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(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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63
tests/testthat/test-antibiogram.R
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@@ -31,19 +31,22 @@
# Traditional antibiogram ----------------------------------------------
ab1 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
antibiotics = c(aminoglycosides(), carbapenems())
)
ab2 <- antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain",
add_total_n = TRUE)
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain",
add_total_n = TRUE
)
ab3 <- antibiogram(example_isolates,
antibiotics = carbapenems(),
ab_transform = "ab",
mo_transform = "name",
formatting_type = 1)
antibiotics = carbapenems(),
ab_transform = "ab",
mo_transform = "name",
formatting_type = 1
)
expect_inherits(ab1, "antibiogram")
expect_inherits(ab2, "antibiogram")
@@ -57,15 +60,17 @@ expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
# combined antibiotics yield higher empiric coverage
ab4 <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain")
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain"
)
ab5 <- antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & ",
add_total_n = FALSE)
antibiotics = c("TZP", "TZP+TOB"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & ",
add_total_n = FALSE
)
expect_inherits(ab4, "antibiogram")
expect_inherits(ab5, "antibiogram")
@@ -76,20 +81,23 @@ expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacill
# the data set could contain a filter for e.g. respiratory specimens
ab6 <- antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward",
ab_transform = NULL)
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward",
ab_transform = NULL
)
# with a custom language, though this will be determined automatically
# (i.e., this table will be in Dutch on Dutch systems)
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
ab7 <- antibiogram(ex1,
antibiotics = aminoglycosides(),
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"IC", "Geen IC"),
language = "nl",
add_total_n = TRUE)
antibiotics = aminoglycosides(),
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"IC", "Geen IC"
),
language = "nl",
add_total_n = TRUE
)
expect_inherits(ab6, "antibiogram")
expect_inherits(ab7, "antibiogram")
@@ -100,8 +108,9 @@ expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikaci
# the data set could contain a filter for e.g. respiratory specimens
ab8 <- suppressWarnings(antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
wisca = TRUE))
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
wisca = TRUE
))
expect_inherits(ab8, "antibiogram")
expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))