tests/testthat/ef.R

In Faskally/ef: Modelling Framework for the Estimation of Salmonid Abundance

context("fitted values")
library(ef)
library(mgcv)

# do a model fit, ef_data

data(ef_data)

ef_data $ pass12 <- factor(replace(ef_data $ pass, ef_data $ pass > 2, 2))
ef_data $ sampleID <- as.numeric(factor(paste(ef_data $ date, ef_data $ siteID,
                                              ef_data $ lifestage, ef_data $ species)))
ef_data $ visitID <- as.numeric(factor(paste(ef_data $ date, ef_data $ siteID)))
m1 <- efp(count ~ pass12 + lifestage + siteID + year,
          data = ef_data, pass = pass, id = sampleID)


test_that("model_output", {
#  expect_equal(str_length("a"), 1)
#  expect_equal(str_length("ab"), 2)
#  expect_equal(str_length("abc"), 3)
})


# Get Predicted Values for _P_
m1_gam <- as.gam(m1)
ef_data $ prob <- predict.gam(m1_gam, newdata=ef_data, type = "response")

test_that("as.gam", {
  #  expect_equal(str_length("a"), 1)
  #  expect_equal(str_length("ab"), 2)
  #  expect_equal(str_length("abc"), 3)
})


# Comparing Models


large_model <- efp(count ~ pass12 + lifestage + siteID + year,
  data = ef_data, pass = pass, id = sampleID
)

od_estimate <- overdispersion(
  data = ef_data, visitID = "visitID",
  siteID = "siteID", sampleID = "sampleID",
  largemodel = large_model
)


test_that("od_estimate", {
  #  expect_equal(str_length("a"), 1)
  #  expect_equal(str_length("ab"), 2)
  #  expect_equal(str_length("abc"), 3)
})

mfull <- efp(count ~ pass12 + lifestage + siteID + year,
  data = ef_data, pass = pass, id = sampleID
)

BICadj(mfull, od_estimate)

test_that("BICadj", {
  #  expect_equal(str_length("a"), 1)
  #  expect_equal(str_length("ab"), 2)
  #  expect_equal(str_length("abc"), 3)
})


mlife <- efp(count ~ pass12 + siteID + year,
  data = ef_data, pass = pass, id = sampleID
)

BICadj(mlife, od_estimate)

test_that("BICadj", {
  #  expect_equal(str_length("a"), 1)
  #  expect_equal(str_length("ab"), 2)
  #  expect_equal(str_length("abc"), 3)
})