tests/testthat/test_multivariate_difference.R

In codyn: Community Dynamics Metrics

context("multivariate_difference")


# prepare data ----------------------------------------


# Load our example dataset
data("pplots", package = "codyn") 

#make a dataset with no time
dat1 <- subset(pplots, year == 2002)

#make missing abundance
bdat <- dat1
bdat$relative_cover[1] <- NA

#repeat a species
x <- c("N1P0", 25, 1, 2002, "senecio plattensis", 0.002123142)
bdat2 <- rbind(dat1, x)

# run tests -------------------------------------------

test_that("multivariate_difference function returns correct result", {
  
  #test the returned result with default setting, no time and reference treatment
  myresults1 <- multivariate_difference(dat1, abundance.var = "relative_cover",
                           species.var = "species",
                           replicate.var = "plot",
                           treatment.var = "treatment",
                           reference.treatment = "N1P0")
  
  
  expect_is(myresults1, "data.frame")
  expect_equal(nrow(myresults1), 2)
  expect_equal(ncol(myresults1), 5)
  expect_equal(myresults1$composition_diff[1], 0.07108743, tolerance = 0.00001)
  expect_equal(myresults1$abs_dispersion_diff[1], 0.01123982, tolerance = 0.000001)

  #test that it works with time and reference treatment
  myresults2 <- multivariate_difference(pplots, abundance.var = "relative_cover",
                                    replicate.var = "plot",
                                    species.var = "species",
                                    time.var = "year",
                                    treatment.var = "treatment",
                                    reference.treatment = "N1P0")
  
  expect_equal(nrow(myresults2), 8)
  expect_equal(ncol(myresults2), 6) 
  
  #test that it works with time 
  myresults2.2 <- multivariate_difference(pplots, abundance.var = "relative_cover",
                                        replicate.var = "plot",
                                        species.var = "species",
                                        time.var = "year",
                                        treatment.var = "treatment")
  
  expect_equal(nrow(myresults2.2), 12)
  expect_equal(ncol(myresults2.2), 6) 
  
  #test that is doesn't work with missing abundance
  expect_error(multivariate_difference(bdat, abundance.var = "relative_cover",
                                   replicate.var = "plot",
                                   species.var = "species",
                                   time.var = "year",
                                   treatment.var = "treatment"), "Abundance column contains missing values")
  
  #test that is doesn't work with a repeated species
  expect_error(multivariate_difference(bdat2, abundance.var = "relative_cover",
                                   replicate.var = "plot",
                                   species.var = "species",
                                   time.var = "year",
                                   treatment.var = "treatment"), "Multiple records for one or more species found at:\n year   plot\n \"2002\" \"25\"")
  
})