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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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32
man/antibiogram.Rd
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@ -183,7 +183,7 @@ Code example:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{antibiogram(your_data,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
wisca = TRUE)
# this is equal to:
wisca(your_data,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
@ -343,12 +343,14 @@ antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "atc",
mo_transform = "gramstain")
mo_transform = "gramstain"
)
antibiogram(example_isolates,
antibiotics = carbapenems(),
ab_transform = "name",
mo_transform = "name")
mo_transform = "name"
)
# Combined antibiogram -------------------------------------------------
@ -356,14 +358,16 @@ antibiogram(example_isolates,
# combined antibiotics yield higher empiric coverage
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain")
mo_transform = "gramstain"
)
# names of antibiotics do not need to resemble columns exactly:
antibiogram(example_isolates,
antibiotics = c("Cipro", "cipro + genta"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & ")
sep = " & "
)
# Syndromic antibiogram ------------------------------------------------
@ -371,7 +375,8 @@ antibiogram(example_isolates,
# the data set could contain a filter for e.g. respiratory specimens
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
syndromic_group = "ward"
)
# now define a data set with only E. coli
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
@ -384,7 +389,8 @@ antibiogram(ex1,
syndromic_group = ifelse(ex1$ward == "ICU",
"UCI", "No UCI"
),
language = "es")
language = "es"
)
# WISCA antibiogram ----------------------------------------------------
@ -393,7 +399,8 @@ antibiogram(ex1,
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
syndromic_group = "ward",
wisca = TRUE)
wisca = TRUE
)
# Print the output for R Markdown / Quarto -----------------------------
@ -401,7 +408,8 @@ antibiogram(example_isolates,
ureido <- antibiogram(example_isolates,
antibiotics = ureidopenicillins(),
syndromic_group = "ward",
wisca = TRUE)
wisca = TRUE
)
# in an Rmd file, you would just need to return `ureido` in a chunk,
# but to be explicit here:
@ -414,11 +422,13 @@ if (requireNamespace("knitr")) {
ab1 <- antibiogram(example_isolates,
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain")
mo_transform = "gramstain"
)
ab2 <- antibiogram(example_isolates,
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
syndromic_group = "ward")
syndromic_group = "ward"
)
if (requireNamespace("ggplot2")) {
ggplot2::autoplot(ab1)