gram_stain_db <- data.frame(
taxon = c(
"Actinobacteria", "Bacteroidetes", "Firmicutes",
"Negativicutes", "Proteobacteria"),
rank = c("Phylum", "Phylum", "Phylum", "Class", "Phylum"),
gram_stain = c(
"Gram-positive", "Gram-negative", "Gram-positive",
"Gram-negative", "Gram-negative"),
stringsAsFactors = FALSE)
gram_stain_aerobic_status_db <- data.frame(
taxon = c(
"Rothia aerobat", "Enterococcus", "Blautia", "Lactobacillus acidophilus",
"Bradyrhizobium", "Rothia", "Actinobacteria"),
rank = c(
"Species", "Genus", "Genus", "Species", "Genus", "Genus", "Phylum"),
aerobic_status = c(
"aerobe", "facultative anaerobe", "obligate anaerobe", NA, "aerobe",
"aerobe", NA),
gram_stain = c(
"Gram-positive", "Gram-positive", "Gram-positive", "Gram-positive",
"Gram-negative", NA, "Gram-positive"),
stringsAsFactors = FALSE)
vancomycin_db <- data.frame(
taxon = c(
"Lactobacillus", "Enterococcus flavescens", "Lactobacillus delbrueckii",
"Lactobacillus lactis", "Lactobacillus casei"),
rank = c("Genus", "Species", "Species", "Species", "Species"),
value = c(
"resistant", "resistant", "susceptible", "susceptible", "resistant"),
antibiotic = "vancomycin",
stringsAsFactors = FALSE)
tetracycline_db <- data.frame(
taxon = c("Escherichia coli", "Enterococcus faecalis", "Klebsiella"),
rank = c("Species", "Species", "Genus"),
value = c("resistant", "resistant", "susceptible"),
antibiotic = "tetracycline",
stringsAsFactors = FALSE)
penicillin_db <-data.frame(
taxon = c(
"Bacteroides", "Stenotrophomonas maltophilia",
"Enterococcus faecalis", "Enterococcus faecium",
"Escherichia coli", "Mycoplasma"),
rank = c("Genus", "Species", "Species", "Species", "Species", "Genus"),
value = c(
"resistant", "resistant", "resistant", "resistant", "resistant",
"resistant"),
antibiotic = "penicillin",
stringsAsFactors = FALSE)
aminoglycoside_db <- data.frame(
taxon = "Staphylococcus",
rank = "Genus",
value = "susceptible",
antibiotic = "aminoglycoside",
stringsAsFactors = FALSE)
test_antibiotic_db <- rbind(
vancomycin_db, tetracycline_db, penicillin_db, aminoglycoside_db)
test_that("antibiotic_susceptibility_vancomycin works for selected taxa", {
lineage <- c(
"Firmicutes; Enterococcus faecalis",
"Firmicutes; Lactobacillus",
"Firmicutes; Lactobacillus; Lactobacillus delbrueckii")
expect_equal(
antibiotic_susceptibility_vancomycin(
lineage = lineage,
antibiotic_db = test_antibiotic_db,
phenotype_db = gram_stain_db),
c("susceptible", "resistant", "susceptible"))
})
test_that("antibiotic_susceptibility_tetracycline works for selected taxa", {
lineage <- c(
"Firmicutes; Enterococcus faecalis",
"Firmicutes; Lactobacillus",
"Proteobacteria; Klebsiella; Klebsiella pneumoniae")
expect_equal(
antibiotic_susceptibility_tetracycline(
lineage = lineage,
antibiotic_db = test_antibiotic_db),
c("resistant", "susceptible", "susceptible"))
})
test_that("antibiotic_susceptibility_penicillin works for selected taxa", {
lineage <- c(
"Firmicutes; Enterococcus faecalis",
"Firmicutes; Lactobacillus",
"Proteobacteria; Klebsiella; Klebsiella pneumoniae")
expect_equal(
antibiotic_susceptibility_penicillin(
lineage = lineage,
antibiotic_db = test_antibiotic_db),
c("resistant", "susceptible", "susceptible"))
})
test_that("antibiotic_susceptibility_aminoglycoside works for selected taxa", {
lineage <- c(
"Staphylococcus epidermidis",
"Rothia", # Not enough info to determine both phenotypes, should be NA
"Actinobacteria; Rothia",
"Bacteroides vulgatus")
expect_equal(
antibiotic_susceptibility_aminoglycoside(
lineage = lineage,
antibiotic_db = test_antibiotic_db,
phenotype_db = gram_stain_aerobic_status_db),
c("susceptible", NA, "resistant", "resistant"))
})
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