tests/testthat/test_poccs_selectOccs.R

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

#### COMPONENT poccs: Process Occurrence Data
#### MODULE: Select Occurrences On Map
context("selectOccs")

### Set parameters

## occurrences
occs <- read.csv(system.file("extdata/Bassaricyon_neblina.csv",
                             package = "wallace"))[, 2:3]
occs$occID <- 1:nrow(occs)

## extention to thin
# set coordinates
longitude <- c(-71.58400, -78.81300, -79.34034, -69.83331, -66.47149, -66.71319,
               -71.11931)
latitude <- c(13.18379, 7.52315, 0.93105, -1.70167, 0.98391, 6.09208, 12.74980)
# generate matrix
expertAddedPoly <- matrix(c(longitude, latitude), byrow = FALSE, ncol = 2)


### run function
out.occs <- poccs_selectOccs(occs, polySelXY = expertAddedPoly, polySelID = 1,
                             logger = NULL)


### test if the error messages appear when they are supposed to
test_that("error checks", {
  # the user has not obtained or loaded the occurrence data
  expect_error(
    poccs_selectOccs(occs = NULL, polySelXY = expertAddedPoly),
    'Before processing occurrences, obtain the data in component 1.')
  # the user has not finished the polygon
  expect_error(
    poccs_selectOccs(occs, polySelXY = NULL),
    paste0('The polygon has not been finished. Please press "Finish" on the ',
           'map toolbar then the "Select Occurrences" button.'))
  })

### test output features
test_that("output type checks", {
   # the output is a data frame
  expect_is(out.occs, "data.frame")
  })

### test function stepts
test_that("output data checks", {
  ##output dataframe has the same columns as original occurrences
  expect_equal(names(occs),names(out.occs))
  ## test if the points out of the extention to thin were removed
  # extract longitude and latitude columns from 'occs' data frame
  points <- occs[, 1:2]
  sp::coordinates(points) <- ~ longitude + latitude
  # create polygon
  Poly <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(expertAddedPoly)),
                                                ID = 1)))
  # check which points overlap with the extention to thin
  overlap <- sp::over(points, Poly)
  # if at least one record was out of the extention to thin
  if ((NA %in% overlap) == TRUE){
    # the original data frame has more records than the thinned one
    expect_true(nrow(occs) > nrow(out.occs))
  } else { # if not,
    # the original data frame has the same amount of records than the "thinned" one
    expect_equal(nrow(occs), nrow(out.occs))
  }
  })