map <- readRDS("map.rds") pop <- population("pop", time = 1000, N = 10, map = map, center = c(0, 40), radius = 500e3) %>% move(trajectory = c(10, 10), start = 900, end = 700, snapshots = 3) test_that("temporal consistency of interaction parameter changes is enforced", { expect_error(set_dispersal(pop, time = 950, competition = 100), "The new event (.*) pre-dates the last specified active event (.*)") expect_silent(set_dispersal(pop, time = 50, competition = 100)) }) test_that("at least one interaction parameter is specified", { expect_error(set_dispersal(pop, time = 1000), "At least one spatial interaction parameter must be specified") }) test_that("interaction parameter must be positive, non-zero values", { msg <- "Spatial interaction parameters can only have positive" expect_error(set_dispersal(pop, time = 1000, competition = -100), msg) expect_error(set_dispersal(pop, time = 1000, mating = -100), msg) expect_error(set_dispersal(pop, time = 1000, dispersal = -100), msg) }) test_that("interaction parameter change is correctly recorded", { x1 <- set_dispersal(pop, time = 100, competition = 100) x2 <- set_dispersal(pop, time = 100, mating = 50) x3 <- set_dispersal(pop, time = 100, dispersal = 20) x4 <- set_dispersal(pop, time = 100, competition = 50, dispersal = 10) hist1 <- attr(x1, "history") %>% .[[length(.)]] expect_true(hist1$pop == pop$pop[1]) expect_true(hist1$time == 100) expect_true(hist1$event == "dispersal") expect_true(hist1$competition == 100) expect_true(is.na(hist1$mating)) expect_true(is.na(hist1$dispersal)) hist2 <- attr(x2, "history") %>% .[[length(.)]] expect_true(hist2$mating == 50) hist3 <- attr(x3, "history") %>% .[[length(.)]] expect_true(hist3$dispersal == 20) hist4 <- attr(x4, "history") %>% .[[length(.)]] expect_true(hist4$competition == 50 && hist4$dispersal == 10) }) test_that("SLiM dispersals match expectations laid by R distributions", { skip_if(!is_slendr_env_present()) seed <- 42 set.seed(seed) map <- world(xrange = c(0, 100), yrange = c(0, 100), landscape = "blank") slim_sim <- function(dispersal_fun, dispersal, seed) { pop <- population("pop", time = 1, N = 3000, map = map, center = c(50, 50), radius = 0.5, dispersal = 0.1) %>% set_range(time = 2, center = c(50, 50), radius = 50) %>% set_dispersal(time = 2, dispersal = dispersal, dispersal_fun = dispersal_fun) model <- compile_model( pop, file.path(tempdir(), paste0("model_", dispersal_fun)), generation_time = 1, competition = 0, mating = 1, simulation_length = 2, resolution = 0.1, overwrite = TRUE, force = TRUE ) locations_file <- tempfile(fileext = ".gz") slim(model, sequence_length = 1, recombination_rate = 0, method = "batch", locations = locations_file, max_attempts = 1, verbose = FALSE, random_seed = seed) locations <- readr::read_tsv(locations_file, show_col_types = FALSE, progress = FALSE) %>% reproject(coords = ., from = "raster", to = "world", model = model, add = TRUE) %>% dplyr::filter(gen == 0) %>% dplyr::mutate(distance = sqrt((newx - 50)^2 + (newy - 50)^2)) %>% dplyr::mutate(fun = dispersal_fun) locations } normal <- slim_sim("normal", 10, seed) uniform <- slim_sim("uniform", 10, seed) cauchy <- slim_sim("cauchy", 10, seed) exp <- slim_sim("exponential", 10, seed) brownian <- slim_sim("brownian", 10, seed) slim_distances <- rbind(normal, uniform, cauchy, exp, brownian) %>% dplyr::select(distance, fun) %>% dplyr::mutate(source = "SLiM") r_sim <- function(param, fun) { if (fun == "rnorm") distance <- rnorm(1, mean = 0, sd = param) else if (fun == "runif") distance <- runif(1, min = 0, max = param) else if (fun == "rcauchy") distance <- rcauchy(1, location = 0, scale = param) else if (fun == "rexp") distance <- rexp(1, rate = 1 / param) else if (fun == "brownian") { y <- rnorm(1, mean = 0, sd = param) x <- rnorm(1, mean = 0, sd = param) distance <- sqrt(x ^ 2 + y ^ 2) } else stop("Unknown distribution function", fun, call. = FALSE) angle <- ifelse(fun == "brownian", tan(y / x), runif(1, min = 0, max = 2 * pi)) x <- distance * cos(angle) y <- distance * sin(angle) c(x, y) } n <- 10000 r_distances <- dplyr::tibble( distance = c( sqrt(colSums(replicate(n, r_sim(10, "rnorm"))^2)), sqrt(colSums(replicate(n, r_sim(10, "runif"))^2)), sqrt(colSums(replicate(n, r_sim(10, "rcauchy"))^2)), sqrt(colSums(replicate(n, r_sim(10, "rexp"))^2)), sqrt(colSums(replicate(n, r_sim(10, "brownian"))^2)) ), fun = c(rep("normal", n), rep("uniform", n), rep("cauchy", n), rep("exponential", n), rep("brownian", n)), source = "R" ) %>% dplyr::filter(distance <= 50) distances <- rbind(slim_distances, r_distances) # library(ggplot2) # p <- ggplot2::ggplot(distances, aes(distance, color = source)) + # geom_density() + # coord_cartesian(xlim = c(0, 50)) + # facet_wrap(~ fun, scales = "free") + # guides(color = guide_legend("simulation")) # # original_png <- "distances.png" # ggsave(original_png, p, width = 8, height = 5) # compare the SLiM dispersal distributions to the distributions randomly # sampled in R using the Kolmogorov-Smirnov test expect_true(ks.test( slim_distances[slim_distances$fun == "normal", ]$distance, r_distances[r_distances$fun == "normal", ]$distance )$p.value > 0.05) expect_true(ks.test( slim_distances[slim_distances$fun == "uniform", ]$distance, r_distances[r_distances$fun == "uniform", ]$distance )$p.value > 0.05) expect_true(ks.test( slim_distances[slim_distances$fun == "cauchy", ]$distance, r_distances[r_distances$fun == "cauchy", ]$distance )$p.value > 0.05) expect_true(ks.test( slim_distances[slim_distances$fun == "exponential", ]$distance, r_distances[r_distances$fun == "exponential", ]$distance )$p.value > 0.05) expect_true(ks.test( slim_distances[slim_distances$fun == "brownian", ]$distance, r_distances[r_distances$fun == "brownian", ]$distance )$p.value > 0.05) # decrease the gigantic table to make the package smaller overall set.seed(42) distances <- distances[sort(sample(1:nrow(distances), size = 5000)), ] # current_tsv <- paste0(tempfile(), ".tsv.gz") # readr::write_tsv(distances, current_tsv, progress = FALSE) original_tsv <- "distances.tsv.gz" # readr::write_tsv(distances, original_tsv, progress = FALSE) orig_distances <- readr::read_tsv(original_tsv, show_col_types = FALSE, progress = FALSE) # make sure that the current distance distribution matches the original one expect_equal(distances, orig_distances, tolerance = 1e-15) })