Nothing
library(DSsim)
library(testthat)
context("Nested Point Transect Simulation Checks")
test_that("Can perform nested point transect simulations", {
#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(5,5,20,20,5), y = c(0,5,5,0,0)))
gaps[[1]] <- list()
gaps[[2]] <- list(data.frame(x = c(10,15,11.5,10), y = c(1,3,4,1)))
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 = 0.25,
y.space = 0.25,
constant = c(0.5,0.5)),
is_a("Density"))
expect_that(density <- add.hotspot(density, c(15,2), 5, 0.5),
is_a("Density"))
#Create Population Description
size <- data.frame(size = c(1,2,3), prob = c(0.25,0.5,0.25))
expect_that(pop.desc <- make.population.description(region,
density,
#cluster.size.table = size,
N = c(150,1000),
fixed.N = TRUE),
is_a("Population.Description"))
#Create Detectability
expect_that(detect <- make.detectability(key.function = "hn",
scale.param = 0.25,
truncation = 0.75),
is_a("Detectability"))
#Create Design
expect_that(design <- make.design(transect.type = "point",
design.details = "nested",
spacing = c(0.75,1),
design.axis = c(0,0),
nested.space = c(2,2)),
is_a("PT.Nested.Design"))
#Create Analyses
analyses <- make.ddf.analysis.list(dsmodel = list(~cds(key = "hn", formula = ~1),~cds(key = "hr", formula = ~1)), method = "ds", truncation = 0.75)
expect_that(analyses, is_a("list"))
expect_that(analyses[[2]], is_a("DDF.Analysis"))
#Create Simulation
expect_that(my.sim <- make.simulation(reps = 3,
single.transect.set = FALSE,
region.obj = region,
design.obj = design,
population.description.obj = pop.desc,
detectability.obj = detect,
ddf.analyses.list = analyses),
is_a("Simulation"))
#Create a population
set.seed(752)
expect_that(pop <- generate.population(pop.desc, detect, region),
is_a("Population"))
expect_that(nrow(pop@population), equals(sum(pop.desc@N)))
set.seed(752)
expect_that(pop2 <- generate.population(my.sim),
is_a("Population"))
expect_that(pop, is_identical_to(pop2))
#Generate transects
set.seed(747)
expect_that(point.transect <- generate.transects(design,
region = region),
is_a("Point.Transect"))
set.seed(747)
expect_that(point.transect2 <- generate.transects(my.sim),
is_a("Point.Transect"))
expect_that(point.transect, is_identical_to(point.transect2))
#plot(density, style = "blocks")
#plot(region, add = T)
#plot(point.transect)
#Generate detections
expect_that(survey.results <- create.survey.results(my.sim,
dht.tables = TRUE),
is_a("Survey.Results"))
expect_that(ddf.data <- survey.results@ddf.data,
is_a("DDF.Data"))
expect_that(length(which(ddf.data@ddf.dat$distance > detect@truncation)), equals(0))
expect_that(obs.table <- survey.results@obs.table,
is_a("Obs.Table"))
expect_that(sample.table <- survey.results@sample.table,
is_a("Sample.Table"))
expect_that(region.table <- survey.results@region.table,
is_a("Region.Table"))
plot(survey.results)
expect_that(nrow(ddf.data@ddf.dat),equals(427))
#equals(448))
with.dists <- ddf.data@ddf.dat[!is.na(ddf.data@ddf.dat$distance),]
expect_that(nrow(with.dists), equals(108))
#equals(119))
})
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