Remove comment argument from setMaxIntakeRate() as proposed in #214

R/newMultispeciesParams.R

@@ -209,7 +209,7 @@ newMultispeciesParams <- function(
 #' @inheritParams setInteraction
 #' @inheritDotParams setPredKernel
 #' @inheritDotParams setSearchVolume
-#' @inheritDotParams setMaxIntakeRate
+#' @inheritDotParams setMaxIntakeRate -reset
 #' @inheritDotParams setMetabolicRate
 #' @inheritDotParams setExtMort
 #' @inheritDotParams setReproduction

R/setMaxIntakeRate.R

@@ -20,10 +20,11 @@
 #' @param intake_max Optional. An array (species x size) holding the maximum
 #'   intake rate for each species at size. If not supplied, a default is set as
 #'   described in the section "Setting maximum intake rate".
-#' @param comment_intake_max `r lifecycle::badge("experimental")`
-#'   A string describing how the value for 'intake_max' was obtained. This is
-#'   ignored if 'intake_max' is not supplied or already has a comment
-#'   attribute.
+#' @param reset If set to TRUE, then the intake rate will be reset to the value
+#'   calculated from the species parameters, even if it was previously 
+#'   overwritten with a custom value. If set to FALSE (default) then a
+#'   recalculation from the species parameters will take place only if no
+#'   custom value has been set.
 #' @param ... Unused
 #' 
 #' @return A `MizerParams` object with updated maximum intake rate. Because
@@ -33,16 +34,29 @@
 #'   `params <- setMaxIntakeRate(params, ...)`.
 #' @export
 #' @family functions for setting parameters
-setMaxIntakeRate <- function(params, 
-                             intake_max = NULL, 
-                             comment_intake_max = "set manually", ...) {
-    assert_that(is(params, "MizerParams"))
+setMaxIntakeRate <- function(params, intake_max = NULL, reset = FALSE, ...) {
+    assert_that(is(params, "MizerParams"),
+                is.logical(reset))
     species_params <- params@species_params
 
+    if (reset) {
+        if (!is.null(intake_max)) {
+            warning("Because you set `reset = TRUE`, the value you provided ", 
+                    "for `intake_max` will be ignored and a value will be ",
+                    "calculated from the species parameters.")
+            intake_max <- NULL
+        }
+        comment(params@intake_max) <- NULL
+    }
+
     # If intake_max array is supplied, check it, store it and return
     if (!is.null(intake_max)) {
         if (is.null(comment(intake_max))) {
-            comment(intake_max) <- comment_intake_max
+            if (is.null(comment(params@intake_max))) {
+                comment(intake_max) <- "set manually"
+            } else {
+                comment(intake_max) <- comment(params@intake_max)
+            }
         }
         assert_that(is.array(intake_max),
                     identical(dim(intake_max), dim(params@intake_max)))
@@ -58,6 +72,7 @@ setMaxIntakeRate <- function(params,
         return(params)
     }
 
+    # Else recalculate from species params
     params@species_params$h <- get_h_default(params)
 
     intake_max <- sweep(outer(params@species_params[["n"]], 

tests/testthat/test-setMaxIntakeRate.R

@@ -1,41 +1,46 @@
-params <- NS_params
-no_sp <- nrow(params@species_params)
-
-## setMaxIntakeRate ----
-test_that("ssetMaxIntakeRate works", {
-    expect_identical(setMaxIntakeRate(params, params@intake_max, 
-                                      comment_intake_max = NULL), params)
+# setMaxIntakeRate ----
+test_that("setMaxIntakeRate works", {
+    params <- NS_params
     params@species_params$h <- 2 * params@species_params$h
     p2 <- setMaxIntakeRate(params)
     expect_identical(2 * params@intake_max, p2@intake_max)
+    # only intake max changed
+    p2@intake_max <- params@intake_max
+    expect_identical(p2, params)
 })
 test_that("Comment works on intake_max", {
+    params <- NS_params
+    # if no comment, it is set automatically
     intake_max <- params@intake_max
+    params <- setMaxIntakeRate(params, intake_max = intake_max)
+    expect_identical(comment(params@intake_max), "set manually")
+
+    # comment is stored
     comment(intake_max) <- "test"
     params <- setMaxIntakeRate(params, intake_max = intake_max)
     expect_identical(comment(params@intake_max), "test")
 
+    # if no comment, previous comment is kept
+    comment(intake_max) <- NULL
+    params <- setMaxIntakeRate(params, intake_max = intake_max)
+    expect_identical(comment(params@intake_max), "test")
+
     # no message when nothing changes
     expect_message(setMaxIntakeRate(params), NA)
     # but message when a change is not stored due to comment
     params@species_params$h <- 1
-    expect_message(setMaxIntakeRate(params),
-                   "has been commented")
-
-    # comment argument is ignored when there is a comment on intake_max
-    params <- setMaxIntakeRate(params, intake_max = intake_max,
-                               comment_intake_max = "overwrite")
-    expect_identical(comment(params@intake_max), "test")
-    # but it is used otherwise
-    comment(intake_max) <- NULL
-    params <- setMaxIntakeRate(params, intake_max = intake_max,
-                               comment_intake_max = "overwrite")
-    expect_identical(comment(params@intake_max), "overwrite")
+    expect_message(setMaxIntakeRate(params),  "has been commented")
+    # Can reset
+    p <- setMaxIntakeRate(params, reset = TRUE)
+    expect_equal(p@intake_max[, 1], params@w[1]^params@species_params$n,
+                 check.attributes = FALSE)
+    expect_warning(setMaxIntakeRate(params, intake_max = intake_max,
+                                    reset = TRUE),
+                   "Because you set `reset = TRUE`, the")
 })
 
 # getMaxIntakeRate ----
 test_that("getMaxIntakeRate works", {
-    p <- setMaxIntakeRate(params, intake_max = getMaxIntakeRate(params), 
-                          comment_intake_max = NULL)
-    expect_identical(params, p)
+    expect_identical(getMaxIntakeRate(NS_params),
+                     NS_params@intake_max)
 })