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(v1.3.0.9001) website update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
parent 0d9602a6a9
commit 7d16bec21f
79 changed files with 2221 additions and 1974 deletions
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58
docs/reference/ab_from_text.html
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@@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@@ -236,12 +236,12 @@
</div>
<pre class="usage"><span class='fu'>ab_from_text</span>(
<span class='no'>text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>thorough_search</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>
<span class='kw'>text</span>,
type = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
collapse = <span class='kw'>NULL</span>,
translate_ab = <span class='fl'>FALSE</span>,
thorough_search = <span class='kw'>NULL</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -312,31 +312,31 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'>ab_from_text</span>(<span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"dose"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type = <span class='st'>"dose"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type = <span class='st'>"admin"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>", "</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, collapse = <span class='st'>", "</span>)
<span class='co'># if you want to know which antibiotic groups were administered, do e.g.:</span>
<span class='no'>abx</span> <span class='kw'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='no'>abx</span><span class='kw'>[[</span><span class='fl'>1</span>]])
<span class='kw'>abx</span> <span class='op'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='kw'>abx</span>[[<span class='fl'>1</span>]])
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
<span class='st'>"started on doxy iv today"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx_codes</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),
<span class='kw'>abx_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>),
<span class='kw'>abx_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>),
<span class='kw'>abx_coll</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx_coll_names</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>),
<span class='kw'>abx_coll_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx_coll_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>))
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='fu'><a href='https://tibble.tidyverse.org/reference/tibble.html'>tibble</a></span>(clinical_text = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
<span class='st'>"started on doxy iv today"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(abx_codes = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>),
abx_doses = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, type = <span class='st'>"doses"</span>),
abx_admin = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, type = <span class='st'>"admin"</span>),
abx_coll = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, collapse = <span class='st'>"|"</span>),
abx_coll_names = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
collapse = <span class='st'>"|"</span>,
translate_ab = <span class='st'>"name"</span>),
abx_coll_doses = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
type = <span class='st'>"doses"</span>,
collapse = <span class='st'>"|"</span>),
abx_coll_admin = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
type = <span class='st'>"admin"</span>,
collapse = <span class='st'>"|"</span>))
}</pre>
</div>
@@ -354,7 +354,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
</footer>