context("STEPCAM")
test_that("STEPCAM: use",{
# skip_on_cran()
set.seed(42)
n_traits <- 1
x <- generate.Artificial.Data(n_species = 10, n_traits = n_traits,
n_communities = 10,
occurence_distribution = 0.5,
average_richness = 1,
sd_richness = 1,
mechanism_random = FALSE)
data_species <- x$traits
data_species$trait1 <- 1:10
data_species <- cbind(data_species,generateFrequencies(x$abundances))
traitnames <- c("1")
names(data_species) <- c("sp",traitnames[1:n_traits], "freq")
data_abundances <- x$abundances
taxa <- nrow(data_species)
community_number <- 1
n_traits <- 1
esppres <- which(data_abundances[community_number, ] > 0)
S <- length(esppres)
species_fallout <- 2
a <- STEPCAM( c(0, species_fallout, 0), data_species, data_abudances,
taxa, esppres, community_number, n_traits, species_fallout)
expect_equal(
a,
c(1,1,1,1,1,1,1,1,0,0),
tol=0.1
)
data_species <- x$traits
data_species$trait1 <- c(1,1.1,2,3,4,5,6,7,7.8,8)
data_species <- cbind(data_species,generateFrequencies(x$abundances))
traitnames <- c("1")
names(data_species) <- c("sp",traitnames[1:n_traits], "freq")
species_fallout <- 2
a <- STEPCAM( c(0,0,species_fallout), data_species, data_abudances,
taxa, esppres, community_number,
n_traits, species_fallout)
expect_equal(
a,
c(1,0,1,1,1,1,1,1,0,1),
tol=0.1
)
data_species <- x$traits
data_species <- cbind(data_species,generateFrequencies(x$abundances))
names(data_species) <- c("sp",traitnames[1:n_traits], "freq")
data_species$freq <- rep(1,length(data_species$freq))
data_species$freq[1] <- 0
species_fallout <- 1
a <- STEPCAM( c(species_fallout,0,0),
data_species, data_abundances,
taxa, esppres, community_number,
n_traits, species_fallout)
expect_equal(
a,
c(0,1,1,1,1,1,1,1,1,1),
tol = 0.1
)
})
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