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(v0.7.0.9006) ab algorithm fix for ATC codes
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Package: AMR
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Version: 0.7.0.9005
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Version: 0.7.0.9006
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Date: 2019-06-11
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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 0.7.0.9005
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# AMR 0.7.0.9006
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#### New
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* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
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15
R/ab.R
15
R/ab.R
@ -203,7 +203,8 @@ as.ab <- function(x) {
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# try by removing all spaces
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if (x[i] %like% " ") {
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found <- suppressWarnings(as.ab(gsub(" +", "", x[i])))
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if (length(found) > 0) {
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print(found)
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if (length(found) > 0 & !is.na(found)) {
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x_new[i] <- found[1L]
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next
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}
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@ -212,7 +213,7 @@ as.ab <- function(x) {
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# try by removing all spaces and numbers
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if (x[i] %like% " " | x[i] %like% "[0-9]") {
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found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i])))
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if (length(found) > 0) {
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if (length(found) > 0 & !is.na(found)) {
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x_new[i] <- found[1L]
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next
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}
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@ -222,6 +223,16 @@ as.ab <- function(x) {
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x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
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}
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# take failed ATC codes apart from rest
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x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
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x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
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if (length(x_unknown_ATCs) > 0) {
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warning("These ATC codes are not (yet) in the antibiotics data set: ",
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paste('"', sort(unique(x_unknown_ATCs)), '"', sep = "", collapse = ', '),
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".",
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call. = FALSE)
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}
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if (length(x_unknown) > 0) {
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warning("These values could not be coerced to a valid antibiotic ID: ",
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paste('"', sort(unique(x_unknown)), '"', sep = "", collapse = ', '),
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@ -78,7 +78,7 @@
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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">0.7.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">0.7.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">0.7.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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">0.7.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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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">0.7.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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</span>
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</div>
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@ -232,9 +232,9 @@
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</div>
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<div id="amr-0709005" class="section level1">
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<div id="amr-0709006" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0709005" class="anchor"></a>AMR 0.7.0.9005<small> Unreleased </small>
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<a href="#amr-0709006" class="anchor"></a>AMR 0.7.0.9006<small> Unreleased </small>
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</h1>
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<div id="new" class="section level4">
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<h4 class="hasAnchor">
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@ -1106,7 +1106,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0709005">0.7.0.9005</a></li>
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<li><a href="#amr-0709006">0.7.0.9006</a></li>
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<li><a href="#amr-070">0.7.0</a></li>
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<li><a href="#amr-061">0.6.1</a></li>
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<li><a href="#amr-060">0.6.0</a></li>
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@ -78,7 +78,7 @@
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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">0.7.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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</span>
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</div>
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@ -30,31 +30,25 @@ if [ -z "$new_version" ]; then
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new_version="$current_tag.9000"
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echo
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echo "** COULD NOT CREATE NEW VERSION NUMBER! **"
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echo "Are there some unpushed changes in a new tag?? Then mind NEWS.md. Assuming sequence number 9000."
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echo "Are there some unpushed changes in a new tag? Then mind NEWS.md. Assuming sequence number 9000."
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echo
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fi
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sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
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# update 1st line of NEWS.md
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sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
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echo "First 3 lines of DESCRIPTION:"
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echo "• First 3 lines of DESCRIPTION:"
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head -3 DESCRIPTION
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echo
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echo "First line of NEWS.md:"
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echo "• First line of NEWS.md:"
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head -1 NEWS.md
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echo
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read -p "Continue (Y/n)? " choice
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case "$choice" in
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n|N ) exit 1;;
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* ) ;;
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esac
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echo
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echo "•••••••••••••••••••••••••••••••••"
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echo "• Reloading/documenting package •"
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echo "•••••••••••••••••••••••••••••••••"
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Rscript -e "devtools::load_all(quiet = TRUE)"
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echo "Documenting..."
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echo "• Documenting..."
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Rscript -e "suppressMessages(devtools::document())"
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echo "Installing..."
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echo "• Installing..."
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Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
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echo
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echo "••••••••••••••••••••••••••"
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@ -73,7 +67,7 @@ echo "••••••••••••••••••••••••
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git status --short
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echo
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read -p "Continue (Y/n)? " choice
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read -p "Pushing version ${new_version}. Continue (Y/n)? " choice
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case "$choice" in
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n|N ) exit 1;;
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* ) ;;
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