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(v1.3.0.9017) small fix
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Package: AMR
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Package: AMR
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Version: 1.3.0.9016
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Version: 1.3.0.9017
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Date: 2020-09-12
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Date: 2020-09-12
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.3.0.9016
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# AMR 1.3.0.9017
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## <small>Last updated: 12 September 2020</small>
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## <small>Last updated: 12 September 2020</small>
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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!
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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!
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74
R/mo.R
74
R/mo.R
@ -282,6 +282,43 @@ exec_as.mo <- function(x,
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check_dataset_integrity()
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check_dataset_integrity()
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lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
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# `column` can be NULL for all columns, or a selection
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# returns a character (vector) - if `column` > length 1 then with columns as names
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if (isTRUE(debug_mode)) {
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cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
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}
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if (length(column) == 1) {
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res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
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res <- as.character(res_df[, column, drop = TRUE])
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if (length(res) == 0) {
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NA_character_
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} else {
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if (length(res) > n) {
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# save the other possible results as well
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uncertainties <<- rbind(uncertainties,
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format_uncertainty_as_df(uncertainty_level = 1,
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input = x_backup[i],
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result_mo = res_df[1, "mo", drop = TRUE],
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candidates = as.character(res_df[, "fullname", drop = TRUE])))
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}
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res[seq_len(min(n, length(res)))]
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}
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} else {
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if (is.null(column)) {
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column <- names(haystack)
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}
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res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
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res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
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if (NROW(res) == 0) {
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res <- rep(NA_character_, length(column))
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}
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res <- as.character(res)
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names(res) <- column
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res
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}
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}
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# start off with replaced language-specific non-ASCII characters with ASCII characters
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# start off with replaced language-specific non-ASCII characters with ASCII characters
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x <- parse_and_convert(x)
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x <- parse_and_convert(x)
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# replace mo codes used in older package versions
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# replace mo codes used in older package versions
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@ -383,43 +420,6 @@ exec_as.mo <- function(x,
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} else if (!all(x %in% microorganisms[, property])) {
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} else if (!all(x %in% microorganisms[, property])) {
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lookup <- function(needle, column = property, haystack = reference_data_to_use, n = 1, debug_mode = debug, input = "") {
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# `column` can be NULL for all columns, or a selection
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# returns a character (vector) - if `column` > length 1 then with columns as names
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if (isTRUE(debug_mode)) {
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cat(font_silver("looking up: ", substitute(needle), "\n", collapse = ""))
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}
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if (length(column) == 1) {
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res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
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res <- as.character(res_df[, column, drop = TRUE])
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if (length(res) == 0) {
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NA_character_
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} else {
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if (length(res) > n) {
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# save the other possible results as well
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uncertainties <<- rbind(uncertainties,
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format_uncertainty_as_df(uncertainty_level = 1,
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input = x_backup[i],
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result_mo = res_df[1, "mo", drop = TRUE],
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candidates = as.character(res_df[, "fullname", drop = TRUE])))
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}
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res[seq_len(min(n, length(res)))]
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}
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} else {
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if (is.null(column)) {
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column <- names(haystack)
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}
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res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
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res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
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if (NROW(res) == 0) {
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res <- rep(NA_character_, length(column))
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}
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res <- as.character(res)
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names(res) <- column
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res
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}
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}
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strip_whitespace <- function(x, dyslexia_mode) {
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strip_whitespace <- function(x, dyslexia_mode) {
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# all whitespaces (tab, new lines, etc.) should be one space
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# all whitespaces (tab, new lines, etc.) should be one space
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# and spaces before and after should be omitted
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# and spaces before and after should be omitted
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -43,7 +43,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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</div>
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<div id="amr-1309016" class="section level1">
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<div id="amr-1309017" class="section level1">
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<h1 class="page-header" data-toc-text="1.3.0.9016">
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<h1 class="page-header" data-toc-text="1.3.0.9017">
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<a href="#amr-1309016" class="anchor"></a>AMR 1.3.0.9016<small> Unreleased </small>
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<a href="#amr-1309017" class="anchor"></a>AMR 1.3.0.9017<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-12-september-2020" class="section level2">
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<div id="last-updated-12-september-2020" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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@ -2,7 +2,7 @@ pandoc: 2.7.3
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pkgdown: 1.5.1.9000
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pkgdown: 1.5.1.9000
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pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
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pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
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articles: []
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articles: []
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last_built: 2020-09-12T06:48Z
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last_built: 2020-09-12T11:54Z
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urls:
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urls:
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reference: https://msberends.github.io/AMR/reference
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reference: https://msberends.github.io/AMR/reference
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article: https://msberends.github.io/AMR/articles
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article: https://msberends.github.io/AMR/articles
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9017</span>
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</span>
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</span>
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</div>
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</div>
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@ -23,3 +23,4 @@ library(testthat)
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library(AMR)
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library(AMR)
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test_check("AMR")
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test_check("AMR")
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unlink("tests/testthat/Rplots.pdf")
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