weiss_sepsis <- subset(weiss2021_data, sample_id %in% "Sepsis.22441.C")
weiss_sepsis$proportion <- round(weiss_sepsis$proportion, 3)
weiss_healthy <- subset(weiss2021_data, sample_id %in% "Healthy.148")
weiss_healthy$proportion <- round(weiss_healthy$proportion, 3)
test_that("antibiotic_susceptibility_vancomycin works on Weiss examples", {
expect_equal(
antibiotic_susceptibility_vancomycin(weiss_sepsis$lineage),
c("resistant", "susceptible", "resistant", "resistant", "resistant"))
expect_equal(
antibiotic_susceptibility_vancomycin(weiss_healthy$lineage),
c("resistant", "susceptible", "resistant", "resistant", "susceptible",
"susceptible", "resistant", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "resistant", "susceptible",
"susceptible", "resistant", "susceptible", "resistant", "susceptible",
"susceptible", "resistant", "susceptible", "susceptible", "susceptible",
"resistant"))
})
test_that("mirix_vancomycin works on Weiss examples", {
expect_equal(
mirix_vancomycin(weiss_sepsis$proportion, weiss_sepsis$lineage),
-0.5670429, tolerance = 1e-5)
expect_equal(
mirix_vancomycin(weiss_healthy$proportion, weiss_healthy$lineage),
-0.3609116, tolerance = 1e-5)
})
test_that("antibiotic_susceptibility_tetracycline works on Weiss examples", {
expect_equal(
antibiotic_susceptibility_tetracycline(weiss_sepsis$lineage),
c("susceptible", "susceptible", "resistant", "susceptible", "susceptible"))
expect_equal(
antibiotic_susceptibility_tetracycline(weiss_healthy$lineage),
c("susceptible", "susceptible", "resistant", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible"))
})
test_that("mirix_doxycycline works on Weiss examples", {
expect_equal(
mirix_doxycycline(weiss_sepsis$proportion, weiss_sepsis$lineage),
1.879934, tolerance = 1e-5)
expect_equal(
mirix_doxycycline(weiss_healthy$proportion, weiss_healthy$lineage),
1.045228, tolerance = 1e-5)
})
test_that("antibiotic_susceptibility_penicillin works on Weiss examples", {
expect_equal(
antibiotic_susceptibility_penicillin(weiss_sepsis$lineage),
c("susceptible", "susceptible", "resistant", "susceptible", "susceptible"))
expect_equal(
antibiotic_susceptibility_penicillin(weiss_healthy$lineage),
c("susceptible", "susceptible", "resistant", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible", "susceptible", "susceptible", "susceptible", "susceptible",
"susceptible"))
})
test_that("mirix_amoxicillin works on Weiss examples", {
expect_equal(
mirix_amoxicillin(weiss_sepsis$proportion, weiss_sepsis$lineage),
1.879934, tolerance = 1e-5)
expect_equal(
mirix_amoxicillin(weiss_healthy$proportion, weiss_healthy$lineage),
1.045228, tolerance = 1e-5)
})
test_that("antibiotic_susceptibility_aminoglycoside works on Weiss examples", {
expect_equal(
antibiotic_susceptibility_aminoglycoside(weiss_sepsis$lineage),
c("susceptible", "resistant", "resistant", "resistant", "resistant"))
expect_equal(
antibiotic_susceptibility_aminoglycoside(weiss_healthy$lineage),
c("resistant", "resistant", "resistant", "resistant", "resistant",
"resistant", "resistant", "resistant", "resistant", "resistant",
"resistant", "resistant", "resistant", "resistant", "resistant",
"resistant", "resistant", "resistant", "resistant", "resistant",
NA, "susceptible", "resistant", "resistant", "resistant", "resistant"))
})
test_that("mirix_gentamicin works on Weiss examples", {
expect_equal(
mirix_gentamicin(weiss_sepsis$proportion, weiss_sepsis$lineage),
0.52420, tolerance = 1e-5)
expect_equal(
mirix_gentamicin(weiss_healthy$proportion, weiss_healthy$lineage),
-2.69373, tolerance = 1e-5)
})
test_that("mirix_metronidazole works on Weiss examples", {
expect_equal(
mirix_metronidazole(weiss_sepsis$proportion, weiss_sepsis$lineage),
-1.788434, tolerance = 1e-5)
expect_equal(
mirix_metronidazole(weiss_healthy$proportion, weiss_healthy$lineage),
2.089021, tolerance = 1e-5)
})
test_that("mirix_metronidazole and mirix_ciprofloxacin are inverses", {
expect_equal(
mirix_metronidazole(weiss_sepsis$proportion, weiss_sepsis$lineage),
-mirix_ciprofloxacin(weiss_sepsis$proportion, weiss_sepsis$lineage))
expect_equal(
mirix_metronidazole(weiss_healthy$proportion, weiss_healthy$lineage),
-mirix_ciprofloxacin(weiss_healthy$proportion, weiss_healthy$lineage))
})
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