P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 18:22:02 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9062@8da2467

Browse Source
This commit is contained in:
github-actions
2022-12-11 23:23:03 +00:00
parent 7b50c6e9f7
commit 64384886d7
101 changed files with 4953 additions and 842 deletions
Download Patch File Download Diff File Expand all files Collapse all files

62
articles/datasets.html
View File

@ -38,7 +38,7 @@
<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="">1.8.2.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9062</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">
@ -187,7 +187,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 48,883 rows and 22 columns, containing the following
<p>A data set with 48,050 rows and 22 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -196,7 +196,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 December 2022 12:37:08 UTC. Find more info
<p>It was last updated on 11 December 2022 23:14:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -204,25 +204,25 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (1.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
text file</a> (10.6 MB)<br>
text file</a> (10.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
Excel workbook</a> (4.8 MB)<br>
Excel workbook</a> (4.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
Feather file</a> (5.1 MB)<br>
Feather file</a> (5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
Parquet file</a> (2.5 MB)<br>
Parquet file</a> (2.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
data file</a> (47.8 MB)<br>
data file</a> (46.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
SPSS Statistics data file</a> (15.8 MB)<br>
SPSS Statistics data file</a> (15.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
DTA file</a> (43.8 MB)</li>
DTA file</a> (43.4 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
the first 50 SNOMED codes per record, as their file size would otherwise
@ -240,9 +240,9 @@ and the Global Biodiversity Information Facility (GBIF):</p>
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
International Journal of Systematic and Evolutionary Microbiology, 70,
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 12 September, 2022.</li>
<li>GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy.
Checklist dataset . Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 12 September, 2022.</li>
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on 11 December, 2022.</li>
<li>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on 11 December, 2022.</li>
<li>Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
@ -261,27 +261,27 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<tbody>
<tr class="odd">
<td align="center">(unknown kingdom)</td>
<td align="center">5</td>
<td align="center">1</td>
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1,524</td>
<td align="center">1,061</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1,237</td>
<td align="center">1,291</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">33,716</td>
<td align="center">34,398</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7,450</td>
<td align="center">6,852</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">4,951</td>
<td align="center">4,447</td>
</tr>
</tbody>
</table>
@ -355,7 +355,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">482</td>
<td align="center"></td>
<td align="center">3221780</td>
<td align="center">4899</td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">407310004, 407251000, 407281008, …</td>
@ -450,7 +450,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
<td align="center">776057</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center">6110934</td>
<td align="center">11286021</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1</td>
@ -1042,37 +1042,37 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134,659 rows and 2 columns, containing the following
<p>A data set with 206,832 rows and 2 columns, containing the following
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 31 October 2022 10:19:06 UTC. Find more info
<p>It was last updated on 11 December 2022 23:14:56 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original
R Data Structure (RDS) file</a> (78 kB)<br>
R Data Structure (RDS) file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
text file</a> (5.1 MB)<br>
text file</a> (7.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.3 MB)<br>
Excel workbook</a> (1.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
Feather file</a> (1.2 MB)<br>
Feather file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.parquet" class="external-link">Apache
Parquet file</a> (0.2 MB)<br>
Parquet file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
data file</a> (9.8 MB)<br>
data file</a> (17.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
SPSS Statistics data file</a> (7.4 MB)<br>
SPSS Statistics data file</a> (11.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
DTA file</a> (9.5 MB)</li>
DTA file</a> (17.2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>