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(v1.2.0.9017) ab_from_text() improvement

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dr. M.S. (Matthijs) Berends
2020-06-26 12:31:27 +02:00
parent b31003c0b6
commit 4f6f056077
19 changed files with 239 additions and 118 deletions
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13
R/first_isolate.R
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@ -291,7 +291,8 @@ first_isolate <- function(x,
# did find some isolates - add new index numbers of rows
x$newvar_row_index_sorted <- seq_len(nrow(x))
scope.size <- row.end - row.start + 1
scope.size <- nrow(x[which(x$newvar_row_index_sorted %in% c(row.start + 1:row.end) &
!is.na(x$newvar_mo)), , drop = FALSE])
identify_new_year <- function(x, episode_days) {
# I asked on StackOverflow:
@ -390,7 +391,7 @@ first_isolate <- function(x,
# handle empty microorganisms
if (any(x$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
message(font_blue(paste0("NOTE: ", ifelse(include_unknown == TRUE, "Included ", "Excluded "),
format(sum(x$newvar_mo == "UNKNOWN"),
format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'UNKNOWN' (column `", font_bold(col_mo), "`)")))
}
@ -398,7 +399,7 @@ first_isolate <- function(x,
# exclude all NAs
if (any(is.na(x$newvar_mo)) & info == TRUE) {
message(font_blue(paste0("NOTE: Excluded ", format(sum(is.na(x$newvar_mo)),
message(font_blue(paste0("NOTE: Excluded ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'NA' (column `", font_bold(col_mo), "`)")))
}
@ -410,18 +411,18 @@ first_isolate <- function(x,
if (info == TRUE) {
n_found <- base::sum(x$newvar_first_isolate, na.rm = TRUE)
p_found_total <- percentage(n_found / nrow(x))
p_found_total <- percentage(n_found / nrow(x[which(!is.na(x$newvar_mo)), , drop = FALSE]))
p_found_scope <- percentage(n_found / scope.size)
# mark up number of found
n_found <- base::format(n_found, big.mark = big.mark, decimal.mark = decimal.mark)
if (p_found_total != p_found_scope) {
msg_txt <- paste0("=> Found ",
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
" (", p_found_scope, " within scope and ", p_found_total, " of total)")
" (", p_found_scope, " within scope and ", p_found_total, " of total where a microbial ID was available)")
} else {
msg_txt <- paste0("=> Found ",
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
" (", p_found_total, " of total)")
" (", p_found_total, " of total where a microbial ID was available)")
}
message(font_black(msg_txt))
}