tuneParams() can now keep the yield matched to observations.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mizerExperimental
 Type: Package
 Title: Extends the mizer package with experimental features
-Version: 2.4.0.9004
+Version: 2.4.0.9005
 Author: Various contributors
 Maintainer: Gustav Delius <[email protected]>
 Description: This mizer extension package collects contributions from the mizer
@@ -36,6 +36,7 @@ Suggests:
 Collate:
     alignResource.R
     manipulateParams.R
+    matchYield.R
     mizerExperimental-package.R
     plotDiet.R
     plotBiomassFlux.R

NAMESPACE

@@ -5,6 +5,7 @@ export(alignResource)
 export(distanceSSLogYield)
 export(getYieldVsF)
 export(markBackground)
+export(matchYield)
 export(plotBiomassFlux)
 export(plotBiomassRelative)
 export(plotBiomassVsSpecies)

R/matchYield.R

@@ -0,0 +1,26 @@
+#' Match observed yields
+#' 
+#' This function matches the observed yields of all the gears for all the
+#' species by scaling the catchabilities by the ratio between current modelled
+#' yield and observed yield. 
+#' 
+#' @param params A MizerParams object
+#' @return A MizerParams object with updated catchabilities
+#' @export
+matchYield <- function(params) {
+    gp <- params@gear_params
+    if (is.null(gp$yield_observed)) {
+        stop("You need to specify `yield_observed` in the gear parameter dataframe.")
+    }
+    gp <- gp[!is.na(gp$yield_observed), ]
+    yields <- getYieldGear(params)
+    for (i in seq_len(nrow(gp))) {
+        gear <- as.character(gp$gear[i])
+        species <- as.character(gp$species[i])
+        ratio <- gp$yield_observed[i] / yields[gear, species]
+        if (!is.nan(ratio)) {
+            gear_params(params)[i, "catchability"] <- gp$catchability[i] * ratio
+        }
+    }
+    return(params)
+}

R/tuneParams_helpers.R

@@ -65,15 +65,15 @@ tuneParams_run_steady <- function(p, params, params_old, logs, session, input,
         progress <- shiny::Progress$new(session)
         on.exit(progress$close())
 
-        if ("yield" %in% input$match) {
-            p <- matchYields(p)
-        }
         if ("biomass" %in% input$match) {
             p <- matchBiomasses(p)
         }
         if ("growth" %in% input$match) {
             p <- matchGrowth(p, keep = "biomass")
         }
+        if ("yield" %in% input$match) {
+            p <- matchYield(p)
+        }
 
         # Run to steady state
         if (return_sim) {

tests/testthat/test-matchYield.R

@@ -0,0 +1,15 @@
+test_that("matchYield works", {
+    params <- NS_params
+    initial_effort(params) <- 1
+    yields <- getYieldGear(params)
+    gp <- params@gear_params
+    # Add yield_observed column but make it twice too large
+    for (i in seq_len(nrow(gp))) {
+        species <- as.character(gp$species[i])
+        gear <- as.character(gp$gear[i])
+        gp$yield_observed[i] <- yields[gear, species] * 2
+    }
+    gear_params(params) <- gp
+    p <- matchYield(params)
+    expect_equal(getYieldGear(params) * 2, getYieldGear(p))
+})