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6
articles/AMR.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">
@@ -847,14 +847,14 @@ language to be Spanish using the <code>language</code> argument:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Gram-negative</td>
<td align="left">Gram negativo</td>
<td align="left">98% (96-99%,N=256)</td>
<td align="left">96% (95-98%,N=684)</td>
<td align="left">0% (0-10%,N=35)</td>
<td align="left">96% (94-97%,N=686)</td>
</tr>
<tr class="even">
<td align="left">Gram-positive</td>
<td align="left">Gram positivo</td>
<td align="left">0% (0-1%,N=436)</td>
<td align="left">63% (60-66%,N=1170)</td>
<td align="left">0% (0-1%,N=436)</td>

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articles/AMR.md
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@@ -672,8 +672,8 @@ antibiogram(example_isolates,
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
|:--------------|:-------------------|:--------------------|:----------------|:-------------------|
| Gram-negative | 98% (96-99%,N=256) | 96% (95-98%,N=684) | 0% (0-10%,N=35) | 96% (94-97%,N=686) |
| Gram-positive | 0% (0-1%,N=436) | 63% (60-66%,N=1170) | 0% (0-1%,N=436) | 34% (31-38%,N=665) |
| Gram negativo | 98% (96-99%,N=256) | 96% (95-98%,N=684) | 0% (0-10%,N=35) | 96% (94-97%,N=686) |
| Gram positivo | 0% (0-1%,N=436) | 63% (60-66%,N=1170) | 0% (0-1%,N=436) | 34% (31-38%,N=665) |
#### Combined Antibiogram

2
articles/AMR_for_Python.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">

2
articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">

2
articles/EUCAST.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">

4
articles/PCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">
@@ -194,7 +194,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

2
articles/PCA.md
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@@ -113,7 +113,7 @@ summary(pca_result)
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> Importance of components:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
```

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articles/WHONET.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">

12
articles/WISCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">
@@ -363,14 +363,14 @@ all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></c
<colgroup>
<col width="12%">
<col width="21%">
<col width="33%">
<col width="34%">
<col width="32%">
</colgroup>
<thead><tr class="header">
<th align="left">Grupo sindrómico</th>
<th align="left">Amoxicillin/ácido clavulánico</th>
<th align="left">Amoxicillin/ácido clavulánico + Ciprofloxacin</th>
<th align="left">Amoxicillin/ácido clavulánico + Gentamicina</th>
<th align="left">Syndromic Grupo</th>
<th align="left">Amoxicilina/clavulanic acid</th>
<th align="left">Amoxicilina/clavulanic acid + Ciprofloxacina</th>
<th align="left">Amoxicilina/clavulanic acid + Gentamicina</th>
</tr></thead>
<tbody>
<tr class="odd">

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articles/WISCA.md
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@@ -207,10 +207,10 @@ wisca(data,
language = "Spanish")
```
| Grupo sindrómico | Amoxicillin/ácido clavulánico | Amoxicillin/ácido clavulánico + Ciprofloxacin | Amoxicillin/ácido clavulánico + Gentamicina |
|:-----------------|:------------------------------|:----------------------------------------------|:--------------------------------------------|
| No UCI | 70% (67.8-72.4%) | 85.3% (83.3-87.2%) | 87% (85.3-88.8%) |
| UCI | 80.9% (77.7-83.9%) | 88.2% (85.5-90.6%) | 90.9% (88.7-93%) |
| Syndromic Grupo | Amoxicilina/clavulanic acid | Amoxicilina/clavulanic acid + Ciprofloxacina | Amoxicilina/clavulanic acid + Gentamicina |
|:----------------|:----------------------------|:---------------------------------------------|:------------------------------------------|
| No UCI | 70% (67.8-72.4%) | 85.3% (83.3-87.2%) | 87% (85.3-88.8%) |
| UCI | 80.9% (77.7-83.9%) | 88.2% (85.5-90.6%) | 90.9% (88.7-93%) |
## Sensible defaults, which can be customised

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articles/datasets.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">

2
articles/index.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9012</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9013</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">