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(v1.1.0.9016) small fix

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dr. M.S. (Matthijs) Berends 2020-05-21 12:28:57 +02:00
parent 743f9a5364
commit 1b1e243d14
18 changed files with 30 additions and 33 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.1.0.9015 Version: 1.1.0.9016
Date: 2020-05-20 Date: 2020-05-21
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.1.0.9015 # AMR 1.1.0.9016
## <small>Last updated: 20-May-2020</small> ## <small>Last updated: 21-May-2020</small>
### Breaking ### Breaking
* Removed code dependency on all other R packages, making this package fully independent on the development process of others. This is a major code change, but will probably not be noticeable by most users. * Removed code dependency on all other R packages, making this package fully independent on the development process of others. This is a major code change, but will probably not be noticeable by most users.

4
R/aa_helper_functions.R
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@ -252,9 +252,9 @@ dataset_UTF8_to_ASCII <- function(df) {
} }
# replace crayon::has_color # replace crayon::has_color, but now also FALSE on non-interactive mode
has_colour <- function() { has_colour <- function() {
if (Sys.getenv("TERM") == "dumb") { if (Sys.getenv("TERM") == "dumb" | !interactive()) {
return(FALSE) return(FALSE)
} }
if (tolower(Sys.info()["sysname"]) == "windows") { if (tolower(Sys.info()["sysname"]) == "windows") {

2
R/ab.R
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@ -215,6 +215,8 @@ as.ab <- function(x, ...) {
x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling) x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
# replace multiple same characters to single one with '+', like "ll" -> "l+" # replace multiple same characters to single one with '+', like "ll" -> "l+"
x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling) x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
# replace spaces and slashes with a possibility on both
x_spelling <- gsub("[ /]", "( |/)", x_spelling)
# try if name starts with it # try if name starts with it
found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab

4
R/atc_online.R
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@ -128,7 +128,7 @@ atc_online_property <- function(atc_code,
returnvalue <- rep(NA_character_, length(atc_code)) returnvalue <- rep(NA_character_, length(atc_code))
} }
progress <- progress_estimated(n = length(atc_code)) progress <- progress_estimated(n = length(atc_code), 3)
on.exit(close(progress)) on.exit(close(progress))
for (i in seq_len(length(atc_code))) { for (i in seq_len(length(atc_code))) {
@ -160,7 +160,7 @@ atc_online_property <- function(atc_code,
as.data.frame(stringsAsFactors = FALSE) as.data.frame(stringsAsFactors = FALSE)
# case insensitive column names # case insensitive column names
colnames(tbl) <- tolower(colnames(tbl)) %>% gsub("^atc.*", "atc", .) colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
if (length(tbl) == 0) { if (length(tbl) == 0) {
warning("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call. = FALSE) warning("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call. = FALSE)

2
R/eucast_rules.R
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@ -599,7 +599,7 @@ eucast_rules <- function(x,
} }
} }
if (!any(c("other", "all") %in% rules, na.rm = TRUE)) { if (info == TRUE & !any(c("other", "all") %in% rules, na.rm = TRUE)) {
cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n")) cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n"))
} }

BIN
R/sysdata.rda
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3
data-raw/eucast_rules.tsv
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@ -16,10 +16,13 @@ genus like .* AMX S AMP S Non-EUCAST: inherit amoxicillin results for unavailabl
genus like .* AMX I AMP I Non-EUCAST: inherit amoxicillin results for unavailable ampicillin Other rules genus like .* AMX I AMP I Non-EUCAST: inherit amoxicillin results for unavailable ampicillin Other rules
genus like .* AMX R AMP R Non-EUCAST: inherit amoxicillin results for unavailable ampicillin Other rules genus like .* AMX R AMP R Non-EUCAST: inherit amoxicillin results for unavailable ampicillin Other rules
genus like .* AMC R AMP, AMX R Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R Other rules genus like .* AMC R AMP, AMX R Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R Other rules
genus like .* SAM R AMP, AMX R Non-EUCAST: set ampicillin = R where ampicillin/sulbactam = R Other rules
genus like .* TZP R PIP R Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R Other rules genus like .* TZP R PIP R Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R Other rules
genus like .* SXT R TMP R Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R Other rules genus like .* SXT R TMP R Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R Other rules
genus like .* AMP S AMC S Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S Other rules genus like .* AMP S AMC S Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S Other rules
genus like .* AMX S AMC S Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S Other rules genus like .* AMX S AMC S Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S Other rules
genus like .* AMP S SAM S Non-EUCAST: set ampicillin/sulbactam = S where ampicillin = S Other rules
genus like .* AMX S SAM S Non-EUCAST: set ampicillin/sulbactam = S where ampicillin = S Other rules
genus like .* PIP S TZP S Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S Other rules genus like .* PIP S TZP S Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S Other rules
genus like .* TMP S SXT S Non-EUCAST: set trimethoprim/sulfa = S where trimethoprim = S Other rules genus like .* TMP S SXT S Non-EUCAST: set trimethoprim/sulfa = S where trimethoprim = S Other rules
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints

Can't render this file because it contains an unexpected character in line 6 and column 96.

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>

12
docs/articles/EUCAST.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to apply EUCAST rules</h1> <h1 data-toc-skip>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 May 2020</h4> <h4 class="date">21 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="hidden name"><code>EUCAST.Rmd</code></div> <div class="hidden name"><code>EUCAST.Rmd</code></div>
@ -218,10 +218,6 @@
<span class="co"># 2 Escherichia S</span> <span class="co"># 2 Escherichia S</span>
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">oops</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>) <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">oops</span>, <span class="kw">info</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
<span class="co"># [31m</span>
<span class="co"># Skipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.</span>
<span class="co"># Use eucast_rules(..., rules = "all") to also apply those rules.</span>
<span class="co"># [39m</span>
<span class="co"># mo ampicillin</span> <span class="co"># mo ampicillin</span>
<span class="co"># 1 Klebsiella R</span> <span class="co"># 1 Klebsiella R</span>
<span class="co"># 2 Escherichia S</span></pre></body></html></div> <span class="co"># 2 Escherichia S</span></pre></body></html></div>
@ -305,10 +301,6 @@
</tbody> </tbody>
</table> </table>
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div> <div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="no">data</span>)</pre></body></html></div>
<pre><code># [31m
# Skipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.
# Use eucast_rules(..., rules = "all") to also apply those rules.
# [39m</code></pre>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="left">mo</th> <th align="left">mo</th>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>

12
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1-1-0-9015" class="section level1"> <div id="amr-1-1-0-9016" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9015"> <h1 class="page-header" data-toc-text="1.1.0.9016">
<a href="#amr-1-1-0-9015" class="anchor"></a>AMR 1.1.0.9015<small> Unreleased </small> <a href="#amr-1-1-0-9016" class="anchor"></a>AMR 1.1.0.9016<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-20-may-2020" class="section level2"> <div id="last-updated-21-may-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-20-may-2020" class="anchor"></a><small>Last updated: 20-May-2020</small> <a href="#last-updated-21-may-2020" class="anchor"></a><small>Last updated: 21-May-2020</small>
</h2> </h2>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-05-20T09:55Z last_built: 2020-05-21T10:28Z
urls: urls:
reference: https://msberends.gitlab.io/AMR/reference reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles article: https://msberends.gitlab.io/AMR/articles

2
docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9016</span>
</span> </span>
</div> </div>