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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -168,7 +168,7 @@
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<li><p><code>Inducible clindamycin resistance</code><br> Clindamycin can be induced?</p></li>
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<li><p><code>Comment</code><br> Other comments</p></li>
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<li><p><code>Date of data entry</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> this data was entered in WHONET</p></li>
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<li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.rsi.html">as.rsi()</a></code>.</p></li>
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<li><p><code>AMP_ND10:CIP_EE</code><br> 0 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.sir.html">as.sir()</a></code>.</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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@ -178,6 +178,90 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">WHONET</span></span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>* Transform your old 'rsi' class to the new 'sir' class with as.sir()</span>
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<span class="r-wrn co"><span class="r-pr">#></span> using e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> your_data %>% mutate_if(is.rsi, as.sir)</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 500 × 53</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identif…¹ Speci…² Organ…³ Country Labor…⁴ Last …⁵ First…⁶ Sex Age Age c…⁷</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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@ -197,7 +281,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Carbapenemase <lgl>, `MRSA screening test` <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Inducible clindamycin resistance` <lgl>, Comment <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Date of data entry` <date>, AMP_ND10 <rsi>, AMC_ED20 <rsi>, …</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Date of data entry` <date>, AMP_ND10 <rsi[!]>, AMC_ED20 <rsi[!]>, …</span></span>
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</code></pre></div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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