tests/testthat/test_fit_geno_cline.R

In tjthurman/BAHZ: Bayesian Analysis of Hybrid Zones

context("fit geno cline")

set.seed(22)
data <- sim_geno_cline(transect_distances = seq(-300,300,75), n_ind = 40, Fis = 0,
                       decrease = F, center = 10, width = 35, pmin = 0.03, pmax = .95)

# Test argument checking
test_that("fit geno cline checks arguments correctly", {
  expect_error(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                              type = "xx", tails = "none", chains = 1), "multi")
  expect_error(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                              type = "bi", tails = "xxx", chains = 1), "ind")
  expect_error(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                              type = "bi", tails = "none", chains = "xxx"), "numeric")
  expect_error(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                              type = "bi", tails = "none", ignore_data = "xxx"), "TRUE")
})

# Test functionality
# Give it a really simple model to fit, and make sure the result is a stanfit.

# z_p <- suppressWarnings(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
#                       type = "bi", tails = "none", chains = 1))
test_that("fit geno cline runs the model and makes a stanfit object", {
  expect_equal(class(suppressWarnings(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                                    type = "bi", tails = "none", chains = 1)))[1], "stanfit")
  expect_equal(class(suppressWarnings(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                                    type = "multi", tails = "none", chains = 1)))[1], "stanfit")
})

test_that("fit_geno_cline works with user-defined init list", {
  expect_equal(class(suppressWarnings(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                                    type = "bi", tails = "none",
                                    chains = 1,
                                    init = list(list(center = 9,
                                                width =  49,
                                                pmin = 0.031,
                                                pmax = .94)))))[1], "stanfit")
})

z_p2 <- suppressWarnings(fit_geno_cline(data = data, prior_file = "prior_config_test1.yaml",
                                        type = "bi", tails = "none", chains = 1, control = list(adapt_delta = 0.85)))
test_that("fit geno cline allows stan control parameters to be changed", {
  expect_equal(attr(z_p2@sim$samples[[1]], "args")$control$adapt_delta, 0.85)
})