Nothing
library(DSsim)
library(testthat)
context("Line Transect Simulation Checks")
test_that("Can perform basic simulation", {
#Create Region
coords <- gaps <- list(2)
coords[[1]] <- list(data.frame(x = c(0,0,5,5,0), y = c(0,5,5,0,0)))
coords[[2]] <- list(data.frame(x = c(5,5,15,15,5), y = c(0,5,5,0,0)))
gaps[[1]] <- list()
gaps[[2]] <- list()
expect_that(region <- make.region(region.name = "Region",
strata.name = c("A", "Total"),
units = "km", coords = coords, gaps = gaps),
throws_error("'Total' is not an accepted strata name, please ammend it."))
expect_that(region <- make.region(region.name = "Region",
strata.name = c("A", "B"),
units = "km", coords = coords, gaps = gaps),
is_a("Region"))
#Create Density
expect_that(density <- make.density(region,
x.space = 0.2,
y.space = 0.2,
constant = c(0.5,0.5)),
is_a("Density"))
expect_that(density <- add.hotspot(density, c(5,2), 5, 0.5),
is_a("Density"))
#Create Population Description
expect_that(pop.desc <- make.population.description(region,
density,
N = c(300,500),
fixed.N = TRUE),
is_a("Population.Description"))
#Create Detectability
expect_that(detect <- make.detectability(key.function = "hn",
scale.param = 0.25,
truncation = 0.5),
is_a("Detectability"))
#Create Design
expect_that(design <- make.design(transect.type = "line",
design.details = c("parallel", "systematic"),
spacing = 1.5,
design.axis = 0,
path = "fortest"),
is_a("LT.Systematic.Design"))
#Create Analyses
analyses <- make.ddf.analysis.list(dsmodel = list(~cds(key = "hn", formula = ~1)), method = "ds", truncation = 0.5)
expect_that(analyses, is_a("list"))
expect_that(analyses[[1]], is_a("DDF.Analysis"))
#Create Simulation
expect_that(my.sim <- make.simulation(reps = 3,
single.transect.set = TRUE,
region.obj = region,
design.obj = design,
population.description.obj = pop.desc,
detectability.obj = detect,
ddf.analyses.list = analyses),
is_a("Simulation"))
#Create a population
expect_that(pop <- generate.population(pop.desc, detect, region),
is_a("Population"))
expect_that(nrow(pop@population), equals(sum(pop.desc@N)))
#Manually make a line transect object
sampler.info <- data.frame(ID = 1:10,
start.X = seq(0.132, 15, by = 1.5),
start.Y = rep(0,10),
end.X = seq(0.132, 15, by = 1.5),
end.Y = rep(5,10),
length = rep(5,10),
region = c(rep("A",4),rep("B",6)),
d7.length = rep(NA,10))
expect_that(line.transect <- new(Class = "Line.Transect",
sampler.info = sampler.info),
is_a("Line.Transect"))
#Manually make a survey object
expect_that(survey <- new(Class = "Single.Obs.LT.Survey",
population = pop,
line.transect = line.transect,
perp.truncation = detect@truncation),
is_a("Single.Obs.LT.Survey"))
#Generate detections
expect_that(survey.results <- create.survey.results(survey,
dht.tables = TRUE,
region = region),
is_a("list"))
expect_that(ddf.data <- survey.results$ddf.data,
is_a("DDF.Data"))
expect_that(length(which(ddf.data@ddf.dat$distance > detect@truncation)), equals(0))
expect_that(obs.table <- survey.results$obs.table,
is_a("Obs.Table"))
expect_that(sample.table <- survey.results$sample.table,
is_a("Sample.Table"))
expect_that(nrow(sample.table@sample.table), equals(10))
expect_that(region.table <- survey.results$region.table,
is_a("Region.Table"))
expect_that(nrow(region.table@region.table), equals(2))
expect_that(region.table@region.table$Area, equals(c(25,50)))
expect_that(survey.results <- new(Class = "Survey.Results",
region = region,
population = pop,
transects = line.transect,
ddf.data = ddf.data,
obs.table = obs.table,
sample.table = sample.table,
region.table = region.table),
is_a("Survey.Results"))
#plot(survey.results)
})
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