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(v2.1.1.9163) cleanup

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This commit is contained in:
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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47
R/custom_microorganisms.R
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@ -250,12 +250,15 @@ add_custom_microorganisms <- function(x) {
"_",
trimws(
paste(abbreviate_mo(x$genus, 5),
abbreviate_mo(x$species, 4, hyphen_as_space = TRUE),
abbreviate_mo(x$subspecies, 4, hyphen_as_space = TRUE),
sep = "_"),
whitespace = "_"))
abbreviate_mo(x$species, 4, hyphen_as_space = TRUE),
abbreviate_mo(x$subspecies, 4, hyphen_as_space = TRUE),
sep = "_"
),
whitespace = "_"
)
)
stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package")
# add to package ----
AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
class(AMR_env$MO_lookup$mo) <- "character"
@ -309,19 +312,25 @@ abbreviate_mo <- function(x, minlength = 5, prefix = "", hyphen_as_space = FALSE
}
# keep a starting Latin ae
suppressWarnings(
gsub("(\u00C6|\u00E6)+",
"AE",
toupper(
paste0(prefix,
abbreviate(
gsub("^ae",
"\u00E6\u00E6",
x,
ignore.case = TRUE),
minlength = minlength,
use.classes = TRUE,
method = "both.sides",
...
))))
gsub(
"(\u00C6|\u00E6)+",
"AE",
toupper(
paste0(
prefix,
abbreviate(
gsub("^ae",
"\u00E6\u00E6",
x,
ignore.case = TRUE
),
minlength = minlength,
use.classes = TRUE,
method = "both.sides",
...
)
)
)
)
)
}