mirror of
https://github.com/msberends/AMR.git
synced 2026-10-01 04:13:33 +02:00
Built site for AMR: 2.1.1.9008@35963ca
This commit is contained in:
github-actions committed
1 parent
1460fadf40
commit
8611815e20
81 files changed
+355
-285
No files matched your search
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9004</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -261,7 +261,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p><strong>Note:</strong> This function does not translate MIC values to SIR values. Use <code><a href="as.sir.html">as.sir()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
|
||||
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until December 11th, 2022, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
|
||||
<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until January 8th, 2024, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
|
||||
<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
|
||||
|
||||
|
||||
@@ -289,7 +289,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
|
||||
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
|
||||
<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href="mdro.html">mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://www.whocc.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
|
||||
<p>Amikacin (<code>AMK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no" class="external-link">J01GB06</a>), amoxicillin (<code>AMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" class="external-link">J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no" class="external-link">J01CR02</a>), ampicillin (<code>AMP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no" class="external-link">J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no" class="external-link">J01CR01</a>), arbekacin (<code>ARB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no" class="external-link">J01GB12</a>), aspoxicillin (<code>APX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no" class="external-link">J01CA19</a>), azidocillin (<code>AZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no" class="external-link">J01CE04</a>), azithromycin (<code>AZM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no" class="external-link">J01FA10</a>), azlocillin (<code>AZL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no" class="external-link">J01CA09</a>), aztreonam (<code>ATM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no" class="external-link">J01DF01</a>), bacampicillin (<code>BAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no" class="external-link">J01CA06</a>), bekanamycin (<code>BEK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no" class="external-link">J01GB13</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no" class="external-link">J01CE08</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no" class="external-link">J01CE10</a>), benzylpenicillin (<code>PEN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no" class="external-link">J01CE01</a>), besifloxacin (<code>BES</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no" class="external-link">S01AE08</a>), biapenem (<code>BIA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no" class="external-link">J01DH05</a>), carbenicillin (<code>CRB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no" class="external-link">J01CA03</a>), carindacillin (<code>CRN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no" class="external-link">J01CA05</a>), cefacetrile (<code>CAC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no" class="external-link">J01DB10</a>), cefaclor (<code>CEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no" class="external-link">J01DC04</a>), cefadroxil (<code>CFR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no" class="external-link">J01DB05</a>), cefalexin (<code>LEX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no" class="external-link">J01DB01</a>), cefaloridine (<code>RID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no" class="external-link">J01DB02</a>), cefalotin (<code>CEP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no" class="external-link">J01DB03</a>), cefamandole (<code>MAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no" class="external-link">J01DC03</a>), cefapirin (<code>HAP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no" class="external-link">J01DB08</a>), cefatrizine (<code>CTZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no" class="external-link">J01DB07</a>), cefazedone (<code>CZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no" class="external-link">J01DB06</a>), cefazolin (<code>CZO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no" class="external-link">J01DB04</a>), cefcapene (<code>CCP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no" class="external-link">J01DD17</a>), cefdinir (<code>CDR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no" class="external-link">J01DD15</a>), cefditoren (<code>DIT</code>, Line truncated
|
||||
<p>Amikacin (<code>AMK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no" class="external-link">J01GB06</a>), amoxicillin (<code>AMX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" class="external-link">J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no" class="external-link">J01CR02</a>), ampicillin (<code>AMP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no" class="external-link">J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no" class="external-link">J01CR01</a>), apramycin (<code>APR</code>, <a href="https://www.whocc.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no" class="external-link">QA07AA92</a>), arbekacin (<code>ARB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no" class="external-link">J01GB12</a>), aspoxicillin (<code>APX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no" class="external-link">J01CA19</a>), azidocillin (<code>AZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no" class="external-link">J01CE04</a>), azithromycin (<code>AZM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no" class="external-link">J01FA10</a>), azlocillin (<code>AZL</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no" class="external-link">J01CA09</a>), aztreonam (<code>ATM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no" class="external-link">J01DF01</a>), bacampicillin (<code>BAM</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no" class="external-link">J01CA06</a>), bekanamycin (<code>BEK</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no" class="external-link">J01GB13</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no" class="external-link">J01CE08</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no" class="external-link">J01CE10</a>), benzylpenicillin (<code>PEN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no" class="external-link">J01CE01</a>), besifloxacin (<code>BES</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no" class="external-link">S01AE08</a>), biapenem (<code>BIA</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no" class="external-link">J01DH05</a>), carbenicillin (<code>CRB</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no" class="external-link">J01CA03</a>), carindacillin (<code>CRN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no" class="external-link">J01CA05</a>), cefacetrile (<code>CAC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no" class="external-link">J01DB10</a>), cefaclor (<code>CEC</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no" class="external-link">J01DC04</a>), cefadroxil (<code>CFR</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no" class="external-link">J01DB05</a>), cefalexin (<code>LEX</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no" class="external-link">J01DB01</a>), cefaloridine (<code>RID</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no" class="external-link">J01DB02</a>), cefalotin (<code>CEP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no" class="external-link">J01DB03</a>), cefamandole (<code>MAN</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no" class="external-link">J01DC03</a>), cefapirin (<code>HAP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no" class="external-link">J01DB08</a>), cefatrizine (<code>CTZ</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no" class="external-link">J01DB07</a>), cefazedone (<code>CZD</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no" class="external-link">J01DB06</a>), cefazolin (<code>CZO</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no" class="external-link">J01DB04</a>), cefcapene (<code>CCP</code>, <a href="https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no" class="external-link">J01DD17</a>), cefdinir (<code>CDR</Line truncated
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
Reference in new issue
Block a user