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unit tests

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dr. M.S. (Matthijs) Berends
2023-02-12 17:10:48 +01:00
parent 68abb00c59
commit 45a9697c84
23 changed files with 438 additions and 406 deletions
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82
man/antibiogram.Rd
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@ -153,39 +153,45 @@ example_isolates
# Traditional antibiogram ----------------------------------------------
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
antibiotics = c(aminoglycosides(), carbapenems())
)
antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain")
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain"
)
antibiogram(example_isolates,
antibiotics = carbapenems(),
ab_transform = "name",
mo_transform = "name")
antibiotics = carbapenems(),
ab_transform = "name",
mo_transform = "name"
)
# Combined antibiogram -------------------------------------------------
# combined antibiotics yield higher empiric coverage
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain")
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain"
)
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & ")
antibiotics = c("TZP", "TZP+TOB"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & "
)
# Syndromic antibiogram ------------------------------------------------
# the data set could contain a filter for e.g. respiratory specimens
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward"
)
# now define a data set with only E. coli
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
@ -193,35 +199,41 @@ ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
# with a custom language, though this will be determined automatically
# (i.e., this table will be in Spanish on Spanish systems)
antibiogram(ex1,
antibiotics = aminoglycosides(),
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"UCI", "No UCI"),
language = "es")
antibiotics = aminoglycosides(),
ab_transform = "name",
syndromic_group = ifelse(ex1$ward == "ICU",
"UCI", "No UCI"
),
language = "es"
)
# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
# the data set could contain a filter for e.g. respiratory specimens
antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"))
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"
)
)
# Generate plots with ggplot2 or base R --------------------------------
ab1 <- antibiogram(example_isolates,
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain")
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain"
)
ab2 <- antibiogram(example_isolates,
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
syndromic_group = "ward")
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
syndromic_group = "ward"
)
plot(ab1)
if (requireNamespace("ggplot2")) {