tests/testthat/test-check_Designs.R

In dssd: Distance Sampling Survey Design

library(dssd)
library(testthat)

context("Check different designs")

test_that("Check designs can generate survey transects", {

  #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

  # Check random points
  design <- make.design(region, transect.type = "point",
                        design = "random",
                        samplers = 30,
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(nrow(transects@samplers), 30)

  design <- make.design(region, transect.type = "point",
                        design = "random",
                        samplers = 40,
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        effort.allocation = c(0.25, 0.25, 0.5),
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@samp.count, c(10,10,20))

  # Check random / systematic combination
  design <- make.design(region, transect.type = "point",
                        design = c("random", "random", "systematic"),
                        samplers = 50,
                        edge.protocol = c("minus"),
                        design.angle = 45,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@samp.count[1:2], c(17,17))

  # Check random / systematic combination
  design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        samplers = 100,
                        edge.protocol = c("minus"),
                        design.angle = 0,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@spacing, rep(2.059126,3))

  design <- make.design(region, transect.type = "point",
                        design = "systematic",
                        samplers = 100,
                        edge.protocol = c("plus"),
                        design.angle = -1,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@spacing, rep(2.059126,3))

  # LINE TRANSECT DESIGNS

  expect_warning(design <- make.design(region, transect.type = "line",
                                       design = "random",
                                       samplers = 100,
                                       edge.protocol = c("minus"),
                                       design.angle = 0,
                                       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.")

  transects <- generate.transects(design)
  expect_equal(nrow(transects@samplers), 100)

  expect_warning(design <- make.design(region, transect.type = "line",
                                       design = c("random", "systematic", "systematic"),
                                       samplers = 60,
                                       edge.protocol = c("minus"),
                                       design.angle = 90,
                                       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.")

  transects <- generate.transects(design)

  design <- make.design(region, transect.type = "line",
                        design = c("systematic", "systematic", "systematic"),
                        samplers = 15,
                        edge.protocol = c("minus"),
                        design.angle = 0,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@spacing, rep(3,3))

  design <- make.design(region, transect.type = "line",
                        design = c("eszigzag"),
                        samplers = 30,
                        edge.protocol = c("minus"),
                        design.angle = 90,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@spacing, rep(1.5,3))

  design <- make.design(region, transect.type = "line",
                        design = c("eszigzagcom"),
                        samplers = 30,
                        edge.protocol = c("minus"),
                        design.angle = 90,
                        truncation = 1)

  transects <- generate.transects(design)
  expect_equal(transects@spacing, rep(3,3))

  design <- make.design(region, transect.type = "line",
                        design = c("eszigzagcom"),
                        line.length = 300,
                        effort.allocation = c(0.25,0.25,0.5),
                        edge.protocol = c("minus"),
                        design.angle = 90,
                        truncation = 1)
  transects <- generate.transects(design)
  area.effort.ratio <- region@area/transects@spacing
  expect_equal(area.effort.ratio[1], area.effort.ratio[2])
  expect_equal(transects@effort.allocation, c(0.25,0.25,0.5))

  design <- make.design(region, transect.type = "line",
                        design = c("eszigzagcom"),
                        line.length = 300,
                        effort.allocation = c(0.25,0.25,0.5),
                        edge.protocol = c("plus"),
                        design.angle = 90,
                        truncation = 1)
  transects <- generate.transects(design)
  expect_equal(transects@edge.protocol, rep("plus",3))

})