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anaerobic codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-04-17 11:26:19 +02:00
parent ad3061c754
commit cabffb22fd
6 changed files with 19 additions and 9 deletions
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R/mo.R
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@ -995,8 +995,10 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
out[x %like_case% "( |^)gram[-]( |$)"] <- "B_GRAMN"
out[x %like_case% "gram[ -]?pos.*"] <- "B_GRAMP"
out[x %like_case% "( |^)gram[+]( |$)"] <- "B_GRAMP"
out[x %like_case% "anaerob[a-z]+ .*gram[ -]?neg.*"] <- "B_ANAER-NEG"
out[x %like_case% "anaerob[a-z]+ .*gram[ -]?pos.*"] <- "B_ANAER-POS"
out[is.na(out) & x %like_case% "anaerob[a-z]+ (micro)?.*organism"] <- "B_ANAER"
# yeasts and fungi
out[x %like_case% "^yeast?"] <- "F_YEAST"
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
@ -1006,7 +1008,7 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
out[x %like_case% "gono[ck]o[ck]"] <- "B_NESSR_GNRR"
out[x %like_case% "pneumo[ck]o[ck]"] <- "B_STRPT_PNMN"
# unexisting names (xxx and con are WHONET codes)
# unexisting names (con is the WHONET code for contamination)
out[x %in% c("con", "other", "none", "unknown") | x %like_case% "virus"] <- "UNKNOWN"
# WHONET has a lot of E. coli and Vibrio cholerae names
@ -1017,18 +1019,23 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
}
italicise <- function(x) {
if (!has_colour()) {
return(x)
}
out <- font_italic(x, collapse = NULL)
# city-like serovars of Salmonella (start with a capital)
out[x %like_case% "Salmonella [A-Z]"] <- paste(
font_italic("Salmonella"),
gsub("Salmonella ", "", x[x %like_case% "Salmonella [A-Z]"])
)
# streptococcal groups
out[x %like_case% "Streptococcus [A-Z]"] <- paste(
font_italic("Streptococcus"),
gsub("Streptococcus ", "", x[x %like_case% "Streptococcus [A-Z]"])
)
if (has_colour()) {
out <- gsub("(Group|group|Complex|complex)(\033\\[23m)?", "\033[23m\\1", out, perl = TRUE)
}
# be sure not to make these italic
out <- gsub("([ -]*)(Group|group|Complex|complex)(\033\\[23m)?", "\033[23m\\1\\2", out, perl = TRUE)
out <- gsub("(\033\\[3m)?(Beta[-]haemolytic|Coagulase[-](postive|negative)) ", "\\2 \033[3m", out, perl = TRUE)
out
}