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(v1.4.0.9038) docu update

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dr. M.S. (Matthijs) Berends
2020-12-13 13:44:04 +01:00
parent c8bcecf232
commit ac22b8d5c1
16 changed files with 62 additions and 66 deletions
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20
R/eucast_rules.R
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@ -539,7 +539,9 @@ eucast_rules <- function(x,
x <- paste(paste0(ab_names, collapse = " and "), "are both")
} else {
# like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment)
x <- paste(paste0(ab_names, collapse = " and "), "are all")
# nolint start
# x <- paste(paste0(ab_names, collapse = " and "), "are all")
# nolint end
}
return(paste0(x, " '", ab_results, "'"))
} else {
@ -869,14 +871,16 @@ eucast_rules <- function(x,
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
error = function(e) integer(0))
} else if (length(source_antibiotics) == 3) {
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like_perl% mo_value
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
& as.rsi_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
error = function(e) integer(0))
# nolint start
# } else if (length(source_antibiotics) == 3) {
# rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like_perl% mo_value
# & as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
# & as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
# & as.rsi_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
# error = function(e) integer(0))
# nolint end
} else {
stop_("only 3 antibiotics supported for source_antibiotics")
stop_("only 2 antibiotics supported for source_antibiotics")
}
}

2
R/globals.R
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@ -40,6 +40,7 @@ globalVariables(c("...length", # for pm_group_split() on R 3.3
"genus",
"gr",
"group",
"guideline",
"hjust",
"input",
"intrinsic_resistant",
@ -47,6 +48,7 @@ globalVariables(c("...length", # for pm_group_split() on R 3.3
"lang",
"language",
"lookup",
"method",
"microorganism",
"microorganisms",
"microorganisms.codes",