P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 13:21:50 +02:00
Code Releases Activity

mo codes for WHONET

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-08 16:06:54 +01:00
parent 3d3366faf7
commit ed30312048
60 changed files with 1103 additions and 615 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
docs/reference/eucast_rules.html
View File

@ -294,7 +294,7 @@
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected</p></td>
<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative <code>data.frame</code> with changes will be returned as output.</p></td>
</tr>
<tr>
<th>amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc</th>
@ -320,7 +320,7 @@
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with verbose info.</p>
<p>The input of <code>tbl</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with all original and new values of the affected bug-drug combinations.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -423,7 +423,9 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># 4 Klebsiella pneumoniae - - - - - S S</span>
<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='st'>"mo"</span>) <span class='co'># 18 results are forced as R or S</span>
<span class='co'># apply EUCAST rules: 18 results are forced as R or S</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>)
<span class='no'>b</span>
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
@ -432,6 +434,11 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='co'># 3 Escherichia coli R - - - - R S</span>
<span class='co'># 4 Klebsiella pneumoniae R R - - - R S</span>
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class='co'># do not apply EUCAST rules, but rather get a a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span>
<span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">