Introduce MizerRate S3 class for rate function outputs

DESCRIPTION

@@ -55,6 +55,7 @@ Collate:
     'helpers.R'
     'MizerParams-class.R'
     'MizerSim-class.R'
+    'MizerRate-class.R'
     'reproduction.R'
     'saveParams.R'
     'species_params.R'

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",MizerRate)
 S3method("catchability<-",MizerParams)
 S3method("diffusion<-",MizerParams)
 S3method("ext_encounter<-",MizerParams)
@@ -23,12 +24,14 @@ S3method("resource_rate<-",MizerParams)
 S3method("search_vol<-",MizerParams)
 S3method("selectivity<-",MizerParams)
 S3method("species_params<-",MizerParams)
+S3method(Ops,MizerRate)
 S3method(addSpecies,MizerParams)
 S3method(age_mat,MizerParams)
 S3method(age_mat_vB,MizerParams)
 S3method(age_mat_vB,data.frame)
 S3method(age_mat_vB,default)
 S3method(animateSpectra,MizerSim)
+S3method(as.data.frame,MizerRate)
 S3method(calculated_species_params,MizerParams)
 S3method(calibrateBiomass,MizerParams)
 S3method(calibrateNumber,MizerParams)
@@ -111,6 +114,9 @@ S3method(matchNumbers,MizerParams)
 S3method(matchYields,MizerParams)
 S3method(maturity,MizerParams)
 S3method(metab,MizerParams)
+S3method(plot,MizerParams)
+S3method(plot,MizerRate)
+S3method(plot,MizerSim)
 S3method(plotBiomass,MizerSim)
 S3method(plotBiomassObservedVsModel,MizerParams)
 S3method(plotBiomassObservedVsModel,MizerSim)
@@ -131,6 +137,8 @@ S3method(plotYieldGear,MizerSim)
 S3method(plotYieldObservedVsModel,MizerParams)
 S3method(plotYieldObservedVsModel,MizerSim)
 S3method(pred_kernel,MizerParams)
+S3method(print,MizerRate)
+S3method(print,summary.MizerRate)
 S3method(project,MizerParams)
 S3method(project,MizerSim)
 S3method(projectToSteady,MizerParams)
@@ -168,6 +176,9 @@ S3method(setSearchVolume,MizerParams)
 S3method(species_params,MizerParams)
 S3method(steady,MizerParams)
 S3method(steadySingleSpecies,MizerParams)
+S3method(summary,MizerParams)
+S3method(summary,MizerRate)
+S3method(summary,MizerSim)
 S3method(w,MizerParams)
 S3method(w_full,MizerParams)
 export("catchability<-")
@@ -197,6 +208,7 @@ export("selectivity<-")
 export("species_params<-")
 export(BevertonHoltRDD)
 export(MizerParams)
+export(MizerRate)
 export(MizerSim)
 export(N)
 export(NOther)
@@ -312,6 +324,7 @@ export(initialNResource)
 export(initial_effort)
 export(intake_max)
 export(interaction_matrix)
+export(is.MizerRate)
 export(knife_edge)
 export(l2w)
 export(log_breaks)
@@ -432,8 +445,6 @@ export(w2l)
 export(w_full)
 exportClasses(MizerParams)
 exportClasses(MizerSim)
-exportMethods(plot)
-exportMethods(summary)
 import(assertthat)
 import(dplyr)
 import(ggplot2)

NEWS.md

@@ -1,5 +1,17 @@
 # Development version 2.5.4.9101
 
+- The `plot()` and `summary()` methods for `MizerParams`, `MizerSim`, and 
+  `MizerRate` objects are now registered as S3 methods rather than S4 methods.
+  This means `plot()` and `summary()` remain plain S3 generics when mizer is
+  loaded, avoiding interference with S4 method dispatch for other packages.
+
+- New `MizerRate` S3 class for the species x size arrays returned by rate
+  functions such as `getEncounter()`, `getFeedingLevel()`, `getEReproAndGrowth()`,
+  etc. A `MizerRate` object behaves like a regular matrix for arithmetic and
+  subsetting, but carries a human-readable `rate_name` and `units` attribute and
+  provides enhanced `print()`, `summary()`, `plot()`, and `as.data.frame()`
+  methods.
+
 - New `expandSizeGrid()` function expands the size grid of a `MizerParams`
   object to a new minimum and/or maximum size while preserving all existing
   species data.