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

sizespectrum · Aug 21, 2021 · f897d4c · f897d4c
1 parent 615419a
commit f897d4c
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Showing 4 changed files with 62 additions and 44 deletions.
diff --git a/R/setMetabolicRate.R b/R/setMetabolicRate.R
@@ -27,10 +27,11 @@
 #' @param p The allometric metabolic exponent. This is only used if `metab`
 #'   is not given explicitly and if the exponent is not specified in a `p`
 #'   column in the `species_params`.
-#' @param comment_metab `r lifecycle::badge("experimental")`
-#'   A string describing how the value for 'metab' was obtained. This is
-#'   ignored if 'metab' is not supplied or already has a comment
-#'   attribute.
+#' @param reset If set to TRUE, then the metabolic 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 MizerParams object with updated metabolic rate. Because of the way
@@ -40,18 +41,33 @@
 #'   `params <- setMetabolicRate(params, ...)`.
 #' @export
 #' @family functions for setting parameters
-setMetabolicRate <- function(params, 
-                             metab = NULL, p = NULL, 
-                             comment_metab = "set manually", ...) {
-    assert_that(is(params, "MizerParams"))
+setMetabolicRate <- function(params, metab = NULL, p = NULL, 
+                             reset = FALSE, ...) {
+    assert_that(is(params, "MizerParams"),
+                is.logical(reset))
     if (!is.null(p)) {
         assert_that(is.numeric(p))
         params <- set_species_param_default(params, "p", p)
     }
     species_params <- params@species_params
+
+    if (reset) {
+        if (!is.null(metab)) {
+            warning("Because you set `reset = TRUE`, the value you provided ", 
+                    "for `metab` will be ignored and a value will be ",
+                    "calculated from the species parameters.")
+            metab <- NULL
+        }
+        comment(params@metab) <- NULL
+    }
+
     if (!is.null(metab)) {
         if (is.null(comment(metab))) {
-            comment(metab) <- comment_metab
+            if (is.null(comment(params@metab))) {
+                comment(metab) <- "set manually"
+            } else {
+                comment(metab) <- comment(params@metab)
+            }
         }
         assert_that(is.array(metab),
                     identical(dim(metab), dim(params@metab)))

diff --git a/man/setMetabolicRate.Rd b/man/setMetabolicRate.Rd
diff --git a/man/setParams.Rd b/man/setParams.Rd
diff --git a/tests/testthat/test-setMetabolicRate.R b/tests/testthat/test-setMetabolicRate.R
@@ -1,13 +1,13 @@
 params <- NS_params
-no_sp <- nrow(params@species_params)
 
-## setMetabolicRate ----
+# setMetabolicRate ----
 test_that("setMetabolicRate works", {
-    expect_identical(setMetabolicRate(params, params@metab, 
-                                      comment_metab = NULL), params)
     params@species_params$ks <- 2 * params@species_params$ks
     p2 <- setMetabolicRate(params)
     expect_identical(2 * params@metab, p2@metab)
+    # only metab changed
+    p2@metab <- params@metab
+    expect_identical(p2, params)
 })
 test_that("setMetabolicRate can set exponent p", {
     # no change where p is already set in species_params
@@ -19,32 +19,38 @@ test_that("setMetabolicRate can set exponent p", {
     expect_identical(params@species_params$p, c(1, rep(0.7, 11)))
 })
 test_that("Comment works on metab", {
+    params <- NS_params
+    # if no comment, it is set automatically
     metab <- params@metab
+    params <- setMetabolicRate(params, metab = metab)
+    expect_identical(comment(params@metab), "set manually")
+
+    # comment is stored
     comment(metab) <- "test"
     params <- setMetabolicRate(params, metab = metab)
     expect_identical(comment(params@metab), "test")
 
+    # if no comment, previous comment is kept
+    comment(metab) <- NULL
+    params <- setMetabolicRate(params, metab = metab)
+    expect_identical(comment(params@metab), "test")
+
     # no message when nothing changes
     expect_message(setMetabolicRate(params), NA)
     # but message when a change is not stored due to comment
-    params@species_params$k <- 1
-    expect_message(setMetabolicRate(params),
-                   "has been commented")
-
-    # comment argument is ignored when there is a comment on intake_max
-    params <- setMetabolicRate(params, metab = metab,
-                               comment_metab = "overwrite")
-    expect_identical(comment(params@metab), "test")
-    # but it is used otherwise
-    comment(metab) <- NULL
-    params <- setMetabolicRate(params, metab = metab,
-                               comment_metab = "overwrite")
-    expect_identical(comment(params@metab), "overwrite")
+    params@species_params$ks <- 1
+    expect_message(setMetabolicRate(params),  "has been commented")
+    # Can reset
+    p <- setMetabolicRate(params, reset = TRUE)
+    expect_equal(p@metab[, 1], params@w[1]^params@species_params$p,
+                 check.attributes = FALSE)
+    expect_warning(setMetabolicRate(params, metab = metab,
+                                    reset = TRUE),
+                   "Because you set `reset = TRUE`, the")
 })
 
 # getMetabolicRate ----
 test_that("getMetabolicRate works", {
-    p <- setMetabolicRate(params, metab = getMetabolicRate(params), 
-                          comment_metab = NULL)
-    expect_identical(params, p)
+    expect_identical(getMetabolicRate(NS_params),
+                     NS_params@metab)
 })