1 files changed, 93 insertions, 0 deletions
diff --git a/tests/testthat/test_occuRN.R b/tests/testthat/test_occuRN.R
new file mode 100644
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+++ b/tests/testthat/test_occuRN.R
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+context("occuRN fitting function")
+skip_on_cran()
+
+test_that("occuRN can fit models",{
+
+  data(birds)
+  woodthrushUMF <- unmarkedFrameOccu(woodthrush.bin)
+
+  # R and C engines give same result
+  fm_R <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="R", K=5, control=list(maxit=1))
+  fm_C <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="C", K=5, control=list(maxit=1))
+  expect_equal(fm_R@AIC, fm_C@AIC)
+
+  # survey occasion-specific detection probabilities
+  fm_C <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="C", K=10)
+  #fm_R <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="R")
+
+  # check that output matches
+  #expect_equivalent(coef(fm_C),coef(fm_R),tol=1e-5)
+
+  # check output is correct
+  expect_equivalent(coef(fm_C),
+    c(0.7921122,-1.8328867,0.4268205,-0.1442194,0.4634105,0.7787513,
+      0.8008794,1.0569827,0.8048578,0.8779660,0.9374874,0.7064848),tol=1e-3)
+
+  # check methods
+  gp <- getP(fm_C)
+  expect_equal(dim(gp), dim(woodthrushUMF@y))
+
+  pr <- predict(fm_C, 'state')
+  expect_equal(dim(pr), c(50,4))
+  expect_equal(pr[1,1], 2.204779, tol=1e-4)
+
+  pr <- predict(fm_C, 'det')
+  expect_equal(dim(pr), c(550,4))
+  expect_equal(pr[1,1], 0.13806, tol=1e-4)
+
+  res <- residuals(fm_C)
+  expect_equal(dim(res), dim(woodthrushUMF@y))
+  expect_equal(res[1,1], 0.73757, tol=1e-4)
+  r <- ranef(fm_C, K=10)
+  expect_equal(dim(r@post), c(50,11,1))
+
+  s <- simulate(fm_C, 2)
+  expect_equal(length(s), 2)
+  expect_equal(dim(s[[1]]), dim(woodthrushUMF@y))
+
+  pb <- parboot(fm_C, nsim=1)
+  expect_is(pb, "parboot")
+
+  # check error if random effect in formula
+  expect_error(occuRN(~(1|dummy)~1, umf))
+})
+
+test_that("occuRN can handle NAs",{
+
+  data(birds)
+  woodthrushUMF <- unmarkedFrameOccu(woodthrush.bin)
+
+  #Remove one observation
+  woodthrushUMF@y[1,1] <- NA
+
+  fm_C <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="C", K=10)
+  #fm_R <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="R")
+
+  # check that output matches
+  #expect_equivalent(coef(fm_C),coef(fm_R),tol=1e-5)
+
+  # check output is correct
+  expect_equivalent(coef(fm_C),
+    c(0.793042, -1.902789, 0.494098, -0.074573, 0.53074, 0.845903,
+    0.867936, 1.123959, 0.871912, 0.944917, 1.004499, 0.773679), tol=1e-3)
+
+  #Remove entire site
+  woodthrush.bin_na <- woodthrush.bin
+  woodthrush.bin_na[1,] <- NA
+  woodthrushUMF <- unmarkedFrameOccu(woodthrush.bin_na)
+
+  expect_warning(fm_C <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="C", K=10))
+  #fm_R <- occuRN(~ obsNum ~ 1, woodthrushUMF, engine="R")
+
+  # check that site was removed
+  expect_equivalent(fm_C@sitesRemoved,1)
+
+  # check that output matches
+  #expect_equivalent(coef(fm_C),coef(fm_R),tol=1e-5)
+
+  # check output is correct
+  expect_equivalent(coef(fm_C),
+    c(0.783066, -1.920232, 0.448369, -0.009701, 0.490085, 0.814767,
+    0.837669, 1.097903, 0.842467, 0.916831, 0.976707, 0.740672), tol=1e-3)
+})
+