tests/testthat/test-fit.R

In ssdtools: Species Sensitivity Distributions

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context("fit")

test_that("fit_dist", {
  dist <- ssd_fit_dist(boron_data)
  expect_true(is.fitdist(dist))
  expect_identical(dist, boron_lnorm)
})

test_that("fit_dists", {
  dist_names <- c("gamma", "gompertz", "lgumbel",
                        "llog", "lnorm", "pareto", "weibull")
  expect_error(ssd_fit_dists(boron_data[1:5,]), "all distributions failed to fit")
  dists <- ssd_fit_dists(boron_data[1:6,], dists = dist_names)
  expect_true(is.fitdists(dists))
  expect_identical(names(dists), dist_names)
  coef <- stats::coef(dists)
  expect_identical(names(coef), dist_names)
})

test_that("fit_dist", {
  expect_error(ssd_fit_dist(boron_data[1:5,]), "data must have at least 6 rows")
  dist <- ssd_fit_dist(boron_data)
  expect_true(is.fitdist(dist))
  expect_identical(dist, boron_lnorm)
  expect_equal(coef(dist), c(meanlog = 2.561645, sdlog = 1.241540), tolerance = 0.0000001)

  boron_data2 <- boron_data[rev(order(boron_data$Conc)),]
  boron_data2$Weight <- 1:nrow(boron_data2)

  dist <- ssd_fit_dist(boron_data2, weight = "Weight")
  expect_true(is.fitdist(dist))
  expect_equal(coef(dist), c(meanlog = 1.879717, sdlog = 1.127537), tolerance = 0.000001)
})

test_that("fluazinam", {
  data(fluazinam, package = "fitdistrplus")
  dist <- ssd_fit_dist(fluazinam, left = "left")
  expect_true(is.fitdist(dist))
  expect_false(is.fitdistcens(dist))
  expect_equal(coef(dist), c(meanlog = 4.660186, sdlog = 2.197562), tolerance = 0.0000001)

  dist <- ssd_fit_dist(fluazinam, left = "left", right = "right")
  expect_false(is.fitdist(dist))
  expect_true(is.fitdistcens(dist))
  expect_equal(coef(dist), c(meanlog = 4.976920, sdlog = 2.687785), tolerance = 0.0000001)

  fluazinam2 <- fluazinam[rev(order(fluazinam$left)),]
  fluazinam2$Weight <- 1:nrow(fluazinam2)

  dist <- ssd_fit_dist(fluazinam2, weight = "Weight", left = "left", right = "right")
  expect_false(is.fitdist(dist))
  expect_true(is.fitdistcens(dist))
  expect_equal(coef(dist), c(meanlog = 3.566750, sdlog = 2.182757), tolerance = 0.000001)
})