Rd
diff --git a/man/getSSB.Rd b/man/getSSB.Rd
diff --git a/man/getZ.Rd b/man/getZ.Rd
diff --git a/man/mizerEGrowth.Rd b/man/mizerEGrowth.Rd
diff --git a/man/mizerERepro.Rd b/man/mizerERepro.Rd
diff --git a/man/mizerEReproAndGrowth.Rd b/man/mizerEReproAndGrowth.Rd