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(v1.7.1.9057) NAs in get_episode()
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Package: AMR
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Version: 1.7.1.9056
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Date: 2021-11-29
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Version: 1.7.1.9057
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Date: 2021-12-02
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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5
NEWS.md
5
NEWS.md
@ -1,5 +1,5 @@
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# `AMR` 1.7.1.9056
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## <small>Last updated: 29 November 2021</small>
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# `AMR` 1.7.1.9057
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## <small>Last updated: 2 December 2021</small>
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### Breaking changes
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* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
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@ -56,6 +56,7 @@
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* The `mdro()` function now returns `NA` for all rows that have no test results
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* The `species_id` column in the `microorganisms` data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and `mo_url()` has been updated to reflect this change.
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* Fixed a small bug in the functions `get_episode()` and `is_new_episode()`
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* `get_episode()` and `is_new_episode()` can now cope with `NA`s
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### Other
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* This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
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12
R/episode.R
12
R/episode.R
@ -105,7 +105,7 @@
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#' }
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#' }
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get_episode <- function(x, episode_days, ...) {
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meet_criteria(x, allow_class = c("Date", "POSIXt"))
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meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
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meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
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exec_episode(x = x,
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@ -117,7 +117,7 @@ get_episode <- function(x, episode_days, ...) {
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#' @rdname get_episode
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#' @export
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is_new_episode <- function(x, episode_days, ...) {
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meet_criteria(x, allow_class = c("Date", "POSIXt"))
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meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
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meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
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exec_episode(x = x,
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@ -131,13 +131,13 @@ exec_episode <- function(x, type, episode_days, ...) {
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# since x is now in seconds, get seconds from episode_days as well
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episode_seconds <- episode_days * 60 * 60 * 24
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if (length(x) == 1) {
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if (length(x) == 1) { # this will also match 1 NA, which is fine
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if (type == "logical") {
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return(TRUE)
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} else if (type == "sequential") {
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return(1)
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}
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} else if (length(x) == 2) {
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} else if (length(x) == 2 && !all(is.na(x))) {
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if (max(x) - min(x) >= episode_seconds) {
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if (type == "logical") {
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return(c(TRUE, TRUE))
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@ -182,5 +182,7 @@ exec_episode <- function(x, type, episode_days, ...) {
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}
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ord <- order(x)
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run_episodes(x[ord], episode_seconds)[order(ord)]
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out <- run_episodes(x[ord], episode_seconds)[order(ord)]
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out[is.na(x) & ord != 1] <- NA # every NA but the first must remain NA
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out
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}
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Binary file not shown.
@ -30,6 +30,8 @@
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<![endif]-->
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</head>
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<body data-spy="scroll" data-target="#toc">
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<div class="container template-article">
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<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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@ -42,7 +44,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9057</span>
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</span>
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</div>
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@ -167,7 +169,7 @@
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</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
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<a href="https://github.com/msberends/AMR">
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<a href="https://github.com/msberends/AMR" class="external-link">
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<span class="fab fa-github"></span>
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Source Code
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@ -183,14 +185,14 @@
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</header><script src="datasets_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
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</header><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 class="date">29 November 2021</h4>
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<h4 data-toc-skip class="date">02 December 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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</div>
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@ -202,42 +204,42 @@
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<p class="dataset-within-r">
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If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
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</p>
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<div id="microorganisms-currently-accepted-names" class="section level2">
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<h2 class="hasAnchor">
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<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
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<div class="section level2">
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<h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
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</h2>
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<p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</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>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
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<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 29 November 2021 10:22:24 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
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<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds">R file</a> (1.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
|
||||
</li>
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||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt">plain text file</a> (13.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas">SAS file</a> (30.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
|
||||
</li>
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||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (16.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (16.3 MB)<br>
|
||||
</li>
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||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (27.5 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (27.5 MB)</li>
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</ul>
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<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
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<div id="source" class="section level3">
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<h3 class="hasAnchor">
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<a href="#source" class="anchor"></a>Source</h3>
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<div class="section level3">
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<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
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</h3>
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<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
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<ul>
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<li>
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<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
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<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
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<li>
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<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
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<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
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<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
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<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
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</ul>
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</div>
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<div id="example-content" class="section level3">
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<h3 class="hasAnchor">
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<a href="#example-content" class="anchor"></a>Example content</h3>
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<div class="section level3">
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<h3 id="example-content">Example content<a class="anchor" aria-label="anchor" href="#example-content"></a>
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</h3>
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<p>Included (sub)species per taxonomic kingdom:</p>
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<table class="table">
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<thead><tr class="header">
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@ -272,24 +274,24 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
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</tbody>
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</table>
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<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
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<table class="table">
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<table style="width:100%;" class="table">
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<colgroup>
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<col width="4%">
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<col width="5%">
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<col width="8%">
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<col width="3%">
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<col width="5%">
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<col width="7%">
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<col width="6%">
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<col width="6%">
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<col width="7%">
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<col width="4%">
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<col width="4%">
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<col width="4%">
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<col width="3%">
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<col width="8%">
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<col width="11%">
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<col width="9%">
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<col width="4%">
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<col width="2%">
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<col width="4%">
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<col width="15%">
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<col width="16%">
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</colgroup>
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<thead><tr class="header">
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<th align="center">mo</th>
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@ -323,8 +325,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<td align="center"></td>
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<td align="center">genus</td>
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<td align="center"></td>
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<td align="center">bc4fdde6867d5ecfc728000b0bfb49a3</td>
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<td align="center">CoL</td>
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<td align="center">515602</td>
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<td align="center">LPSN</td>
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<td align="center">1</td>
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<td align="center">64735005</td>
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</tr>
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@ -341,8 +343,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<td align="center"></td>
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<td align="center">species</td>
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<td align="center">Huys et al., 2003</td>
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<td align="center">36618b1ed3b8b7e5a61f40eb9386e63c</td>
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<td align="center">CoL</td>
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<td align="center">776053</td>
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<td align="center">LPSN</td>
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<td align="center">1</td>
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<td align="center">419388003</td>
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</tr>
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@ -359,8 +361,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<td align="center"></td>
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<td align="center">species</td>
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<td align="center">Castellani et al., 1919</td>
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<td align="center">3254b3db31bf16fdde669ac57bf8c4fe</td>
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<td align="center">CoL</td>
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<td align="center">776057</td>
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<td align="center">LPSN</td>
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<td align="center">1</td>
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<td align="center">1095001000112106, 715307006, 737528008, …</td>
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</tr>
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@ -377,8 +379,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<td align="center"></td>
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<td align="center">species</td>
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<td align="center">Farmer et al., 1985</td>
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<td align="center">82d98b10c456ce5f4c8c515f4e1567e2</td>
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<td align="center">CoL</td>
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<td align="center">776059</td>
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<td align="center">LPSN</td>
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<td align="center">1</td>
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<td align="center">72461005</td>
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</tr>
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@ -395,8 +397,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<td align="center"></td>
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<td align="center">species</td>
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<td align="center">Brenner et al., 1983</td>
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<td align="center">b16086aee36e3b46b565510083ab4b65</td>
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<td align="center">CoL</td>
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<td align="center">776060</td>
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<td align="center">LPSN</td>
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<td align="center">1</td>
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<td align="center">85786000</td>
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</tr>
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@ -422,41 +424,41 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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</table>
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</div>
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</div>
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<div id="microorganisms-previously-accepted-names" class="section level2">
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<h2 class="hasAnchor">
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<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
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<div class="section level2">
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<h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
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</h2>
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<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
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<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
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||||
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.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/microorganisms.old.rds">R file</a> (0.2 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx">Excel file</a> (0.5 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt">plain text file</a> (1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas">SAS file</a> (2.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav">SPSS file</a> (1.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta">Stata file</a> (2 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
|
||||
</ul>
|
||||
<div id="source-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#source-1" class="anchor"></a>Source</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
|
||||
</h3>
|
||||
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
|
||||
<li>
|
||||
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="example-content-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#example-content-1" class="anchor"></a>Example content</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
|
||||
</h3>
|
||||
<p>Example rows when filtering on <em>Escherichia</em>:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
@ -488,41 +490,41 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div id="antibiotic-agents" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
|
||||
</h2>
|
||||
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 28 November 2021 15:08:22 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.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/antibiotics.rds">R file</a> (32 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx">Excel file</a> (65 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt">plain text file</a> (0.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas">SAS file</a> (1.8 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (0.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta">Stata file</a> (0.3 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
|
||||
</ul>
|
||||
<div id="source-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#source-2" class="anchor"></a>Source</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
|
||||
</h3>
|
||||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
|
||||
<li><a href="https://whonet.org">WHONET software 2019</a></li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
|
||||
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="example-content-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#example-content-2" class="anchor"></a>Example content</h3>
|
||||
<table class="table">
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-2">Example content<a class="anchor" aria-label="anchor" href="#example-content-2"></a>
|
||||
</h3>
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="1%">
|
||||
<col width="2%">
|
||||
@ -656,39 +658,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div id="antiviral-agents" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
|
||||
</h2>
|
||||
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.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/antivirals.rds">R file</a> (5 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx">Excel file</a> (14 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt">plain text file</a> (16 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas">SAS file</a> (80 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav">SPSS file</a> (68 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta">Stata file</a> (67 kB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
|
||||
</ul>
|
||||
<div id="source-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#source-3" class="anchor"></a>Source</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
|
||||
</h3>
|
||||
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="example-content-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#example-content-3" class="anchor"></a>Example content</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="4%">
|
||||
@ -783,34 +785,34 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div id="intrinsic-bacterial-resistance" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
|
||||
</h2>
|
||||
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</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 6 October 2021 14:38:29 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">R file</a> (69 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (69 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel file</a> (0.9 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt">plain text file</a> (3.5 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (3.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas">SAS file</a> (7.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (7.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file</a> (5.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (5.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta">Stata file</a> (7 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (7 MB)</li>
|
||||
</ul>
|
||||
<div id="source-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#source-4" class="anchor"></a>Source</h3>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2</a> (2020).</p>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
</h3>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2</a> (2020).</p>
|
||||
</div>
|
||||
<div id="example-content-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#example-content-4" class="anchor"></a>Example content</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
|
||||
</h3>
|
||||
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
@ -998,34 +1000,34 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
|
||||
</h2>
|
||||
<p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.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/rsi_translation.rds">R file</a> (37 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (37 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.8 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.8 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (2.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.5 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
|
||||
</ul>
|
||||
<div id="source-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#source-5" class="anchor"></a>Source</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
|
||||
</h3>
|
||||
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
|
||||
</div>
|
||||
<div id="example-content-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#example-content-5" class="anchor"></a>Example content</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="8%">
|
||||
@ -1128,35 +1130,35 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
<div id="dosage-guidelines-from-eucast" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
|
||||
</h2>
|
||||
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.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/dosage.rds">R file</a> (3 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx">Excel file</a> (14 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt">plain text file</a> (15 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas">SAS file</a> (52 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav">SPSS file</a> (45 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta">Stata file</a> (44 kB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
|
||||
</ul>
|
||||
<div id="source-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#source-6" class="anchor"></a>Source</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
|
||||
</h3>
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
|
||||
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
</div>
|
||||
<div id="example-content-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#example-content-6" class="anchor"></a>Example content</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">ab</th>
|
||||
@ -1253,11 +1255,13 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
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|
||||
|
||||
</footer>
|
||||
@ -1266,5 +1270,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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||||
|
||||
|
||||
|
||||
|
||||
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|
||||
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|
||||
|
||||
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Reference in New Issue
Block a user