Merge pull request #365 from sizespectrum/copilot/plotbiomassobservedvsmodel-fix-default-ratio

Unify `plotBiomassObservedVsModel` default `ratio` behavior to `FALSE`

Author: gustavdelius

NEWS.md

@@ -334,6 +334,11 @@ the mathematical details.
 
 ## Breaking changes
 
+- The default `ratio` argument in `plotBiomassObservedVsModel()` and
+  `plotlyBiomassObservedVsModel()` is now consistently `FALSE` for all object
+  types. Calls that relied on the previous default ratio plot should now set
+  `ratio = TRUE`.
+
 - The first argument of `plotBiomass()`, `plotYield()`, `plotYieldGear()` and
   their `MizerSim` methods and `plotly*` wrappers has been renamed from `sim`
   to `object` for consistency with other plot generics. Calls using

R/plotBiomassObservedVsModel.R

@@ -5,8 +5,8 @@
 #' `biomass_observed` column in the species parameter data frame, this function
 #' plots the biomass of each species in the model against the observed
 #' biomasses. When called with a MizerSim object, the plot will use the model
-#' biomasses predicted for the final time step in the simulation. For the
-#' MizerSim and plotly methods, `ratio` defaults to `FALSE`.
+#' biomasses predicted for the final time step in the simulation. `ratio`
+#' defaults to `FALSE`.
 #'
 #' Before you can use this function you will need to have added a
 #' `biomass_observed` column to your model which gives the observed biomass in
@@ -30,7 +30,7 @@
 #'   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 TRUE.
+#'   the ratio of model : observed biomass (TRUE). Default is FALSE.
 #' @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.
@@ -65,14 +65,14 @@
 #' plotBiomassObservedVsModel(params, show_unobserved = TRUE, ratio = FALSE)
 #'
 #' # Show the ratio instead
-#' plotBiomassObservedVsModel(params)
-plotBiomassObservedVsModel <- function(object, species = NULL, ratio = TRUE,
+#' plotBiomassObservedVsModel(params, ratio = TRUE)
+plotBiomassObservedVsModel <- function(object, species = NULL, ratio = FALSE,
                                       log_scale = TRUE, return_data = FALSE, 
                                       labels = TRUE, show_unobserved = FALSE, ...) {
     UseMethod("plotBiomassObservedVsModel")
 }
 #' @export
-plotBiomassObservedVsModel.MizerParams <- function(object, species = NULL, ratio = TRUE,
+plotBiomassObservedVsModel.MizerParams <- function(object, species = NULL, ratio = FALSE,
                                       log_scale = TRUE, return_data = FALSE, 
                                       labels = TRUE, show_unobserved = FALSE, ...) {
     # preliminary checks

tests/testthat/test-plotBiomassObservedVsModel.R

@@ -41,18 +41,18 @@ expect_equal(nrow(dummy), length(sp_select))
 expect_equal(dummy$observed, 
              species_params(params)$biomass_observed[sp_select])
 
-# Finally, look at plot of ratio
+# Finally, look at default plot (model biomass vs observed biomass)
 dummy <- plotBiomassObservedVsModel(params, return_data = TRUE)
 p <- plotBiomassObservedVsModel(params)
 expect_true(is_ggplot(p))
 expect_identical(p$labels$x, "observed biomass [g]")
-expect_identical(p$labels$y, "model biomass / observed biomass")
+expect_identical(p$labels$y, "model biomass [g]")
 expect_identical(p$data, dummy)
 
-# Look at plot as model biomass vs. observed biomass
-dummy <- plotBiomassObservedVsModel(params, ratio = F, return_data = TRUE)
-p <- plotBiomassObservedVsModel(params, ratio = F)
-expect_identical(p$labels$y, "model biomass [g]")
+# Look at plot of ratio
+dummy <- plotBiomassObservedVsModel(params, ratio = TRUE, return_data = TRUE)
+p <- plotBiomassObservedVsModel(params, ratio = TRUE)
+expect_identical(p$labels$y, "model biomass / observed biomass")
 expect_identical(p$data, dummy)
 
 vdiffr::expect_doppelganger("plotBiomassObservedVsModel", p)