Catch all messages

tests/testthat/test-MizerSim-class.R

@@ -1,4 +1,4 @@
-params <- newMultispeciesParams(NS_species_params_gears, inter)
+params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
 
 # basic constructor sets dimensions properly ----
 test_that("basic constructor sets dimensions properly", {

tests/testthat/test-analytic_results.R

@@ -1,7 +1,9 @@
 # Initialise power law ----
 no_w <- 100
 no_sp <- 2
-p <- newTraitParams(no_sp = no_sp, perfect_scaling = TRUE, no_w = no_w)
+expect_message(p <- newTraitParams(no_sp = no_sp, perfect_scaling = TRUE, 
+                                   no_w = no_w),
+               "Note: Negative resource abundances")
 p@species_params$pred_kernel_type <- "truncated_lognormal"
 n0 <- p@initial_n
 n0[] <- 0

tests/testthat/test-backwards_compatibility.R

@@ -7,7 +7,7 @@ data(inter)
 test_that("MizerParams() works as in version 2.5.1", {
   # expect_warning(params <- MizerParams(NS_species_params_gears, inter), "deprecated") 
   # warning no longer thrown - NS_species_params_gears is now 2.5.1 (see `params@mizer_version`)
-  params <- newMultispeciesParams(NS_species_params_gears, inter)
+  params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
   # expect_known_value(params@search_vol, "values/set_multispecies_model_search_vol")
   # expect_known_value(params@intake_max, "values/set_multispecies_model_intake_max")
   # expect_known_value(params@psi,        "values/set_multispecies_model_psi")

tests/testthat/test-get_initial_n.R

@@ -1,6 +1,6 @@
 # get_initial_n ----
 test_that("get_initial_n is working properly", {
-    params <- newMultispeciesParams(NS_species_params_gears, inter)
+    params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     n <- get_initial_n(params)
     no_sp <- nrow(params@species_params)
     for (i in 1:no_sp) {

tests/testthat/test-manipulate_species.R

@@ -6,7 +6,7 @@ test_that("addSpecies works when adding a second identical species", {
     species_params <- p@species_params[5, ]
     species_params$species <- "new"
     # Adding species 5 again should lead two copies of the species
-    pa <- addSpecies(p, species_params)
+    expect_message(pa <- addSpecies(p, species_params))
     expect_identical(pa@metab[5, ], pa@metab[no_sp + 1, ])
     expect_identical(pa@psi[5, ], pa@psi[no_sp + 1, ])
     expect_identical(pa@ft_pred_kernel_e[5, ], pa@ft_pred_kernel_e[no_sp + 1, ])
@@ -36,23 +36,29 @@ test_that("addSpecies handles gear params correctly", {
     # If no initial_effort for new gear is provided, it is 0
     # Wrapping in `expect_warning()` to ignore warnings about unrealistic
     # reproductive efficiency
-    expect_warning(pa <- addSpecies(p, sp, gp))
+    (pa <- addSpecies(p, sp, gp)) |>
+        expect_message() |>
+        expect_warning()
     expect_identical(pa@initial_effort,
                      c(knife_edge_gear = 0, gear1 = 0, gear2 = 0))
     expect_identical(nrow(pa@gear_params), 5L)
 
     # effort for existing gear is not changed
     extra_effort <- c(gear1 = 2, gear2 = 3)
-    expect_warning(pa <- addSpecies(p, sp, gp, initial_effort = extra_effort))
+    (pa <- addSpecies(p, sp, gp, initial_effort = extra_effort)) |>
+        expect_message() |>
+        expect_warning()
     expect_identical(pa@initial_effort, c(knife_edge_gear = 0, extra_effort))
 
     effort <- 2
-    expect_error(addSpecies(p, sp, gp, initial_effort = effort),
-                 "The `initial_effort` must be a named list or vector")
+    addSpecies(p, sp, gp, initial_effort = effort) |>
+        expect_message() |>
+        expect_error("The `initial_effort` must be a named list or vector")
 
     effort <- c(knife_edge_gear = 1)
-    expect_error(addSpecies(p, sp, gp, initial_effort = effort),
-                 "The names of the `initial_effort` do not match the names of the new gears.")
+    addSpecies(p, sp, gp, initial_effort = effort) |>
+        expect_message() |>
+        expect_error("The names of the `initial_effort` do not match the names of the new gears.")
 })
 
 test_that("addSpecies handles interaction matrix correctly", {
@@ -66,19 +72,23 @@ test_that("addSpecies handles interaction matrix correctly", {
 
     interaction <- matrix(1:4/4, ncol = 2)
     ones <- matrix(rep(1, 4), ncol = 2)
-    expect_warning(pa <- addSpecies(p, sp, interaction = interaction))
+    (pa <- addSpecies(p, sp, interaction = interaction)) |>
+        expect_message() |>
+        expect_warning()
     expect_equal(pa@interaction[3:4, 3:4], interaction, ignore_attr = TRUE)
     expect_equal(pa@interaction[1:2, 3:4], ones, ignore_attr = TRUE)
     expect_equal(pa@interaction[3:4, 1:2], ones, ignore_attr = TRUE)
     expect_equal(pa@interaction[1:2, 1:2], p@interaction, ignore_attr = TRUE)
 
     interaction <- matrix(1:16/16, ncol = 4)
-    expect_warning(pa <- addSpecies(p, sp, interaction = interaction))
+    (pa <- addSpecies(p, sp, interaction = interaction)) |>
+        expect_message() |>
+        expect_warning("The following species require an unrealistic reproductive efficiency greater than 1: new2")
     expect_equal(pa@interaction, interaction, ignore_attr = TRUE)
 
-    expect_error(addSpecies(p, sp,
-                            interaction = matrix(1:9, ncol = 3)),
-                 "Interaction matrix has invalid dimensions.")
+    addSpecies(p, sp, interaction = matrix(1:9, ncol = 3)) |>
+        expect_warning() |>
+        expect_error("Interaction matrix has invalid dimensions.")
 })
 test_that("addSpecies works when adding a species with a larger w_max", {
     sp <- data.frame(species = "Blue whale", w_max = 5e4,
@@ -88,7 +98,8 @@ test_that("addSpecies works when adding a species with a larger w_max", {
     # change a slot to test that such changes will be preserved
     params <- setMaxIntakeRate(params, 2 * getMaxIntakeRate(params))
 
-    p <- addSpecies(params, sp)
+    (p <- addSpecies(params, sp)) |>
+        expect_message()
     expect_identical(p@w[1:100], params@w)
     expect_identical(p@w_full[seq_along(params@w_full)], params@w_full)
     expect_lte(5e4, max(p@w))
@@ -104,7 +115,8 @@ test_that("addSpecies works when adding a species with a smaller w_min", {
     # change a slot to test that such changes will be preserved
     params <- setMaxIntakeRate(params, 2 * getMaxIntakeRate(params))
 
-    p <- addSpecies(params, sp)
+    (p <- addSpecies(params, sp)) |>
+        expect_message()
     expect_equal(p@w[28:127], params@w)
     expect_equal(p@w_full[seq_along(params@w_full)], params@w_full)
     expect_gte(1e-5, min(p@w))
@@ -119,7 +131,8 @@ test_that("addSpecies has other documented properties", {
                      k_vb = c(4, 1),
                      n = 2 / 3,
                      p = 2 / 3)
-    p <- addSpecies(NS_params, sp)
+    (p <- addSpecies(NS_params, sp)) |>
+        expect_message()
 
     # New species have 0 reproduction level
     expect_equal(getReproductionLevel(p)[13:14],
@@ -144,7 +157,7 @@ test_that("Added species stay at low abundance", {
         a = 0.0085,
         b = 3.11
     )
-    params <- addSpecies(params, species_params)
+    expect_message(params <- addSpecies(params, species_params))
     no_sp <- nrow(params@species_params)
     sim <- project(params, t_max = 1, progress_bar = FALSE)
     expect_lt(finalN(sim)[no_sp, 1] / initialN(sim)[no_sp, 1], 1.04)
@@ -156,11 +169,12 @@ test_that("removeSpecies works", {
     remove <- NS_species_params$species[2:11]
     reduced <- NS_species_params[!(NS_species_params$species %in% remove), ]
     params <- newMultispeciesParams(NS_species_params, no_w = 20,
-                                    max_w = 39900, min_w_pp = 9e-14)
+                                    max_w = 39900, min_w_pp = 9e-14, 
+                                    info_level = 0)
     p1 <- removeSpecies(params, species = remove)
     expect_equal(nrow(p1@species_params), nrow(params@species_params) - 10)
     p2 <- newMultispeciesParams(reduced, no_w = 20,
-                                max_w = 39900, min_w_pp = 9e-14)
+                                max_w = 39900, min_w_pp = 9e-14, info_level = 0)
     p2@linecolour[2] = "#a08dfb" # update line colour
     expect_equal(p1, p2, ignore_attr = TRUE)
     sim1 <- project(p1, t_max = 0.4, t_save = 0.4)
@@ -206,8 +220,9 @@ test_that("adding and then removing species leaves params unaltered", {
     comment(params@pred_kernel) <- NULL
     comment(params@catchability) <- NULL
     comment(params@selectivity) <- NULL
-    params2 <- addSpecies(params, sp) %>%
-        removeSpecies(c("new1", "new2"))
+    (params2 <- addSpecies(params, sp) |>
+        removeSpecies(c("new1", "new2"))) |>
+        expect_message()
 
     # For now the linecolour and linetype are not preserved
     # TODO: fix this in the next overhaul of linecolour and linetype code
@@ -225,11 +240,11 @@ test_that("adding and then removing species leaves params unaltered", {
 # renameSpecies ----
 test_that("renameSpecies works", {
     sp <- NS_species_params
-    p <- newMultispeciesParams(sp)
+    p <- newMultispeciesParams(sp, info_level = 0)
     sp$species <- tolower(sp$species)
     replace <- NS_species_params$species
     names(replace) <- sp$species
-    p2 <- newMultispeciesParams(sp)
+    p2 <- newMultispeciesParams(sp, info_level = 0)
     p2 <- renameSpecies(p2, replace)
     p2@time_modified <- p@time_modified
     p2@time_created <- p@time_created

tests/testthat/test-newMultispeciesParams.R

@@ -1,23 +1,24 @@
 # newMultispeciesParams ----
 # * Dimensions are correct ----
 test_that("constructor with species_params and interaction signature gives the right dimensions", {
-    params <- newMultispeciesParams(NS_species_params, inter)
+    params <- newMultispeciesParams(NS_species_params, inter, info_level = 0)
     # expect_that(params, is_a("MizerParams")) # deprecated, trying to find alternative
     expect_equal(class(params)[1], "MizerParams") # alternative?
     expect_equal(dim(params@psi)[1], nrow(NS_species_params))
     expect_equal(dimnames(params@psi)$sp, as.character(NS_species_params$species))
-    params_gears <- newMultispeciesParams(NS_species_params_gears, inter)  
+    params_gears <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)  
     expect_equal(unique(dimnames(params_gears@selectivity)$gear), 
                  as.character(unique(params_gears@species_params$gear)))
     # pass in other arguments
-    params_gears <- newMultispeciesParams(NS_species_params_gears, inter, no_w = 50)  
+    params_gears <- newMultispeciesParams(NS_species_params_gears, 
+                                          inter, no_w = 50, info_level = 0)  
     expect_length(params_gears@w, 50)
     expect_equal(dimnames(params_gears@selectivity)$gear,
                  unique(NS_species_params_gears$gear))
 })
 
 test_that("constructor with only species_params signature gives the right dimensions", {
-    params <- newMultispeciesParams(NS_species_params)  
+    params <- newMultispeciesParams(NS_species_params, info_level = 0)  
     expect_true(all(params@interaction == 1))
     expect_equal(dim(params@interaction), c(dim(params@psi)[1],
                                             dim(params@psi)[1]))
@@ -26,23 +27,24 @@ test_that("constructor with only species_params signature gives the right dimens
 # * w_min_idx is correct ----
 test_that("w_min_idx is being set correctly", {
     # default - no w_min in params data so set to first size
-    params <- newMultispeciesParams(NS_species_params_gears, inter)
+    params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     expect_true(all(params@species_params$w_min == params@w[1]))
     expect_true(all(params@w_min_idx == 1))
     # Set w_min to be the min by hand
     NS_species_params_gears$w_min <- 0.001
-    params <- newMultispeciesParams(NS_species_params_gears, inter)
+    params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     expect_true(all(params@w_min_idx == 1))
     # Change w_min of one of the species
     NS_species_params_gears$w_min <- 0.001
     NS_species_params_gears$w_min[7] <- 10
-    params <- newMultispeciesParams(NS_species_params_gears, inter)
+    params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     expect_true(all(params@w_min_idx[c(1:6, 8:12)] == 1))
     expect_equal(as.integer(params@w_min_idx[7]), max(which(params@w <= 10)))
 })
 
 test_that("Errors are reported", {
-    expect_error(newMultispeciesParams(NS_species_params, min_w_pp = 1),
+    expect_error(newMultispeciesParams(NS_species_params, min_w_pp = 1, 
+                                       info_level = 0),
                  "min_w_pp must be larger than min_w")
 })
 

tests/testthat/test-plots.R

@@ -3,8 +3,10 @@ species_params <- NS_species_params_gears
 # Make species names numeric because that created problems in the past
 species_params$species <- seq_len(nrow(species_params))
 species_params$pred_kernel_type <- "truncated_lognormal"
-params <- newMultispeciesParams(species_params, inter, no_w = 30,
-                                n = 2 / 3, p = 0.7, lambda = 2.8 - 2 / 3)
+(params <- newMultispeciesParams(species_params, inter, no_w = 30,
+                                n = 2 / 3, p = 0.7, lambda = 2.8 - 2 / 3, 
+                                info_level = 0)) |>
+    expect_message("Note: Dimnames of interaction matrix do not match")
 sim <- project(params, effort = 1, t_max = 3, dt = 1, t_save = 1)
 sim0 <- project(params, effort = 0, t_max = 3, dt = 1, t_save = 1)
 species <- c(11, 10)
@@ -13,7 +15,7 @@ params_bkgrd <- params
 params_bkgrd@A[1:3] <- NA
 # params object with single species
 sp_single <- data.frame(species = 1, w_max = 1000, h = 30)
-params_single <- newMultispeciesParams(sp_single, no_w = 30)
+params_single <- newMultispeciesParams(sp_single, no_w = 30, info_level = 0)
 
 # Need to use vdiffr conditionally
 expect_doppelganger <- function(title, fig, ...) {

tests/testthat/test-project.R

@@ -1,4 +1,4 @@
-params <- newMultispeciesParams(NS_species_params_gears, inter)
+params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
 
 # time dimension ----
 test_that("time dimension is dealt with properly", {
@@ -112,7 +112,7 @@ test_that("Can pass in initial species", {
 test_that("w_min array reference is working OK", {
     NS_species_params_gears$w_min <- 0.001
     NS_species_params_gears$w_min[1] <- 1
-    params2 <- newMultispeciesParams(NS_species_params_gears, inter)
+    params2 <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     sim <- project(params2, effort = 1, t_max = 5)
     expect_equal(sim@n[6, 1, 1:(sim@params@w_min_idx[1] - 1)],
                       rep(0, sim@params@w_min_idx[1] - 1), ignore_attr = TRUE)
@@ -219,7 +219,7 @@ test_that("Gear checking and sorting is OK", {
 # same numerical results as previously ----
 test_that("Simulation gives same numerical results as previously",{
   params <- newMultispeciesParams(NS_species_params_gears, inter,
-                                  n = 2/3, p = 0.7, lambda = 2.8 - 2/3)
+                                  n = 2/3, p = 0.7, lambda = 2.8 - 2/3, info_level = 0)
   sim <- project(params, t_max = 1)
   # expect_known_value(sim@n[2, 3, ], "values/projectn")
   # expect_known_value(sim@n_pp[2, ], "values/projectp")

tests/testthat/test-project_methods.R

@@ -2,7 +2,8 @@
 
 # North sea
 params <- newMultispeciesParams(NS_species_params_gears, inter,
-                                n = 2/3, p = 0.7, lambda = 2.8 - 2/3)
+                                n = 2/3, p = 0.7, lambda = 2.8 - 2/3,
+                                info_level = 0)
 no_gear <- dim(params@catchability)[1]
 no_sp <- dim(params@catchability)[2]
 no_w <- length(params@w)
@@ -215,7 +216,7 @@ test_that("getPredMort passes correct time", {
 
 test_that("interaction is right way round in getPredMort function", {
     inter[, "Dab"] <- 0  # Dab not eaten by anything
-    params <- newMultispeciesParams(NS_species_params_gears, inter)
+    params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     m2 <- getPredMort(params, get_initial_n(params), params@cc_pp)
     expect_true(all(m2["Dab", ] == 0))
 })
@@ -535,7 +536,9 @@ test_that("Test that fft based integrator gives similar result as old code", {
     species_params$beta[5] <- species_params$beta[5] / 1000
     # and use different egg sizes
     species_params$w_min <- seq(0.001, 1, length.out = no_sp)
-    params <- newMultispeciesParams(species_params, inter, no_w = 30, min_w_pp = 1e-12)
+    params <- newMultispeciesParams(species_params, inter, 
+                                        no_w = 30, min_w_pp = 1e-12,
+                                        info_level = 0)
     # create a second params object that does not use fft
     params2 <- setPredKernel(params, pred_kernel = getPredKernel(params))
     # Test encounter rate integral

tests/testthat/test-selectivity_funcs.R

@@ -11,7 +11,7 @@ test_that("knife-edge selectivity function is working properly", {
     NS_species_params_gears$knife_edge_size[NS_species_params_gears$gear == "Industrial"] <- 500
     # Chop off l25, l50, a and b columns - the trawl selectivity
     NS_species_params_gears <- NS_species_params_gears[,!(colnames(NS_species_params_gears) %in% c("l25","l50","a","b"))]
-    params <- newMultispeciesParams(NS_species_params_gears, inter)
+    params <- newMultispeciesParams(NS_species_params_gears, inter, info_level = 0)
     industrial_species <- as.character(NS_species_params_gears$species[NS_species_params_gears$gear == "Industrial"])
     pelagic_species <- as.character(NS_species_params_gears$species[NS_species_params_gears$gear == "Pelagic"])
     beam_trawl_species <- as.character(NS_species_params_gears$species[NS_species_params_gears$gear == "Beam"])

tests/testthat/test-setFishing.R

@@ -76,7 +76,7 @@ test_that("validEffort works", {
 })
 test_that("validEffortParams works when no gears are set up", {
     params <- newMultispeciesParams(NS_species_params,
-                                    gear_params = data.frame())
+                                    gear_params = data.frame(), info_level = 0)
     expect_length(validEffortVector(1, params), 0)
     expect_length(validEffortVector(NULL, params), 0)
 })

tests/testthat/test-setInitialValues.R

@@ -24,14 +24,14 @@ test_that("We can set and get initial values from sim object", {
 })
 
 test_that("setInitialValues gives correct errors", {
-    params1 <- newMultispeciesParams(NS_species_params, no_w = 20)
+    params1 <- newMultispeciesParams(NS_species_params, no_w = 20, info_level = 0)
     sim <- project(params1, t_max = 2, dt = 1)
-    params2 <- newMultispeciesParams(NS_species_params, no_w = 30)
+    params2 <- newMultispeciesParams(NS_species_params, no_w = 30, info_level = 0)
     expect_error(setInitialValues(params2, sim),
                  "The consumer size spectrum of the simulation in `sim` has a different size from that in `params`")
 
     params3 <- newMultispeciesParams(NS_species_params, no_w = 20,
-                                     min_w_pp = 1e-4)
+                                     min_w_pp = 1e-4, info_level = 0)
     expect_error(setInitialValues(params3, sim),
                  "The resource size spectrum of the simulation in `sim` has a different size from that in `params`.")
     params4 <- setComponent(params1, "test",
@@ -49,7 +49,7 @@ test_that("setInitialValues gives correct errors", {
 
 test_that("Can set initial values in a model with a single species", {
     species_params <- NS_species_params[1, ]
-    params <- newMultispeciesParams(species_params)
+    params <- newMultispeciesParams(species_params, info_level = 0)
     sim <- project(params, t_max = 0.1, t_save = 0.1)
     p <- setInitialValues(params, sim)
     expect_identical(finalN(sim), initialN(p))

tests/testthat/test-single_species.R

@@ -1,5 +1,5 @@
 # We choose the largest species for our single-species
-params <- newMultispeciesParams(NS_species_params_gears[12, ])
+params <- newMultispeciesParams(NS_species_params_gears[12, ], info_level = 0)
 n <- params@initial_n
 npp <- params@initial_n_pp
 effort <- array(abs(rnorm(10)), dim = c(10, 1))
@@ -39,6 +39,6 @@ test_that("Can set up model with minimal information", {
                      stringsAsFactors = FALSE)
     sp$w_max <- 1000
     sp$k_vb <- 10
-    params <- newMultispeciesParams(sp)
+    params <- newMultispeciesParams(sp, info_level = 0)
     expect_error(project(params, t_max = 1), NA)
 })