test-check_UserInput.R
In dssd: Distance Sampling Survey Design

library(dssd)
library(testthat)

context("User Input Checks")

test_that("Can deal with XYZ polygons", {
  
  #Setup region
  outer <- matrix(c(0,0,1,
                    15,0,1,
                    15,10,2,
                    0,10,2,
                    0,0,1),ncol=3, byrow=TRUE)
  pol1 <- sf::st_polygon(list(outer))
  pol2 <- sf::st_polygon(list(outer + 15))
  sfc <- sf::st_sfc(pol1,pol2)
  strata.names <- c("SW", "NE")
  mp1 <- sf::st_sf(strata = strata.names, geom = sfc)
  region <- make.region(region.name = "study.area",
                        strata.name = strata.names,
                        shape = mp1)
  
  # This used to display an error when region was XYZ, now that info is removed
  cover <- make.coverage(region, n.grid.points = 50)
  
  expect_true(is(cover, "Coverage.Grid"))
  
})

test_that("Can deal with various forms of user input", {

  #Setup region
  outer <- matrix(c(0,0,15,0,15,10,0,10,0,0),ncol=2, byrow=TRUE)
  hole1 <- matrix(c(2,2,2,3,3,3,3,2,2,2),ncol=2, byrow=TRUE)
  hole2 <- matrix(c(5,5,5,6,7,6,8,5.5,7,5,5,5),ncol=2, byrow=TRUE)
  pol1 <- sf::st_polygon(list(outer, hole1*1.5, hole2))
  pol2 <- sf::st_polygon(list(outer + 15, hole2*1.5 + 12))
  pol3 <- sf::st_polygon(list(outer + 30, hole2*2.5 + 20))
  sfc <- sf::st_sfc(pol1,pol2,pol3)
  strata.names <- c("SW", "central", "NE")
  mp1 <- sf::st_sf(strata = strata.names, geom = sfc)
  region <- make.region(region.name = "study.area",
                        strata.name = strata.names,
                        shape = mp1)


  #POINT TRANSECT DESIGNS
  #Test make.design for random points
  design <- make.design(region, transect.type = "point",
                        design = "random",
                        samplers = 30,
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@design, rep("random",3))
  expect_equal(design@edge.protocol, rep("minus",3))
  expect_equal(design@design.angle, rep(45,3))
  expect_equal(design@samplers, 30)

  design <- make.design(region, transect.type = "point",
                        design = "random",
                        truncation = 1)
  expect_equal(design@samplers, 20)

  #Test make.design for systematic points
  design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        samplers = 30,
                        edge.protocol = c("plus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@design, rep("systematic",3))
  expect_equal(design@edge.protocol, rep("plus",3))
  expect_equal(design@design.angle, rep(45,3))
  expect_equal(design@samplers, 30)

  design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        spacing = 2,
                        edge.protocol = c("plus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@design, rep("systematic",3))
  expect_equal(design@edge.protocol, rep("plus",3))
  expect_equal(design@design.angle, rep(45,3))
  expect_equal(design@spacing, rep(2,3))

  design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        samplers = 30,
                        effort.allocation = c(0.25,0.25,0.5),
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@effort.allocation, c(0.25,0.25,0.5))

  expect_error(design <- make.design(region, transect.type = "point",
                                       design = "systematic",
                                       samplers = 30,
                                       effort.allocation = c(0.5,0.25,0.5),
                                       edge.protocol = c("minus"),
                                       design.angle = 45,
                                       truncation = 1),
               "Effort allocation should either be omitted or sum to 1")

  expect_error(design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        samplers = c(30,10),
                        effort.allocation = c(0.25,0.25,0.5),
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1),
               "No sampler or spacing argument has been specified for strata 3.")

  expect_error(design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        samplers = 30,
                        effort.allocation = c(0.5,0.5),
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1),
               "The length of the effort allocation argument should be equal to the number of strata.")

  expect_error(design <- make.design(region, transect.type = "point",
                                       design = c("systematic","random"),
                                       samplers = 30,
                                       design.angle = 45,
                                       truncation = 1),
                 "Design description argument has a different number of values than there are strata, please supply a single global value or one value per stratum.")


  expect_error(design <- make.design(region, transect.type = "point",
                                       design = c("systematic"),
                                       samplers = 30,
                                       design.angle = c(45,0),
                                       truncation = 1),
                 "Design angle argument has a different number of values than there are strata, please supply a single global value or one value per stratum.")

  #Check point transect works when design is systematic and only spacing provided
  expect_warning(design <- make.design(region, transect.type = "point",
                                       design = c("systematic"),
                                       #samplers = 30,
                                       spacing = 2.5,
                                       effort.allocation = c(0.25,0.25,0.5),
                                       edge.protocol = c("minus"),
                                       design.angle = -1,
                                       truncation = 1),
                 "Effort allocation not applicable when effort is determined by spacing, it will be ignored.")
  temp <- generate.transects(design)
  expect_equal(length(design@effort.allocation), 0)

  #Check point transect works when design is mix of random and systematic and design angle is -1
  expect_error(design <- make.design(region, transect.type = "point",
                        design = c("systematic", "random", "systematic"),
                        samplers = c(NA,20,NA),
                        spacing = 2.5,
                        effort.allocation = c(0.25,0.25,0.5),
                        edge.protocol = c("minus"),
                        design.angle = c(-1,NA,-1),
                        truncation = 1),
               "NA values supplied for design angle. Please supply values >= 0 and < 180 or the value -1 to indicate a random design angle selection.")

  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  #LINE TRANSECT DESIGNS
  #Test make.design for random line
  expect_warning(design <- make.design(region, transect.type = "line",
                                       design = "random",
                                       samplers = 30,
                                       edge.protocol = c("minus"),
                                       design.angle = 45,
                                       truncation = 1),
                 "The default allocation of samplers to strata \\(i.e. the number of samplers per stratum are in proportion to stratum areas\\) may lead to an unequal effort design as average sampler lengths could vary between strata.")
  expect_equal(design@design, rep("random",3))
  expect_equal(design@edge.protocol, rep("minus",3))
  expect_equal(design@design.angle, rep(45,3))
  expect_equal(design@samplers, 30)

  expect_warning(design <- make.design(region, transect.type = "line",
                                       design = "random",
                                       truncation = 1),
                 "The default allocation of samplers to strata \\(i.e. the number of samplers per stratum are in proportion to stratum areas\\) may lead to an unequal effort design as average sampler lengths could vary between strata.")
  expect_equal(design@samplers, 20)

  design <- make.design(region, transect.type = "line",
                        design = "random",
                        line.length = 150,
                        truncation = 1)
  expect_equal(design@line.length, 150)

  #Test make.design for systematic line
  design <- make.design(region, transect.type = "line",
                        design = "systematic",
                        samplers = 30,
                        edge.protocol = c("plus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@design, rep("systematic",3))
  expect_equal(design@edge.protocol, rep("plus",3))
  expect_equal(design@design.angle, rep(45,3))
  expect_equal(design@samplers, 30)

  samps <- generate.transects(design, region)
  expect_true(length(unique(samps@spacing)) == 1)

  design <- make.design(region, transect.type = "line",
                        design = "systematic",
                        spacing = 2,
                        edge.protocol = c("plus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@design, rep("systematic",3))
  expect_equal(design@edge.protocol, rep("plus",3))
  expect_equal(design@design.angle, rep(45,3))
  expect_equal(design@spacing, rep(2,3))

  design <- make.design(region, transect.type = "line",
                        design = "systematic",
                        samplers = 30,
                        effort.allocation = c(0.25,0.25,0.5),
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1)
  expect_equal(design@effort.allocation, c(0.25,0.25,0.5))

  expect_error(design <- make.design(region, transect.type = "line",
                        design = c("systematic", "random", "segmentedgrid"),
                        spacing = c(1,NA,1),
                        samplers = c(NA,30,NA),
                        edge.protocol = c("minus"),
                        design.angle = c(-1,-1,45),
                        truncation = 1), "Segment length argument has a different number of values than there are strata, please supply a single global value or one value per stratum.")


  design <- make.design(region, transect.type = "line",
                        design = c("systematic", "random", "segmentedgrid"),
                        spacing = c(2,NA,2),
                        samplers = c(NA,10,NA),
                        seg.length = c(NA,NA,1),
                        edge.protocol = c("minus"),
                        design.angle = -1,
                        truncation = 1)
  temp <- generate.transects(design)

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     samplers = 30,
                                     effort.allocation = c(0.5,0.25,0.5),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "Effort allocation should either be omitted or sum to 1")

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     samplers = c(30,10),
                                     effort.allocation = c(0.25,0.25,0.5),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "No sampler, spacing or line.length arguments have been specified for stratum 3.")

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     line.length = c(50,50),
                                     effort.allocation = c(0.25,0.25,0.5),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "No sampler, spacing or line.length arguments have been specified for stratum 3.")


  # CHECK EFFORT ALLOCATION

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     samplers = 30,
                                     effort.allocation = c(0.5,0.5),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "The length of the effort allocation argument should be equal to the number of strata.")

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     samplers = 30,
                                     effort.allocation = c(0.5,0.5, NA),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "Sorry, effort allocation is only applied across all strata at present. NA values are not permitted.")

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     samplers = 30,
                                     effort.allocation = c(0.5,0.5, "c"),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "Effort allocation values must be numeric.")

  expect_error(design <- make.design(region, transect.type = "line",
                                     design = "systematic",
                                     samplers = 30,
                                     effort.allocation = c(0.5,0.5, 0.1),
                                     edge.protocol = c("minus"),
                                     design.angle = 45,
                                     truncation = 1),
               "Effort allocation should either be omitted or sum to 1.")

  # CHECK EDGE PROTOCOL

  expect_error(design <- make.design(region, transect.type = "line",
                                       design = "systematic",
                                       samplers = 30,
                                       edge.protocol = c("minus", "plus"),
                                       design.angle = 45,
                                       truncation = 1),
                 "Edge protocol argument has a different number of values than there are strata, please either supply a single global value or one value per stratum.")

  expect_error(design <- make.design(region, transect.type = "line",
                                       design = c("systematic","random"),
                                       samplers = 30,
                                       design.angle = 45,
                                       truncation = 1),
                 "Design description argument has a different number of values than there are strata, please supply a single global value or one value per stratum.")

  expect_error(design <- make.design(region, transect.type = "line",
                                       design = c("systematic"),
                                       samplers = 30,
                                       design.angle = c(45,0),
                                       truncation = 1),
                 "Design angle argument has a different number of values than there are strata, please supply a single global value or one value per stratum.")


})