tests/testthat/test_richness.R

In jeremiaheb/rvc: A statistical package for the Reef Visual Census

context("SSU richness")

load('../test_data.Rdata')
ssu = subset(fk2012, PRIMARY_SAMPLE_UNIT == PRIMARY_SAMPLE_UNIT[1] & STATION_NR == 1)
ssr = ssu_richness(ssu)

test_that('returns a data.frame',
          expect_true(is.data.frame(ssr))
          )
test_that('has richness column',
          expect_true('richness' %in% names(ssr)))

test_that('returns correct richness',
          expect_equal(ssr$richness, 14))

context("PSU richness")

psu = subset(fk2012, PRIMARY_SAMPLE_UNIT == PRIMARY_SAMPLE_UNIT[1])
psr = psu_richness(ssu_richness(psu))

test_that('returns a data.frame', expect_true(is.data.frame(psr)))
test_that('has richness/var column', expect_true(all(c('var','richness') %in% names(psr))))
test_that('returns correct richness', expect_equal(psr$richness, 23.5))
test_that('returns correct variance', expect_equal(psr$var, 180.5))

context("STRAT richness")

strat = subset(fk2012, STRAT == STRAT[1] & PROT == 0)
str = strat_richness(psu_richness(ssu_richness(strat)), ntot = ntot2012)

test_that('returns a data.frame', expect_true(is.data.frame(str)))
test_that('returns a richness, var, n, nm, N, NM column',
          expect_true(all(c('richness', 'var', 'n', 'nm', 'N', 'NM') %in% names(str))))
test_that('returns correct richness', expect_equal(signif(str$richness), 26.3750))
test_that('returns correct variance', expect_equal(signif(str$var, 4),0.5125))

context("DOMAIN richness")
dr = domain_richness(strat_richness(psu_richness(ssu_richness(fk2012)), ntot2012), ntot2012)

test_that('returns a data.frame', expect_true(is.data.frame(dr)))
test_that('returns a richness, var, n, nm, N, and NM column',
          expect_true(all(c('richness', 'var', 'n', 'nm', 'N', 'NM') %in% names(dr))))
test_that('returns correct richness',
          expect_equal(signif(dr$richness), 28.5211))
test_that('returns correct variance',
          expect_equal(signif(dr$var), 0.110390))