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Built site for AMR@3.0.1.9067: 935071a

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2026-06-24 17:55:11 +00:00
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2
reference/AMR-deprecated.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</small>
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2
reference/WHOCC.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</small>
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2
reference/WHONET.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</small>
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2
reference/ab_from_text.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/ab_property.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/add_custom_antimicrobials.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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">

8
reference/add_custom_microorganisms.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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">
@@ -132,12 +132,6 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_info</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Since <span style="color: #0000BB;">AMR v3.1.0</span>, `mo_kingdom()` returns the taxonomic kingdom as defined by</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Göker and Oren (2024), who formally introduced a new kingdom rank into</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prokaryotic nomenclature (DOI: 10.1099/ijsem.0.006242</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (<span style="color: #0000BB; font-style: italic;">&lt;https://doi.org/10.1099/ijsem.0.006242&gt;</span>)). <span style="font-weight: bold;">The former kingdom of Bacteria</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> was divided into four new kingdoms under the <span style="font-weight: bold;">new domain of Bacteria</span>. For the</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> old behaviour, use `mo_domain()`. This note will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $mo</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "CUSTOM1_ENTRB_ASB/"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>

6
reference/add_custom_microorganisms.md
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@@ -121,12 +121,6 @@ mo_gramstain("Enterobacter asburiae/cloacae")
#> [1] "Gram-negative"
mo_info("Enterobacter asburiae/cloacae")
#> ℹ Since AMR v3.1.0, `mo_kingdom()` returns the taxonomic kingdom as defined by
#> Göker and Oren (2024), who formally introduced a new kingdom rank into
#> prokaryotic nomenclature (DOI: 10.1099/ijsem.0.006242
#> (<https://doi.org/10.1099/ijsem.0.006242>)). The former kingdom of Bacteria
#> was divided into four new kingdoms under the new domain of Bacteria. For the
#> old behaviour, use `mo_domain()`. This note will be shown once per session.
#> $mo
#> [1] "CUSTOM1_ENTRB_ASB/"
#>

2
reference/age.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/age_groups.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/amr-tidymodels.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/amr_course.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/antibiogram.html
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@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/as.ab.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/as.av.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/as.disk.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/as.mic.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/as.mo.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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">

10
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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">
@@ -458,10 +458,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-24 <span style="color: #949494;">17:04:09</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-24 <span style="color: #949494;">17:04:09</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-24 <span style="color: #949494;">17:04:10</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-24 <span style="color: #949494;">17:04:10</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-24 <span style="color: #949494;">17:50:57</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-24 <span style="color: #949494;">17:50:57</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-24 <span style="color: #949494;">17:50:58</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-24 <span style="color: #949494;">17:50:58</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

8
reference/as.sir.md
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@@ -705,10 +705,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-06-24 17:04:09 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-24 17:04:09 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-24 17:04:10 1 DISK tobra Escherich… human 16
#> 4 2026-06-24 17:04:10 1 DISK genta Escherich… human 18
#> 1 2026-06-24 17:50:57 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-24 17:50:57 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-24 17:50:58 1 DISK tobra Escherich… human 16
#> 4 2026-06-24 17:50:58 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/av_from_text.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</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
reference/av_property.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</small>
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2
reference/availability.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</small>
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2
reference/bug_drug_combinations.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="">3.0.1.9065</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9067</small>
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2
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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@@ -7,7 +7,7 @@
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reference/microorganisms.groups.html
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reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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@@ -108,11 +108,10 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
<p>For convenience, some entries were added manually:</p><ul><li><p>~1 500 entries of <em>Salmonella</em>, such as the city-like serovars and groups A to H</p></li>
<li><p>37 species groups (such as the beta-haemolytic <em>Streptococcus</em> groups A to K, coagulase-negative <em>Staphylococcus</em> (CoNS), <em>Mycobacterium tuberculosis</em> complex, etc.), of which the group compositions are stored in the <a href="microorganisms.groups.html">microorganisms.groups</a> data set</p></li>
<p>For convenience, some entries were added manually:</p><ul><li><p>All 37 groups and complexes of the <a href="microorganisms.groups.html">microorganisms.groups</a> data set, for cross-reference (examples include beta-haemolytic <em>Streptococcus</em> groups A to K, coagulase-negative <em>Staphylococcus</em> (CoNS), <em>Mycobacterium tuberculosis</em> complex, etc.)</p></li>
<li><p>~1 500 entries of <em>Salmonella</em>, such as the city-like serovars and groups A to H</p></li>
<li><p>1 entry of <em>Blastocystis</em> (<em>B. hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
<li><p>8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)</p></li>
<li><p>9 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)</p></li>
</ul><p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R" class="external-link">found here</a>.</p>
</div>

19
reference/microorganisms.md
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@@ -188,24 +188,19 @@ are:
For convenience, some entries were added manually:
- All 37 groups and complexes of the
[microorganisms.groups](https://amr-for-r.org/reference/microorganisms.groups.md)
data set, for cross-reference (examples include beta-haemolytic
*Streptococcus* groups A to K, coagulase-negative *Staphylococcus*
(CoNS), *Mycobacterium tuberculosis* complex, etc.)
- ~1 500 entries of *Salmonella*, such as the city-like serovars and
groups A to H
- 37 species groups (such as the beta-haemolytic *Streptococcus* groups
A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium
tuberculosis* complex, etc.), of which the group compositions are
stored in the
[microorganisms.groups](https://amr-for-r.org/reference/microorganisms.groups.md)
data set
- 1 entry of *Blastocystis* (*B. hominis*), although it officially does
not exist (Noel *et al.* 2005, PMID 15634993)
- 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named
*Branhamella catarrhalis* (Catlin, 1970) though this change was never
accepted within the field of clinical microbiology
- 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown
- 9 other 'undefined' entries (unknown, unknown Gram-negatives, unknown
Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic
Gram-pos/Gram-neg bacteria)

2
reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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reference/mo_property.html
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@@ -7,7 +7,7 @@
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@@ -428,6 +428,8 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># taxonomic tree -----------------------------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_domain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
<span class="r-in"><span><span class="fu">mo_phylum</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
@@ -445,6 +447,35 @@
<span class="r-in"><span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># all in one go</span></span></span>
<span class="r-in"><span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $domain</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadota"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $class</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gammaproteobacteria"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $order</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacterales"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $family</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacteriaceae"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $genus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Klebsiella"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "pneumoniae"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $subspecies</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># full names and short names -----------------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
@@ -482,6 +513,8 @@
<span class="r-in"><span><span class="fu">mo_is_yeast</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Candida"</span>, <span class="st">"Trichophyton"</span>, <span class="st">"Klebsiella"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_group_members</span><span class="op">(</span><span class="st">"Streptococcus group A"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Streptococcus pyogenes"</span>
<span class="r-in"><span><span class="fu">mo_group_members</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="st">"Streptococcus group A"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Streptococcus group C"</span>,</span></span>
@@ -572,6 +605,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Staphylococcus epidermidis"</span>
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Staph epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Staph epidermidis"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "S. epidermidis"</span>
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Staph epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
@@ -584,6 +618,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Streptococcus agalactiae"</span>
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Streptococcus Group B"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "S. agalactiae"</span>
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
@@ -603,13 +638,13 @@
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Грамнегативні"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated</span></span></span>
<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
<span class="r-in"><span><span class="co"># mo_type is equal to mo_domain, but mo_domain will remain untranslated</span></span></span>
<span class="r-in"><span><span class="fu">mo_domain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, no effect</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Pseudomonadati"</span>
<span class="r-in"><span><span class="fu">mo_domain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, no effect</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, translated</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "细菌"</span>
<span class="r-in"><span></span></span>

45
reference/mo_property.md
View File

@@ -564,6 +564,8 @@ Data set
``` r
# taxonomic tree -----------------------------------------------------------
mo_domain("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Pseudomonadati"
mo_phylum("Klebsiella pneumoniae")
@@ -581,6 +583,35 @@ mo_species("Klebsiella pneumoniae")
mo_subspecies("Klebsiella pneumoniae")
#> [1] ""
# all in one go
mo_taxonomy("Klebsiella pneumoniae")
#> $domain
#> [1] "Bacteria"
#>
#> $kingdom
#> [1] "Pseudomonadati"
#>
#> $phylum
#> [1] "Pseudomonadota"
#>
#> $class
#> [1] "Gammaproteobacteria"
#>
#> $order
#> [1] "Enterobacterales"
#>
#> $family
#> [1] "Enterobacteriaceae"
#>
#> $genus
#> [1] "Klebsiella"
#>
#> $species
#> [1] "pneumoniae"
#>
#> $subspecies
#> [1] ""
#>
# full names and short names -----------------------------------------------
@@ -618,6 +649,8 @@ mo_url("Klebsiella pneumoniae")
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
#> [1] TRUE FALSE FALSE
mo_group_members("Streptococcus group A")
#> [1] "Streptococcus pyogenes"
mo_group_members(c(
"Streptococcus group A",
"Streptococcus group C",
@@ -708,6 +741,7 @@ mo_fullname("Staph epidermidis")
#> [1] "Staphylococcus epidermidis"
mo_fullname("Staph epidermidis", Becker = TRUE)
#> [1] "Coagulase-negative Staphylococcus (CoNS)"
mo_shortname("Staph epidermidis")
#> [1] "S. epidermidis"
mo_shortname("Staph epidermidis", Becker = TRUE)
@@ -720,6 +754,7 @@ mo_fullname("Strep agalactiae")
#> [1] "Streptococcus agalactiae"
mo_fullname("Strep agalactiae", Lancefield = TRUE)
#> [1] "Streptococcus Group B"
mo_shortname("Strep agalactiae")
#> [1] "S. agalactiae"
mo_shortname("Strep agalactiae", Lancefield = TRUE)
@@ -739,13 +774,13 @@ mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#> [1] "Грамнегативні"
# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
mo_kingdom("Klebsiella pneumoniae")
#> [1] "Pseudomonadati"
# mo_type is equal to mo_domain, but mo_domain will remain untranslated
mo_domain("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae")
#> [1] "Bacteria"
mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#> [1] "Pseudomonadati"
mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
#> [1] "Bacteria"
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
#> [1] "细菌"

2
reference/mo_source.html
View File

@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -7,7 +7,7 @@
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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