mirror of https://github.com/msberends/AMR.git
(v1.0.1.9007) small bugfix
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Package: AMR
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Version: 1.0.1.9006
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Version: 1.0.1.9007
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Date: 2020-04-14
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.0.1.9006
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# AMR 1.0.1.9007
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## <small>Last updated: 14-Apr-2020</small>
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### New
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44
R/mo.R
44
R/mo.R
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@ -178,7 +178,7 @@ as.mo <- function(x,
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check_dataset_integrity()
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# start off with replaced language-specific non-ASCII characters with ASCII characters
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x <- parse_encoding(x)
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x <- parse_and_convert(x)
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# WHONET: xxx = no growth
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x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
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@ -263,7 +263,7 @@ exec_as.mo <- function(x,
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check_dataset_integrity()
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# start off with replaced language-specific non-ASCII characters with ASCII characters
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x <- parse_encoding(x)
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x <- parse_and_convert(x)
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# WHONET: xxx = no growth
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x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
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@ -277,27 +277,7 @@ exec_as.mo <- function(x,
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options(mo_renamed = NULL)
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}
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options(mo_renamed_last_run = NULL)
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if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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# paste these columns together
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x_vector <- vector("character", NROW(x))
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for (i in seq_len(NROW(x))) {
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x_vector[i] <- paste(pull(x[i, ], 1), pull(x[i, ], 2), sep = " ")
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}
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x <- x_vector
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} else {
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if (NCOL(x) > 2) {
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stop("`x` can be 2 columns at most", call. = FALSE)
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}
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x[is.null(x)] <- NA
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# support tidyverse selection like: df %>% select(colA)
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if (!is.vector(x) & !is.null(dim(x))) {
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x <- pull(x, 1)
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}
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}
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uncertainties <- data.frame(uncertainty = integer(0),
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input = character(0),
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fullname = character(0),
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@ -1977,9 +1957,23 @@ trimws2 <- function(x) {
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trimws(gsub("[\\s]+", " ", x, perl = TRUE))
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}
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parse_encoding <- function(x) {
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parse_and_convert <- function(x) {
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tryCatch({
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x <- unname(unlist(x))
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if (!is.null(dim(x))) {
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if (NCOL(x) > 2) {
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stop("A maximum of two columns is allowed.", call. = FALSE)
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} else if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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# paste these columns together
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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colnames(x) <- c("A", "B")
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x <- paste(x$A, x$B)
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} else {
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# support tidyverse selection like: df %>% select(colA)
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x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
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}
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}
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x[is.null(x)] <- NA
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parsed <- iconv(x, to = "UTF-8")
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parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
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parsed <- gsub('"', "", parsed, fixed = TRUE)
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.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">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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@ -229,9 +229,9 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1019006" class="section level1">
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<h1 class="page-header" data-toc-text="1.0.1.9006">
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<a href="#amr-1019006" class="anchor"></a>AMR 1.0.1.9006<small> Unreleased </small>
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<div id="amr-1019007" class="section level1">
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<h1 class="page-header" data-toc-text="1.0.1.9007">
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<a href="#amr-1019007" class="anchor"></a>AMR 1.0.1.9007<small> Unreleased </small>
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</h1>
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<div id="last-updated-14-apr-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-04-14T12:12Z
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last_built: 2020-04-14T12:56Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -81,7 +81,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9007</span>
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</span>
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</div>
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