Nothing
# variance exercise tests
context("variance")
test_that("variance 2",{
data(Systematic_variance_2)
# how to convert units
convert.units <- Systematic_variance_2_units
cu <- convert.units[, 3]
cu <- 1/(cu[3]/(cu[1]*cu[2]))
# first fit a model
sysvar_df <- ds(Systematic_variance_2, adjustment="cos", convert_units=cu)
systematic_var2 <- Systematic_variance_2
unflat <- unflatten(systematic_var2)
# make variance groupings
vargroups <- data.frame(Sample.Label = 1:20,
grouping = sort(rep(1:10, 2)))
unflat$sample.table <- merge(unflat$sample.table, vargroups,
by="Sample.Label")
# Remove these labels as they confuse the merge()
unflat$sample.table$Region.Label <- NULL
unflat$obs.table$Region.Label <- NULL
unflat$sample.table$Sample.Label <-
as.numeric(unflat$sample.table$Sample.Label)
unflat$obs.table$Sample.Label <- as.numeric(unflat$obs.table$Sample.Label)
unflat$data$Sample.Label <- as.numeric(unflat$data$Sample.Label)
# fit the detection function
sysvar_df <- ds(unflat$data, adjustment="cos", convert_units=cu)
## no stratification
#Nhat_nostrat_eff <- dht2(sysvar_df, transects=unflat$sample.table,
# geo_strat=unflat$region.table, observations=unflat$obs.table,
# strat_formula=~1, convert_units=cu, er_est="R3")
# using the Fewster et al 2009, "O2" estimator "Post-stratify, grouping adjacent pairs of samplers"
expect_warning(Nhat_O2 <- dht2(sysvar_df, transects=unflat$sample.table,
geo_strat=unflat$region.table,
observations=unflat$obs.table,
strat_formula=~1, convert_units=cu,
er_est="O2"),
"Using O2 or O3 encounter rate variance estimator, assuming that sorting on Sample.Label is meaningful")
lr <- Nhat_O2[nrow(Nhat_O2), , drop=FALSE]
expect_equal(lr$Abundance, 1022, tol=1e-1)
expect_equal(lr$Abundance_CV, 8.64/100, tol=1e-2)
expect_equal(lr$LCI, 858, tol=1e-1)
expect_equal(lr$UCI, 1219, tol=1e-1)
expect_equal(lr$df, 75.87, tol=1e-2)
# stratified estimate, weighting by effort
# (this is doing the effort weighted variance, combining the individual
# variance estimates)
# Nhat_strat_eff <- dht2(sysvar_df, transects=unflat$sample.table,
# geo_strat=unflat$region.table,
# observations=unflat$obs.table,
# strat_formula=~grouping, convert_units=cu,
# er_est="R3", stratification="effort_sum")
})
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