tests/testthat/test-match.R

In mizer: Dynamic Multi-Species Size Spectrum Modelling

local_edition(3)

test_that("matchBiomasses works", {
    params <- setBevertonHolt(NS_params)
    
    # Does nothing when no observed biomass
    expect_unchanged(matchBiomasses(params), params)
    species_params(params)$biomass_observed <- NA
    expect_unchanged(matchBiomasses(params), params)
    # Does nothing if observed already equals model
    species_params(params)$biomass_cutoff <- 1e-4
    biomass_actual <-
        rowSums(sweep(params@initial_n, 2, params@w * params@dw, "*"))
    species_params(params)$biomass_observed <- biomass_actual
    expect_unchanged(matchBiomasses(params), params)
    # Even if only partially observed
    species_params(params)$biomass_observed[1:5] <- NA
    expect_unchanged(matchBiomasses(params), params)
    
    # If we double the observations, we get twice the abundance
    species <- 1:9
    species_params(params)$biomass_observed <- 
        species_params(params)$biomass_observed * 2
    params2 <- matchBiomasses(params, species)
    expect_equal(params2@initial_n[6:9, ], params@initial_n[6:9, ] * 2)
    # but unobserved species don't change
    expect_equal(params2@initial_n[1:5, ], params@initial_n[1:5, ])
    # and unselected species don't change
    expect_equal(params2@initial_n[10:12, ], params@initial_n[10:12, ])
})

test_that("matchNumbers works", {
    params <- setBevertonHolt(NS_params)
    
    # Does nothing when no observed numbers
    expect_unchanged(matchNumbers(params), params)
    species_params(params)$number_observed <- NA
    expect_unchanged(matchNumbers(params), params)
    # Does nothing if observed already equals model
    species_params(params)$number_cutoff <- 1e-4
    number_actual <-
        rowSums(sweep(params@initial_n, 2, params@dw, "*"))
    species_params(params)$number_observed <- number_actual
    expect_unchanged(matchNumbers(params), params)
    # Even if only partially observed
    species_params(params)$number_observed[1:5] <- NA
    expect_unchanged(matchNumbers(params), params)
    
    # If we double the observations, we get twice the abundance
    species <- 1:9
    species_params(params)$number_observed <- 
        species_params(params)$number_observed * 2
    params2 <- matchNumbers(params, species)
    expect_equal(params2@initial_n[6:9, ], params@initial_n[6:9, ] * 2)
    # but unobserved species don't change
    expect_equal(params2@initial_n[1:5, ], params@initial_n[1:5, ])
    # and unselected species don't change
    expect_equal(params2@initial_n[10:12, ], params@initial_n[10:12, ])
})

test_that("matchYields works", {
    params <- setBevertonHolt(NS_params)
    
    # Does nothing when no observed yield
    expect_unchanged(matchYields(params), params)
    species_params(params)$yield_observed <- NA
    expect_message(
        expect_unchanged(matchYields(params), params),
        "not be changed: Sprat, Sandeel, N.pout, Herring, Dab, Whiting, Sole, Gurnard, Plaice, Haddock, Cod, Saithe.")
    # Does nothing if observed already equals model
    biomass <- sweep(params@initial_n, 2, params@w * params@dw, "*")
    yield_model <- rowSums(biomass * getFMort(params))
    species_params(params)$yield_observed <- yield_model
    expect_message(
        expect_unchanged(matchYields(params), params),
        "not be changed: Sprat, Sandeel, N.pout.")
    # Even if only partially observed
    species_params(params)$yield_observed[1:5] <- NA
    expect_message(
        expect_unchanged(matchYields(params), params),
        "not be changed: Sprat, Sandeel, N.pout, Herring, Dab.")
    
    # If we double the observations, we get twice the abundance
    species <- 1:9
    species_params(params)$yield_observed <- 
        species_params(params)$yield_observed * 2
    expect_message(
        params2 <- matchYields(params, species),
        "not be changed: Sprat, Sandeel, N.pout, Herring, Dab.")
    expect_equal(params2@initial_n[6:9, ], params@initial_n[6:9, ] * 2)
    # but unobserved species don't change
    expect_equal(params2@initial_n[1:5, ], params@initial_n[1:5, ])
    # and unselected species don't change
    expect_equal(params2@initial_n[10:12, ], params@initial_n[10:12, ])
})