tests/testthat/test-backwards_compatibility.R

In mizer: Dynamic Multi-Species Size Spectrum Modelling

context("Backwards compatibility")

# The known values below were calculated with mizer version 1.0.1

# In version 1.0.1 it was still necessary to use data()
data(NS_species_params_gears)
data(inter)

test_that("MizerParams() works as in version 1", {
    expect_warning(params <- MizerParams(NS_species_params_gears, inter), "deprecated")
    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")
    #expect_known_value(params@std_metab + params@activity, "values/set_multispecies_model_metab")
    expect_known_value(params@metab,      "values/set_multispecies_model_metab")
    expect_known_value(params@mu_b,      "values/set_multispecies_model_mu_b")
    expect_known_value(params@rr_pp, "values/set_multispecies_model_rr_pp")
    expect_known_value(params@cc_pp, "values/set_multispecies_model_cc_pp")
    expect_known_value(params@initial_n, "values/set_multispecies_model_initial_n")
    expect_known_value(params@initial_n_pp, "values/set_multispecies_model_initial_n_pp")
    # The predation rate is different because in the old version the predation
    # kernel was cut off at beta + 3 sigma
    # new <- getPredRate(params)
    # df <- melt(new) %>% mutate(type = "new")
    # old <- readRDS("values/set_multispecies_model_pred_rate")
    # dimnames(old) <- dimnames(new)
    # dfo <- melt(old) %>% mutate(type = "old")
    # dfs <- rbind(df, dfo)
    # dfs$sp <- as.factor(dfs$sp)
    # ggplot(dfs) +
    #     geom_line((aes(x = w_prey, y = value, colour = sp, linetype = type))) +
    #     scale_x_log10() +
    #     scale_y_log10()
    # max(abs(old - new))
    expect_warning(gpp <- getPhiPrey(params, n = initialN(params), 
                                     n_pp = initialNResource(params)),
                   "deprecated")
    expect_known_value(gpp, "values/set_multispecies_model_phi_prey",
                       check.attributes = FALSE,
                       tolerance = 0.0005)
    # The discrepancy is small, see the following graph:
    # new <- getPhiPrey(params, n = initialN(params), n_pp = initialNResource(params))
    # df <- melt(new) %>% mutate(type = "new")
    # old <- readRDS("values/set_multispecies_model_phi_prey")
    # dimnames(old) <- dimnames(new)
    # dfo <- melt(old) %>% mutate(type = "old")
    # dfs <- rbind(df, dfo)
    # dfs$sp <- as.factor(dfs$sp)
    # ggplot(dfs) +
    #     geom_line((aes(x = w, y = value, colour = sp, linetype = type))) +
    #     scale_x_log10() +
    #     scale_y_log10()
    # max(abs(old - new))
})

test_that("set_trait_model() works as in version 1", {
    expect_warning(params <- set_trait_model(), "deprecated")
    expect_known_value(params@search_vol, "values/set_trait_model_search_vol")
    expect_known_value(params@intake_max, "values/set_trait_model_intake_max")
    expect_known_value(params@psi,        "values/set_trait_model_psi")
    #expect_known_value(params@std_metab + params@activity, "values/set_trait_model_metab")
    expect_known_value(params@metab,      "values/set_trait_model_metab")
    expect_known_value(params@mu_b,      "values/set_trait_model_mu_b")
    expect_known_value(params@rr_pp, "values/set_trait_model_rr_pp")
    expect_known_value(params@cc_pp, "values/set_trait_model_cc_pp")
    expect_known_value(params@initial_n, "values/set_trait_model_initial_n")
    expect_known_value(params@initial_n_pp, "values/set_trait_model_initial_n_pp")
    # The predation rate is different because in the old version the predation
    # kernel was cut off at beta + 3 sigma
    # new <- getPredRate(params)
    # df <- melt(new) %>% mutate(type = "new")
    # old <- readRDS("values/set_trait_model_pred_rate")
    # dimnames(old) <- dimnames(new)
    # dfo <- melt(old) %>% mutate(type = "old")
    # dfs <- rbind(df, dfo)
    # dfs$sp <- as.factor(dfs$sp)
    # ggplot(dfs) +
    #     geom_line((aes(x = w_prey, y = value, colour = sp, linetype = type))) +
    #     scale_x_log10() +
    #     scale_y_log10()
    expect_known_value(getPhiPrey(params, n = initialN(params), n_pp = initialNResource(params)), 
                       "values/set_trait_phi_prey",
                       check.attributes = FALSE,
                       tolerance = 1e-5)
    # The discrepancy is too small to see in the following graph:
    # new <- getPhiPrey(params, n = initialN(params), n_pp = initialNResource(params))
    # df <- melt(new) %>% mutate(type = "new")
    # old <- readRDS("values/set_trait_phi_prey")
    # dimnames(old) <- dimnames(new)
    # dfo <- melt(old) %>% mutate(type = "old")
    # dfs <- rbind(df, dfo)
    # dfs$sp <- as.factor(dfs$sp)
    # ggplot(dfs) +
    #     geom_line((aes(x = w, y = value, colour = sp, linetype = type))) +
    #     scale_x_log10() +
    #     scale_y_log10()
    # max(abs(old - new))
})

test_that("set_community_model() works as in version 1", {
    expect_warning(params <- set_community_model(), "deprecated")
    expect_known_value(params@search_vol, "values/set_community_model_search_vol")
    expect_known_value(params@intake_max, "values/set_community_model_intake_max")
    expect_known_value(params@psi,        "values/set_community_model_psi")
    #expect_known_value(params@std_metab + params@activity, "values/set_community_model_metab")
    expect_known_value(params@metab,      "values/set_community_model_metab")
    expect_known_value(params@mu_b,      "values/set_community_model_mu_b")
    expect_known_value(params@rr_pp, "values/set_community_model_rr_pp")
    expect_known_value(params@cc_pp, "values/set_community_model_cc_pp")
    expect_known_value(params@initial_n, "values/set_community_model_initial_n")
    expect_known_value(params@initial_n_pp, "values/set_community_model_initial_n_pp")
    # The predation rate is different because in the old version the predation
    # kernel was cut off at beta + 3 sigma, see following graph
    # new <- getPredRate(params)
    # df <- melt(new) %>% mutate(type = "new")
    # old <- readRDS("values/set_community_model_pred_rate")
    # dimnames(old) <- dimnames(new)
    # dfo <- melt(old) %>% mutate(type = "old")
    # dfs <- rbind(df, dfo)
    # dfs$sp <- as.factor(dfs$sp)
    # ggplot(dfs) +
    #     geom_line((aes(x = w_prey, y = value, colour = sp, linetype = type))) +
    #     scale_x_log10() +
    #     scale_y_log10()
    # max(abs(new - old))
    expect_known_value(getPhiPrey(params, n = initialN(params), n_pp = initialNResource(params)), 
                       "values/set_community_phi_prey",
                       check.attributes = FALSE,
                       tolerance = 42)
    # The discrepancy is small, see the following graph:
    # new <- getPhiPrey(params, n = initialN(params), n_pp = initialNResource(params))
    # df <- melt(new) %>% mutate(type = "new")
    # old <- readRDS("values/set_community_phi_prey")
    # dimnames(old) <- dimnames(new)
    # dfo <- melt(old) %>% mutate(type = "old")
    # dfs <- rbind(df, dfo)
    # dfs$sp <- as.factor(dfs$sp)
    # ggplot(dfs) +
    #     geom_line((aes(x = w, y = value, colour = sp, linetype = type))) +
    #     scale_x_log10() +
    #     scale_y_log10()
    # max(abs(new - old))
})