Nothing
# test calculate complexities --------------------------------------------------
data(P_sojae_survey)
complexities <- calculate_complexities(
x = P_sojae_survey,
cutoff = 60,
control = "susceptible",
sample = "Isolate",
gene = "Rps",
perc_susc = "perc.susc"
)
test_that("calculate_complexities() works properly", {
expect_s3_class(complexities, "hagis.complexities")
expect_length(complexities, 2)
expect_named(complexities,
c("grouped_complexities",
"indvidual_complexities"))
# test summary.hagis.complexities
expect_length(summary(complexities), 3)
expect_equal(summary(complexities)[[1]], 8.714286,
tolerance = 1e-3)
expect_equal(summary(complexities)[[2]], 2.003568,
tolerance = 1e-3)
expect_equal(summary(complexities)[[3]], 0.4372144,
tolerance = 1e-3)
expect_named(summary(complexities), c("mean", "sd", "se"))
})
test_that("calculate_complexities() stops if lacking all params", {
expect_error(
calculate_complexities(
x = "y",
cutoff = 60,
control = "susceptible",
sample = "Isolate",
gene = "Rps",
perc_susc = "perc.susc"
),
regexp = "You have failed to provide all necessary inputs"
)
expect_error(
calculate_complexities(
x = P_sojae_survey,
cutoff = "sixty",
control = "susceptible",
sample = "Isolate",
gene = "Rps",
perc_susc = "perc.susc"
),
regexp = "You have failed to provide all necessary inputs"
)
expect_error(
calculate_complexities(
x = P_sojae_survey,
cutoff = 60,
control = NULL,
sample = "Isolate",
gene = "Rps",
perc_susc = "perc.susc"
),
regexp = "You have failed to provide all necessary inputs"
)
expect_error(
calculate_complexities(
x = P_sojae_survey,
cutoff = 60,
control = "susceptible",
sample = NULL,
gene = "Rps",
perc_susc = "perc.susc"
),
regexp = "You have failed to provide all necessary inputs"
)
expect_error(
calculate_complexities(
x = P_sojae_survey,
cutoff = 60,
control = "susceptible",
sample = "isolate",
gene = NULL,
perc_susc = "perc.susc"
),
regexp = "You have failed to provide all necessary inputs"
)
expect_error(
calculate_complexities(
x = P_sojae_survey,
cutoff = 60,
control = "susceptible",
sample = "isolate",
gene = "Rps",
perc_susc = 60
),
regexp = "You have failed to provide all necessary inputs"
)
})
test_that("print.summary.complexities() returns a proper summary", {
x <- capture.output(summary(complexities))
expect_type(x, "character")
expect_equal(x[[2]], "Mean of Complexities")
expect_equal(x[[3]], "8.714286 ")
expect_equal(x[[5]], "Standard Deviation of Complexities")
expect_equal(x[[6]], "2.003568 ")
expect_equal(x[[8]], "Standard Error of Complexities")
expect_equal(x[[9]], "0.4372144")
})
test_that("print.hagis.complexities() returns a proper summary", {
x <- capture.output(print(complexities))
expect_type(x, "character")
expect_equal(x[[2]], "Grouped Complexities")
expect_equal(x[[3]], " complexity frequency distribution")
expect_equal(tail(x),
c(
"18: 18 10",
"19: 19 11",
"20: 20 11",
"21: 21 13",
" sample N_samp",
""
))
})
test_that("pander.summary.complexities returns a properly formatted table", {
x <- capture.output(pander(summary(complexities)))
expect_type(x, "character")
expect_equal(x[[1]], "")
expect_equal(x[[2]], "------------------------")
expect_equal(x[[3]], " Mean SD SE ")
expect_equal(x[[4]], "------- ------- --------")
expect_equal(x[[5]], " 8.714 2.004 0.4372 ")
expect_equal(x[[6]], "------------------------")
})
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