library(dplyr)
test_that("link function works", {
sagebrush2 <-
sagebrush %>%
filter(Species == 'Artemisia tridentata') %>%
add_presence(cover_class_col = `Cover Class`) %>%
mutate(
`Dist. to Bound` = `Dist. to Bound` / 1000,
Topography2 = Topography^2
) %>%
top_n(10)
## Link Function Not Found
expect_error({
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + `Dist. to Bound`,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
link_function = 'not a link function',
iter = 0
)
})
})
test_that("prior values work", {
sagebrush2 <-
sagebrush %>%
filter(Species == 'Artemisia tridentata') %>%
add_presence(cover_class_col = `Cover Class`) %>%
mutate(
`DistToBound` = `Dist. to Bound` / 1000,
Topography2 = Topography^2
) %>%
top_n(10)
### Default Run
result <-
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + DistToBound,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
iter=0
)
## Single Value Run
result2 <-
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + DistToBound,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
prior_presence_mean = 1,
prior_abundance_mean = 2,
prior_presence_var = 3,
prior_abundance_var = 4,
iter = 0
)
## Multiple Value Run
result3 <-
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + DistToBound,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
prior_presence_mean = c(1, 2, 3, 4),
prior_abundance_mean = c(1, 2, 3, 4),
prior_presence_var = c(4, 3, 2, 1),
prior_abundance_var = c(4, 3, 2, 1),
iter = 0
)
# prior presence mean
## default works
expect_equal(
attr(result, 'prior')$`presence_(Intercept)`,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$presence_Topography,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$presence_Fire,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$presence_DistToBound,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$`abundance_(Intercept)`,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$abundance_Topography,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$abundance_Topography2,
c(0, 10)
)
expect_equal(
attr(result, 'prior')$abundance_Fire,
c(0, 10)
)
## single value works
expect_equal(
attr(result2, 'prior')$`presence_(Intercept)`,
c(1, 3)
)
expect_equal(
attr(result2, 'prior')$presence_Topography,
c(1, 3)
)
expect_equal(
attr(result2, 'prior')$presence_Fire,
c(1, 3)
)
expect_equal(
attr(result2, 'prior')$presence_DistToBound,
c(1, 3)
)
expect_equal(
attr(result2, 'prior')$`abundance_(Intercept)`,
c(2, 4)
)
expect_equal(
attr(result2, 'prior')$abundance_Topography,
c(2, 4)
)
expect_equal(
attr(result2, 'prior')$abundance_Topography2,
c(2, 4)
)
expect_equal(
attr(result2, 'prior')$abundance_Fire,
c(2, 4)
)
## multiple value works
expect_equal(
attr(result3, 'prior')$`presence_(Intercept)`,
c(1, 4)
)
expect_equal(
attr(result3, 'prior')$presence_Topography,
c(2, 3)
)
expect_equal(
attr(result3, 'prior')$presence_Fire,
c(3, 2)
)
expect_equal(
attr(result3, 'prior')$presence_DistToBound,
c(4, 1)
)
expect_equal(
attr(result3, 'prior')$`abundance_(Intercept)`,
c(1, 4)
)
expect_equal(
attr(result3, 'prior')$abundance_Topography,
c(2, 3)
)
expect_equal(
attr(result3, 'prior')$abundance_Topography2,
c(3, 2)
)
expect_equal(
attr(result3, 'prior')$abundance_Fire,
c(4, 1)
)
## expect error on mismatched dims
expect_error({
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + `Dist. to Bound`,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
prior_presence_mean = c(1, 3),
iter = 0
)
})
# prior abundance mean
## expect error on mismatched dims
expect_error({
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + `Dist. to Bound`,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
prior_abundance_mean = c(1, 3),
iter = 0,
refresh = 0
)
})
## expect error on mismatched dims
expect_error({
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + `Dist. to Bound`,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
prior_presence_var = c(1, 3),
iter = 0,
refresh = 0
)
})
## error on different dims
expect_error({
ozab(
sagebrush2,
`Presence` ~ Topography + Fire + `Dist. to Bound`,
`Cover Class` ~ Topography + Topography2 + Fire,
cutpoint_scheme = daubenmire(),
prior_abundance_var = c(1, 2),
iter = 0,
refresh = 0
)
})
})
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