Nothing
# More test_that code for occSS series of functions
# library(testthat)
context("Multi-season occupancy")
test_that("occMS0 gives right answers", {
require(wiqid)
data(GrandSkinks)
DH <- GrandSkinks[, 1:15]
res1 <- occMS0(DH, 3)
expect_that(class(res1), equals(c("wiqid", "list")))
expect_that(names(res1),
equals(c("call", "beta", "beta.vcv", "real", "logLik", "ci", "link", "index")))
expect_true(is.call(res1$call))
expect_that(dim(res1$beta), equals(c(4, 4)))
expect_that(colnames(res1$beta),
equals(c("est", "SE", "lowCI", "uppCI")))
expect_that(rownames(res1$beta),
equals(c("psi1", "gamma", "epsilon", "p")))
expect_that(round(as.vector(res1$beta), 4),
equals(c(-0.4284, -2.6133, -2.1971, 0.7962, 0.1318, 0.1865, 0.2029,
0.1077, -0.6868, -2.9788, -2.5947, 0.5850, -0.1701, -2.2478,
-1.7995, 1.0073)))
expect_that(dim(res1$real), equals(c(4, 3)))
expect_that(colnames(res1$real),
equals(c("est", "lowCI", "uppCI")))
# Check against PRESENCE results:
expect_that(round(as.vector(res1$real), 4),
equals(c(0.3945, 0.0683, 0.1, 0.6892, 0.3348, 0.0484, 0.0695,
0.6422, 0.4576, 0.0955, 0.1419, 0.7325)))
expect_that(round(AIC(res1), 4),
equals(1775.0155))
res1a <- occMS0(DH, 3, ci=0.85)
expect_that(round(as.vector(res1a$real), 4),
equals(c(0.3945, 0.0683, 0.1, 0.6892, 0.3502, 0.0531, 0.0766,
0.655, 0.4406, 0.0875, 0.1295, 0.7214)))
})
test_that("occMStime gives right answers", {
require(wiqid)
data(GrandSkinks)
DH <- GrandSkinks[, 1:15]
res1 <- occMStime(DH, 3)
expect_that(class(res1), equals(c("wiqid", "list")))
expect_that(names(res1),
equals(c("call", "beta", "beta.vcv", "real", "logLik")))
expect_true(is.call(res1$call))
expect_that(dim(res1$beta), equals(c(4, 4)))
expect_that(colnames(res1$beta),
equals(c("est", "SE", "lowCI", "uppCI")))
expect_that(rownames(res1$beta),
equals(c("psi1", "gam: Intrcpt", "eps: Intrcpt", "p: Intrcpt" )))
expect_that(round(as.vector(res1$beta), 4),
equals(c(-0.4284, -2.6133, -2.1971, 0.7962, 0.1318, 0.1865, 0.2029,
0.1077, -0.6868, -2.9788, -2.5947, 0.5850, -0.1701, -2.2478,
-1.7995, 1.0073)))
expect_that(dim(res1$real), equals(c(14, 3)))
expect_that(colnames(res1$real),
equals(c("est", "lowCI", "uppCI")))
# Check against PRESENCE results:
expect_that(round(as.vector(res1$real[1, ]), 4),
equals(c(0.3945, 0.3348, 0.4576)))
expect_that(round(as.vector(res1$real[3, ]), 4),
equals(c(0.0683, 0.0484, 0.0955)))
expect_that(round(as.vector(res1$real[8, ]), 4),
equals(c(0.1, 0.0695, 0.1419)))
expect_that(round(as.vector(res1$real[14, ]), 4),
equals(c(0.6892, 0.6422, 0.7325)))
expect_that(round(AIC(res1), 4),
equals(1775.0155))
res2 <- occMStime(DH, 3, list(gamma ~ .interval, epsilon~.interval, p~.season))
expect_that(dim(res2$beta), equals(c(14, 4)))
expect_that(dim(res2$real), equals(c(14, 3)))
# Check against PRESENCE results:
expect_that(round(as.vector(res2$real), 4),
equals(c( 0.3834, 0.1176, 0.0135, 0.0706, 0.0958,
0.0704, 0.0730, 0.1388, 0.1703,
0.6950, 0.6506, 0.6888, 0.8424, 0.6643,
0.3191, 0.0611, 0.0008, 0.0362, 0.0531,
0.0302, 0.0318, 0.0766, 0.0836,
0.5730, 0.5602, 0.6032, 0.7403, 0.5403,
0.4520, 0.2147, 0.1854, 0.1329, 0.1667,
0.1557, 0.1586, 0.2384, 0.3158,
0.7946, 0.7313, 0.7632, 0.9092, 0.7692)))
# Same as PRESENCE +/- 0.0001
expect_that(round(AIC(res2), 4),
equals(1773.8787)) # Same as PRESENCE
})
test_that("occMS gives right answers", {
require(wiqid)
data(GrandSkinks)
DH <- GrandSkinks[, 1:15]
if(TRUE) { # Don't do this regularly, too slow
res1 <- occMS(DH, 3) # this invokes occMS0
expect_that(class(res1), equals(c("wiqid", "list")))
expect_that(names(res1),
equals(c("call", "beta", "beta.vcv", "real", "logLik", "ci", "link", "index")))
expect_true(is.call(res1$call))
expect_that(dim(res1$beta), equals(c(4, 4)))
expect_that(colnames(res1$beta),
equals(c("est", "SE", "lowCI", "uppCI")))
expect_that(rownames(res1$beta),
equals(c("psi1", "gamma", "epsilon", "p" )))
# equals(c("psi1: Intrcpt", "gam: Intrcpt", "eps: Intrcpt", "p: Intrcpt" )))
expect_that(round(as.vector(res1$beta), 4),
equals(c(-0.4284, -2.6133, -2.1971, 0.7962, 0.1318, 0.1865, 0.2029,
0.1077, -0.6868, -2.9788, -2.5947, 0.5850, -0.1701, -2.2478,
-1.7995, 1.0073)))
expect_that(dim(res1$real), equals(c(4, 3)))
expect_that(colnames(res1$real),
equals(c("est", "lowCI", "uppCI")))
# Check against PRESENCE results:
expect_that(as.vector(t(round(unique(res1$real), 4))),
equals(c(0.3945, 0.3348, 0.4576,
0.0683, 0.0484, 0.0955,
0.1000, 0.0695, 0.1419,
0.6892, 0.6422, 0.7325)))
expect_that(round(AIC(res1), 4),
equals(1775.0155))
} # if FALSE
res2 <- occMS(DH, 3,
model=list(psi1~habitat, gamma ~ habitat, epsilon~habitat),
data=GrandSkinks)
expect_that(dim(res2$beta), equals(c(7, 4)))
expect_that(dim(res2$real), equals(c(5353, 3)))
# Check against PRESENCE results:
expect_that(as.vector(t(round(unique(res2$real), 4))),
equals(c(0.2315, 0.1601, 0.3224,
0.5075, 0.4239, 0.5906,
0.0434, 0.0242, 0.0769,
0.1004, 0.0663, 0.1491,
0.1557, 0.0914, 0.2527,
0.0844, 0.0523, 0.1335,
0.6882, 0.6412, 0.7316)))
# Same as PRESENCE +/- 0.0001
expect_that(round(AIC(res2), 4),
equals(1745.0000))
})
test_that("occMScovSite gives right answers", {
require(wiqid)
data(GrandSkinks)
DH <- GrandSkinks[, 1:15]
res1 <- occMScovSite(DH, 3)
expect_that(class(res1), equals(c("wiqid", "list")))
expect_that(names(res1),
equals(c("call", "beta", "beta.vcv", "real", "logLik", "ci")))
expect_true(is.call(res1$call))
expect_that(dim(res1$beta), equals(c(4, 4)))
expect_that(colnames(res1$beta),
equals(c("est", "SE", "lowCI", "uppCI")))
expect_that(rownames(res1$beta),
# equals(c("ps1: Intrcpt", "gam: Intrcpt", "eps: Intrcpt", "p: Intrcpt" )))
equals(c("psi1: Intrcpt", "gam: Intrcpt", "eps: Intrcpt", "p: Intrcpt" )))
expect_that(round(as.vector(res1$beta), 4),
equals(c(-0.4284, -2.6133, -2.1971, 0.7962, 0.1318, 0.1865, 0.2029,
0.1077, -0.6868, -2.9788, -2.5947, 0.5850, -0.1701, -2.2478,
-1.7995, 1.0073)))
expect_that(dim(res1$real), equals(c(4732, 3)))
expect_that(colnames(res1$real),
equals(c("est", "lowCI", "uppCI")))
# Check against PRESENCE results:
expect_that(as.vector(t(round(unique(res1$real), 4))),
equals(c(0.3945, 0.3348, 0.4576,
0.0683, 0.0484, 0.0955,
0.1000, 0.0695, 0.1419,
0.6892, 0.6422, 0.7325)))
expect_that(round(AIC(res1), 4),
equals(1775.0155))
res2 <- occMScovSite(DH, 3,
model=list(psi1~habitat, gamma ~ habitat, epsilon~habitat),
data=GrandSkinks)
expect_that(dim(res2$beta), equals(c(7, 4)))
expect_that(dim(res2$real), equals(c(4732, 3)))
# Check against PRESENCE results:
expect_that(as.vector(t(round(unique(res2$real), 4))),
equals(c(0.2315, 0.1601, 0.3224,
0.5075, 0.4239, 0.5906,
0.0434, 0.0242, 0.0769,
0.1004, 0.0663, 0.1491,
0.1557, 0.0914, 0.2527,
0.0844, 0.0523, 0.1335,
0.6882, 0.6412, 0.7316)))
# Same as PRESENCE +/- 0.0001
expect_that(round(AIC(res2), 4),
equals(1745.0000))
})
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