diff --git a/DESCRIPTION b/DESCRIPTION
index e3418f58..7dd2cacb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.3.0.9016
+Version: 1.3.0.9017
Date: 2020-09-12
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index c18501a8..6c57494a 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.3.0.9016
+# AMR 1.3.0.9017
## Last updated: 12 September 2020
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
diff --git a/R/mo.R b/R/mo.R
index b0700fda..75e2dceb 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -281,6 +281,43 @@ exec_as.mo <- function(x,
reference_data_to_use = MO_lookup) {
check_dataset_integrity()
+
+ lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
+ # `column` can be NULL for all columns, or a selection
+ # returns a character (vector) - if `column` > length 1 then with columns as names
+ if (isTRUE(debug_mode)) {
+ cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
+ }
+ if (length(column) == 1) {
+ res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+ res <- as.character(res_df[, column, drop = TRUE])
+ if (length(res) == 0) {
+ NA_character_
+ } else {
+ if (length(res) > n) {
+ # save the other possible results as well
+ uncertainties <<- rbind(uncertainties,
+ format_uncertainty_as_df(uncertainty_level = 1,
+ input = x_backup[i],
+ result_mo = res_df[1, "mo", drop = TRUE],
+ candidates = as.character(res_df[, "fullname", drop = TRUE])))
+ }
+ res[seq_len(min(n, length(res)))]
+ }
+ } else {
+ if (is.null(column)) {
+ column <- names(haystack)
+ }
+ res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+ res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
+ if (NROW(res) == 0) {
+ res <- rep(NA_character_, length(column))
+ }
+ res <- as.character(res)
+ names(res) <- column
+ res
+ }
+ }
# start off with replaced language-specific non-ASCII characters with ASCII characters
x <- parse_and_convert(x)
@@ -383,43 +420,6 @@ exec_as.mo <- function(x,
} else if (!all(x %in% microorganisms[, property])) {
- lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
- # `column` can be NULL for all columns, or a selection
- # returns a character (vector) - if `column` > length 1 then with columns as names
- if (isTRUE(debug_mode)) {
- cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
- }
- if (length(column) == 1) {
- res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
- res <- as.character(res_df[, column, drop = TRUE])
- if (length(res) == 0) {
- NA_character_
- } else {
- if (length(res) > n) {
- # save the other possible results as well
- uncertainties <<- rbind(uncertainties,
- format_uncertainty_as_df(uncertainty_level = 1,
- input = x_backup[i],
- result_mo = res_df[1, "mo", drop = TRUE],
- candidates = as.character(res_df[, "fullname", drop = TRUE])))
- }
- res[seq_len(min(n, length(res)))]
- }
- } else {
- if (is.null(column)) {
- column <- names(haystack)
- }
- res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
- res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
- if (NROW(res) == 0) {
- res <- rep(NA_character_, length(column))
- }
- res <- as.character(res)
- names(res) <- column
- res
- }
- }
-
strip_whitespace <- function(x, dyslexia_mode) {
# all whitespaces (tab, new lines, etc.) should be one space
# and spaces before and after should be omitted
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diff --git a/docs/404.html b/docs/404.html
index 1287c7c6..942ccef7 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
NEWS.md
-