# Initialise power law ---- no_w <- 100 no_sp <- 2 expect_message(p <- newTraitParams(no_sp = no_sp, perfect_scaling = TRUE, no_w = no_w), "Note: Negative resource abundances") p@species_params$pred_kernel_type <- "truncated_lognormal" n0 <- p@initial_n n0[] <- 0 n_pp <- p@initial_n_pp n_pp[] <- p@resource_params$kappa * p@w_full^(-p@resource_params$lambda) sp <- 1 # check first species sigma <- p@species_params$sigma[sp] beta <- p@species_params$beta[sp] gamma <- p@species_params$gamma[sp] q <- p@species_params[["q"]][sp] n <- p@species_params[["n"]][sp] lm2 <- p@resource_params$lambda - 2 # getEncounter ---- test_that("getEncounter approximates analytic result when feeding on resource only", { e <- getEncounter(p, n0, n_pp)[sp, ] * p@w^(lm2 - q) # Check that this is constant expect_equal(e, rep(e[1], length(e)), ignore_attr = TRUE) # Check that it agrees with analytic result Dx <- p@w[2] / p@w[1] - 1 dx <- log(p@w[2] / p@w[1]) encounter_analytic <- p@resource_params$kappa * exp(lm2^2 * sigma^2 / 2) * beta^lm2 * sqrt(2 * pi) * sigma * gamma * # The following factor takes into account the discretisation scheme Dx / dx #* # The following factor takes into account the cutoff in the integral # (pnorm(3 - lm2 * sigma) + pnorm(log(beta)/sigma + lm2 * sigma) - 1) # The Riemann sum is not precise enough expect_equal(e[1], encounter_analytic, tolerance = 1e-3, ignore_attr = TRUE) # Check that it agrees with left Riemann sum from w-Beta-3*sigma to w Beta <- log(beta) x_full <- log(p@w_full) dx <- x_full[2] - x_full[1] # Choose some predator weight w[i] i <- 100 ear <- 0 # Calculate left Riemann sum for (j in 1:(i - 1)) { ear <- ear + p@w_full[j]^(2 - p@resource_params$lambda) * exp(-(x_full[i] - x_full[j] - Beta)^2 / (2 * sigma^2)) } ear <- ear * p@resource_params$kappa * p@w_full[i]^(p@resource_params$lambda - 2) * dx * gamma expect_equal(e[1], ear * Dx / dx, ignore_attr = TRUE) }) # getDiet ---- test_that("getDiet approximates analytic result when feeding on resource only", { # n and n_pp are power laws n <- p@initial_n n[] <- rep(p@resource_params$kappa * p@w^(-p@resource_params$lambda), each = 2) n_pp <- p@initial_n_pp n_pp[] <- p@resource_params$kappa * p@w_full^(-p@resource_params$lambda) # switch of interaction between species p0 <- setInteraction(p, interaction = matrix(0, nrow = no_sp, ncol = no_sp)) diet <- getDiet(p0, n, n_pp, proportion = FALSE)[sp, , ] # None of the diet should come from fish expect_true(all(diet[, 1:2] == 0)) # Check that diet from resource is power law diet_coeff <- diet[, 3] * p@w^(lm2 - q) expect_equal(diet_coeff, rep(diet_coeff[1], no_w), ignore_attr = TRUE) # and agrees with result from getEncounter feeding_level <- getFeedingLevel(p0, n0, n_pp)[sp, ] encounter <- getEncounter(p0, n0, n_pp)[sp, ] expect_equal(diet[, 3], encounter * (1 - feeding_level), ignore_attr = TRUE) }) test_that("getFeedingLevel approximates analytic result", { f <- getFeedingLevel(p)[sp, ] # Check that this is constant expect_equal(f, rep(f[1], length(f)), tolerance = 1e-12, ignore_attr = TRUE) # Still to imprecise expect_equal(f[1], 0.6, tolerance = 2e-2, ignore_attr = TRUE) }) # TODO: fix this # test_that("getPredRate approximates analytic result", { # # We use a power law for the species spectrum # p@initial_n[sp, ] <- p@resource_params$kappa * p@w^(-p@resource_params$lambda) # # and constant feeding level # f0 <- 0.6 # f <- matrix(f0, nrow = 2, ncol = no_w) # # Calculate the coefficient of the power law # pr <- getPredRate(p, feeding_level = f)[sp, ] * p@w_full^(1 - n) # # Check that this is constant in the feeding range of the predator # sel <- (p@w_full > min(p@w) / beta * exp(3 * sigma)) & # (p@w_full < max(p@w) / beta / exp(3 * sigma)) # pr <- pr[sel] # # The first three entries of pr are still different. Why? # # For now we just cut them off # pr <- pr[4:length(pr)] # expect_equivalent(pr, rep(pr[1], length(pr))) # # Check that it agrees with analytic result # n1 <- n - 1 # Dx <- p@w[2] / p@w[1] - 1 # dx <- log(p@w[2] / p@w[1]) # pred_rate_analytic <- p@resource_params$kappa * gamma * (1 - f0) * # exp(n1^2 * sigma^2 / 2) * # beta^n1 * sqrt(2 * pi) * sigma * # # The following factor takes into account the discretisation scheme # Dx / dx #* # # The following factor takes into account the cutoff in the integral # #(pnorm(3 - n1 * sigma) + pnorm(log(beta)/sigma + n1 * sigma) - 1) # # This is still too imprecise # expect_equivalent(pr[1], pred_rate_analytic, tolerance = 1e-3) # # # Check that it agrees with Riemann sum from w to w+Beta-3*sigma # Beta <- log(beta) # x_full <- log(p@w_full) # dx <- x_full[2] - x_full[1] # rr <- Beta + 3*sigma # jj <- ceiling(rr/dx) # # Choose some prey weight w[i] # i <- which.max(sel) + 10 # pra <- 0 # # The following corresponds to the right Riemann sum because the sum # # goes all the way to the right limit of j == i # for (j in i:(i + jj)) { # pra <- pra + p@w_full[j]^(n - 1) * # exp(-(x_full[j] - x_full[i] - Beta)^2 / (2 * sigma^2)) # } # pra <- pra * (1 - f0) * p@resource_params$kappa * gamma * p@w_full[i]^(1 - n) * dx # # TODO: Still need to understand this # # expect_equal(unname(pr[1]), pra, tolerance = 1e-14) # }) # # Analytic steady-state solution ---- # test_that("Analytic steady-state solution is well approximated", { # # Choose some parameters # f0 <- 0.6 # alpha <- 0.4 # r_pp <- 10^18 # Choosing a high value because we want the resource to stay # # at its power-law steady state # n <- 2/3 # p <- n # q <- 0.95 # lambda <- 2 + q - n # erepro <- 0.1 # R <- 1e10 # The rate of reproduction # # beta <- 100 # sigma <- 1.3 # h <- 30 # ks <- 4 # kappa <- 1e11 # # w_min <- 1e-3 # w_max <- 1e3 # w_mat <- 1e2 # min_w_pp <- 1e-7 # Only have to make sure the smallest fish are perfectly fed # # Chose number of gridpoints so that w_mat and w_max lie on gridpoints # no_w <- log10(w_max / w_min) * 100 + 1 # # species_params <- data.frame( # species = "Single", # w_min = w_min, # w_max = w_max, # w_mat = w_mat, # f0 = f0, # h = h, # ks = ks, # beta = beta, # sigma = sigma, # z0 = 0, # alpha = alpha, # erepro = erepro, # sel_func = "knife_edge", # not used but required # knife_edge_size = 1000, # stringsAsFactors = FALSE # ) # # params <- newMultispeciesParams(species_params, p = p, n = n, lambda = lambda, # kappa = kappa, min_w = w_min, max_w = w_max, # no_w = no_w, min_w_pp = min_w_pp, w_pp_cutoff = w_max, # r_pp = r_pp) # # gamma <- params@species_params$gamma[1] # w <- params@w # # # mu0 w^(n-1) is the death rate that is produced by predation if the predators # # follow the same power law as the resource. # # We could equally well have chosen any other constant # mu0 <- (1 - f0) * sqrt(2 * pi) * kappa * gamma * sigma * # (beta ^ (n - 1)) * exp(sigma ^ 2 * (n - 1) ^ 2 / 2) # params@mu_b[1,] <- mu0 * w ^ (n - 1) # # hbar w^n is the rate at which energy is available for growth and reproduction # hbar <- alpha * h * f0 - ks # # n_exact is calculated using the analytic expression for the solution # pow <- mu0 / hbar / (1 - n) # n_mult <- (1 - (w / w_max) ^ (1 - n)) ^ (pow - 1) * # (1 - (w_mat / w_max) ^ (1 - n)) ^ (-pow) # n_mult[w < w_mat] <- 1 # n_exact <- params@psi # Just to get array with correct dimensions and names # n_exact[] <- R * (w_min/w)^(mu0/hbar) / (hbar * w^n) * n_mult # # # Make sure that the rate of reproduction is R # params@rates_funcs$RDD <- "constantRDD" # params@species_params$constant_reproduction <- R # # We use a step function for the maturity function # params@psi[1,] <- (params@w / w_max) ^ (1 - n) # params@psi[1, params@w < w_mat] <- 0 # # We switch off the self-interaction # params@interaction[] <- 0 # # # We start the simulation with the exact steady-state solution # sim <- project(params, t_max = 5, effort = 0, initial_n = n_exact) # # If all is well, it should stay close to the steady-state solution # relative_error <- abs((n_exact[1,] - sim@n[6, 1, ]) / n_exact[1, ]) # # TODO: Unfortunately there is a significant difference at the maximum weight, # # so we only test the others # # expect_lt(max(relative_error[1:(no_w - 1)]), 0.02) # })