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(v1.2.0.9006) improve auto col-determination

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dr. M.S. (Matthijs) Berends
2020-06-11 20:03:13 +02:00
parent 352508889c
commit 4f94e1312f
12 changed files with 38 additions and 40 deletions
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39
R/aa_helper_functions.R
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@ -103,60 +103,55 @@ search_type_in_df <- function(x, type) {
# -- mo
if (type == "mo") {
if ("mo" %in% lapply(x, class)) {
found <- colnames(x)[lapply(x, class) == "mo"][1]
if (any(sapply(x, is.mo))) {
found <- sort(colnames(x)[sapply(x, is.mo)])[1]
} else if ("mo" %in% colnames(x) &
suppressWarnings(
all(x$mo %in% c(NA,
microorganisms$mo,
microorganisms.translation$mo_old)))) {
found <- "mo"
} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$")) {
found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$"][1]
} else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)")) {
found <- colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)"][1]
} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1]
} else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
found <- sort(colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)"])[1]
} else if (any(colnames(x) %like% "species")) {
found <- colnames(x)[colnames(x) %like% "species"][1]
found <- sort(colnames(x)[colnames(x) %like% "species"])[1]
}
}
# -- key antibiotics
if (type == "keyantibiotics") {
if (any(colnames(x) %like% "^key.*(ab|antibiotics)")) {
found <- colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"][1]
found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"])[1]
}
}
# -- date
if (type == "date") {
if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) {
# WHONET support
found <- colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"][1]
found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
if (!any(class(pull(x, found)) %in% c("Date", "POSIXct"))) {
stop(font_red(paste0("ERROR: Found column `", font_bold(found), "` to be used as input for `col_", type,
"`, but this column contains no valid dates. Transform its values to valid dates first.")),
"`, but this column contains no valid dates. Transform its values to valid dates first.")),
call. = FALSE)
}
} else {
for (i in seq_len(ncol(x))) {
if (any(class(pull(x, i)) %in% c("Date", "POSIXct"))) {
found <- colnames(x)[i]
break
}
}
} else if (any(sapply(x, function(x) inherits(x, c("Date", "POSIXct"))))) {
found <- sort(colnames(x)[sapply(x, function(x) inherits(x, c("Date", "POSIXct")))])[1]
}
}
# -- patient id
if (type == "patient_id") {
if (any(colnames(x) %like% "^(identification |patient|patid)")) {
found <- colnames(x)[colnames(x) %like% "^(identification |patient|patid)"][1]
found <- sort(colnames(x)[colnames(x) %like% "^(identification |patient|patid)"])[1]
}
}
# -- specimen
if (type == "specimen") {
if (any(colnames(x) %like% "(specimen type|spec_type)")) {
found <- colnames(x)[colnames(x) %like% "(specimen type|spec_type)"][1]
found <- sort(colnames(x)[colnames(x) %like% "(specimen type|spec_type)"])[1]
} else if (any(colnames(x) %like% "^(specimen)")) {
found <- colnames(x)[colnames(x) %like% "^(specimen)"][1]
found <- sort(colnames(x)[colnames(x) %like% "^(specimen)"])[1]
}
}
# -- UTI (urinary tract infection)
@ -164,13 +159,13 @@ search_type_in_df <- function(x, type) {
if (any(colnames(x) == "uti")) {
found <- colnames(x)[colnames(x) == "uti"][1]
} else if (any(colnames(x) %like% "(urine|urinary)")) {
found <- colnames(x)[colnames(x) %like% "(urine|urinary)"][1]
found <- sort(colnames(x)[colnames(x) %like% "(urine|urinary)"])[1]
}
if (!is.null(found)) {
# this column should contain logicals
if (!is.logical(x[, found, drop = TRUE])) {
message(font_red(paste0("NOTE: Column `", font_bold(found), "` found as input for `col_", type,
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.")))
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.")))
found <- NULL
}
}