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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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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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@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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, Chinese, Czech, Danish, Dutch, Finnish,
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">

13
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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -74,10 +74,13 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Meropenem"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"flucloxacillin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "culpen" "floxacillin" "floxacillinsodium" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "floxapen" "floxapensodiumsalt" "fluclox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "flucloxacilina" "flucloxacilline" "flucloxacillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "fluorochloroxacillin" "staphylex" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "bactopen" "cloxacap" "cloxacillinhydrate" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "cloxypen" "floxacillin" "floxacillinanhydrous"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "floxapen" "floxapensalt" "fluclomix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "flucloxacilina" "flucloxacilline" "flucloxacillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "flucloxin" "fluorochloroxacillin" "galfloxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "latocillin" "orbeninhydrate" "rimaflox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "staphobristol" "zoxin" </span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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_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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">

128
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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -175,43 +175,55 @@
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 33613</span>
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillinhydrate" "amoxicillinum" "amoxiden" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxil" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxycillin" "amoxyke" "anemolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "aspenil" "atoksilin" "biomox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "bristamox" "cemoxin" "clamoxyl" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "damoxy" "delacillin" "demoksil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "dispermox" "efpenix" "flemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "hiconcil" "histocillin" "hydroxyampicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "ibiamox" "imacillin" "lamoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "largopen" "metafarmacapsules" "metifarmacapsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "moksilin" "moxacin" "moxatag" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "ospamox" "pamoxicillin" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "promoxil" "remoxil" "robamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "sawamoxpm" "tolodina" "topramoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "unicillin" "utimox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "acuotricina" "alfamox" "alfida" "amitron" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "amoclen" "amodex" "amoksicillin" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "amopen" "amopenixin" "amophar" "amoran" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxi" "amoxicaps" "amoxicilina" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "amoxicillinum" "amoxidal" "amoxiden" "amoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "amoxillat" "amoxina" "amoxine" "amoxipen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "amoxivet" "amoxycillin" "amoxycillinsalt" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "anemolin" "aspenil" "atoksilin" "bristamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [33] "cemoxin" "ciblor" "clamoxyl" "damoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "danoxillin" "delacillin" "demoksil" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "efpenix" "eupen" "flemoxin" "flemoxine" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [45] "galenamox" "gramidil" "hiconcil" "himinomax" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "histocillin" "ibiamox" "imacillin" "izoltil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [53] "kentrocyllin" "lamoxy" "largopen" "larotid" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [57] "matasedrin" "metifarma" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "moxal" "moxaline" "moxatag" "neotetranase" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [65] "novabritine" "ospamox" "pacetocin" "pamocil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [69] "paradroxil" "pasetocin" "penamox" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "promoxil" "quimiopen" "remoxil" "riotapen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [77] "robamox" "sawacillin" "siganopen" "simplamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [81] "sintopen" "sumox" "topramoxin" "trifamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] "trimox" "unicillin" "utimox" "velamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [89] "vetramox" "wymox" "zamocillin" "zamocilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [93] "zimox" </span>
<span class="r-in"><span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillinhydrate" "amoxicillinum" "amoxiden" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxil" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxycillin" "amoxyke" "anemolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "aspenil" "atoksilin" "biomox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "bristamox" "cemoxin" "clamoxyl" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "damoxy" "delacillin" "demoksil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "dispermox" "efpenix" "flemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "hiconcil" "histocillin" "hydroxyampicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "ibiamox" "imacillin" "lamoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "largopen" "metafarmacapsules" "metifarmacapsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "moksilin" "moxacin" "moxatag" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "ospamox" "pamoxicillin" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "promoxil" "remoxil" "robamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "sawamoxpm" "tolodina" "topramoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "unicillin" "utimox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "acuotricina" "alfamox" "alfida" "amitron" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "amoclen" "amodex" "amoksicillin" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "amopen" "amopenixin" "amophar" "amoran" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxi" "amoxicaps" "amoxicilina" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "amoxicillinum" "amoxidal" "amoxiden" "amoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "amoxillat" "amoxina" "amoxine" "amoxipen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "amoxivet" "amoxycillin" "amoxycillinsalt" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "anemolin" "aspenil" "atoksilin" "bristamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [33] "cemoxin" "ciblor" "clamoxyl" "damoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "danoxillin" "delacillin" "demoksil" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "efpenix" "eupen" "flemoxin" "flemoxine" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [45] "galenamox" "gramidil" "hiconcil" "himinomax" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "histocillin" "ibiamox" "imacillin" "izoltil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [53] "kentrocyllin" "lamoxy" "largopen" "larotid" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [57] "matasedrin" "metifarma" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "moxal" "moxaline" "moxatag" "neotetranase" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [65] "novabritine" "ospamox" "pacetocin" "pamocil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [69] "paradroxil" "pasetocin" "penamox" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "promoxil" "quimiopen" "remoxil" "riotapen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [77] "robamox" "sawacillin" "siganopen" "simplamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [81] "sintopen" "sumox" "topramoxin" "trifamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] "trimox" "unicillin" "utimox" "velamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [89] "vetramox" "wymox" "zamocillin" "zamocilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [93] "zimox" </span>
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactams/penicillins"</span>
<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
@ -261,24 +273,30 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Penicillins with extended spectrum"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $tradenames</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillinhydrate" "amoxicillinum" "amoxiden" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxil" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxycillin" "amoxyke" "anemolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "aspenil" "atoksilin" "biomox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "bristamox" "cemoxin" "clamoxyl" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "damoxy" "delacillin" "demoksil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "dispermox" "efpenix" "flemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "hiconcil" "histocillin" "hydroxyampicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "ibiamox" "imacillin" "lamoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "largopen" "metafarmacapsules" "metifarmacapsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "moksilin" "moxacin" "moxatag" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "ospamox" "pamoxicillin" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "promoxil" "remoxil" "robamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "sawamoxpm" "tolodina" "topramoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "unicillin" "utimox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "acuotricina" "alfamox" "alfida" "amitron" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "amoclen" "amodex" "amoksicillin" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "amopen" "amopenixin" "amophar" "amoran" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxi" "amoxicaps" "amoxicilina" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "amoxicillinum" "amoxidal" "amoxiden" "amoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "amoxillat" "amoxina" "amoxine" "amoxipen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "amoxivet" "amoxycillin" "amoxycillinsalt" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "anemolin" "aspenil" "atoksilin" "bristamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [33] "cemoxin" "ciblor" "clamoxyl" "damoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "danoxillin" "delacillin" "demoksil" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "efpenix" "eupen" "flemoxin" "flemoxine" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [45] "galenamox" "gramidil" "hiconcil" "himinomax" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "histocillin" "ibiamox" "imacillin" "izoltil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [53] "kentrocyllin" "lamoxy" "largopen" "larotid" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [57] "matasedrin" "metifarma" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "moxal" "moxaline" "moxatag" "neotetranase" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [65] "novabritine" "ospamox" "pacetocin" "pamocil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [69] "paradroxil" "pasetocin" "penamox" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "promoxil" "quimiopen" "remoxil" "riotapen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [77] "robamox" "sawacillin" "siganopen" "simplamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [81] "sintopen" "sumox" "topramoxin" "trifamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] "trimox" "unicillin" "utimox" "velamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [89] "vetramox" "wymox" "zamocillin" "zamocilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [93] "zimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $loinc</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "101498-4" "15-8" "16-6" "16365-9" "17-4" "18-2" </span>

4
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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -99,7 +99,7 @@
<span class="r-in"><span><span class="co"># returns a wildly guessed result:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] THA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] CTE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
<span class="r-in"><span><span class="co"># all ab_*() functions</span></span></span>

2
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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">

22
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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -113,16 +113,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.71233 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.12877 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.27945 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.04384 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.37260 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.08493 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.07123 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.18082 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.55342 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.13699 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.71507 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.13151 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.28219 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.04658 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.37534 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.08767 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.07397 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.18356 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.55616 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.13973 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">

53
reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -69,13 +69,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antimicrobials <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, add_total_n <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
<span> conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> sep <span class="op">=</span> <span class="st">" + "</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
<span> interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">retrieve_wisca_parameters</span><span class="op">(</span><span class="va">wisca_model</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@ -108,7 +106,19 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-antimicrobials">antimicrobials<a class="anchor" aria-label="anchor" href="#arg-antimicrobials"></a></dt>
<dd><p>vector of any antimicrobial name or code (will be evaluated with <code><a href="as.ab.html">as.ab()</a></code>, column name of <code>x</code>, or (any combinations of) <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> or <code><a href="antimicrobial_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be set to values separated with <code>"+"</code>, such as <code>"TZP+TOB"</code> or <code>"cipro + genta"</code>, given that columns resembling such antimicrobials exist in <code>x</code>. See <em>Examples</em>.</p></dd>
<dd><p>a vector specifying the antimicrobials to include in the antibiogram (see <em>Examples</em>). Will be evaluated using <code><a href="guess_ab_col.html">guess_ab_col()</a></code>. This can be:</p><ul><li><p>Any antimicrobial name or code</p></li>
<li><p>A column name in <code>x</code> that contains SIR values</p></li>
<li><p>Any <a href="antimicrobial_selectors.html">antimicrobial selector</a>, such as <code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> or <code><a href="antimicrobial_selectors.html">carbapenems()</a></code></p></li>
<li><p>A combination of the above, using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>, e.g.:</p><ul><li><p><code>c(aminoglycosides(), "AMP", "AMC")</code></p></li>
<li><p><code>c(aminoglycosides(), carbapenems())</code></p></li>
</ul></li>
<li><p>Combination therapy, indicated by using <code>"+"</code>, with or without <a href="antimicrobial_selectors.html">antimicrobial selectors</a>, e.g.:</p><ul><li><p><code>"TZP+TOB"</code></p></li>
<li><p><code>"cipro + genta"</code></p></li>
<li><p><code>carbapenems() + "GEN"</code></p></li>
<li><p><code>carbapenems() + c("", "GEN")</code></p></li>
<li><p><code>carbapenems() + c("", aminoglycosides())</code></p></li>
</ul></li>
</ul></dd>
<dt id="arg-mo-transform">mo_transform<a class="anchor" aria-label="anchor" href="#arg-mo-transform"></a></dt>
@ -480,6 +490,23 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># you can use any antimicrobial selector with `+` too:</span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antimicrobials <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</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">""</span>, <span class="st">"GEN"</span>, <span class="st">"tobra"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">ureidopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span>
<span class="r-out co"><span class="r-pr">#&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> Gram-neg… 88% (85-91%,N=641) 99% (97-99%,N=691) 98% (97-99%,N=693) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-pos… 86% (82-89%,N=345) 98% (96-98%,N=1044) 95% (93-97%,N=550) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Piperacillin/tazobactam`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Piperacillin/tazobactam + Gentamicin`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`Piperacillin/tazobactam + Tobramycin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># names of antimicrobials do not need to resemble columns exactly:</span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antimicrobials <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">"Cipro"</span>, <span class="st">"cipro + genta"</span><span class="op">)</span>,</span></span>
@ -563,9 +590,9 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
<span class="r-out co"><span class="r-pr">#&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> Clinical 76.2% (59.9-88.6%) 94.9% (85.2-99.2%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 60.3% (42.8-78.9%) 90.9% (77.4-98.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 67.2% (39-92%) 89.9% (68.6-99.4%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 76.5% (60.8-88%) 95.3% (86.4-99.2%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 60.3% (42.1-80.7%) 90.6% (76.4-98.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 66.8% (38.4-91.3%) 89.7% (69.9-99.5%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@ -591,8 +618,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |76% (60-88.6%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |59.8% (40.7-80.1%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |66.2% (38.1-91.3%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |59.8% (40.7-79.7%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |66.2% (37.9-91.3%) |</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>

8
reference/antimicrobial_selectors.html
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@ -1,10 +1,10 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:
library(dplyr)
my_data_with_all_these_columns %&amp;gt;%
select(cephalosporins())
'><meta property="og:description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.
'><meta property="og:description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:
library(dplyr)
my_data_with_all_these_columns %&amp;gt;%
@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -61,7 +61,7 @@ my_data_with_all_these_columns %&amp;gt;%
</div>
<div class="ref-description section level2">
<p>These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.</p>
<p>These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base <span style="R">R</span>, tidyverse, tidymodels, and <code>data.table</code>.</p>
<p>In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="va">my_data_with_all_these_columns</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>

2
reference/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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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37
reference/as.sir.html
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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -718,18 +718,17 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming </span><span style="color: #0000BB; background-color: #EEEEEE;">breakpoint_type = "animal"</span><span style="color: #0000BB;">, since </span><span style="color: #0000BB; background-color: #EEEEEE;">host</span><span style="color: #0000BB;"> is set.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic), </span><span style="color: #0000BB; font-weight: bold;">CLSI</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin), </span><span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No CLSI 2024 MIC breakpoints available for test Antibiotic (TESTAB).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No CLSI 2024 MIC breakpoints available for acetylspiramycin (ASP).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (TESTAB, test Antibiotic),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No CLSI 2024 DISK breakpoints available for acetylspiramycin (ASP).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: '</span><span style="color: #0000BB; font-weight: bold;">antibiotic</span><span style="color: #0000BB;">' (ASP, acetylspiramycin),</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; font-weight: bold;">CLSI 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFAFAF;"> WARNING </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No CLSI 2024 DISK breakpoints available for test Antibiotic (TESTAB).</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • No CLSI 2024 DISK breakpoints available for acetylspiramycin (ASP).</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
@ -768,6 +767,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting disk diffusion zones: column '</span><span style="color: #0000BB; font-weight: bold;">nitrofuratoin</span><span style="color: #0000BB;">' (NIT,</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">nitrofurantoin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Cleaning values in column '</span><span style="color: #0000BB; font-weight: bold;">specimen</span><span style="color: #0000BB;">' (ACM, acetylmidecamycin)...</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 2 results in index 'nitrofuratoin' truncated (100%) that</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> were invalid antimicrobial interpretations: "blood" and "urine"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> OK </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> afterwards to retrieve a logbook with</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;"> all the details of the breakpoint interpretations.</span></span>
@ -816,16 +819,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-17 <span style="color: #949494;">08:01:05</span> 1 ampicillin Strep p… human AMP <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-17 <span style="color: #949494;">08:01:05</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-17 <span style="color: #949494;">08:01:05</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-18 <span style="color: #949494;">15:55:52</span> 1 ampicillin Strep p… human AMP <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-18 <span style="color: #949494;">15:55:52</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-18 <span style="color: #949494;">15:55:52</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-17 <span style="color: #949494;">08:01:06</span> 1 GEN Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-17 <span style="color: #949494;">08:01:06</span> 1 TOB Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-17 <span style="color: #949494;">08:01:07</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-17 <span style="color: #949494;">08:01:07</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-17 <span style="color: #949494;">08:01:07</span> 2 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-17 <span style="color: #949494;">08:01:07</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-18 <span style="color: #949494;">15:55:52</span> 1 GEN Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-18 <span style="color: #949494;">15:55:53</span> 1 TOB Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-18 <span style="color: #949494;">15:55:53</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-18 <span style="color: #949494;">15:55:54</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-18 <span style="color: #949494;">15:55:54</span> 2 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-18 <span style="color: #949494;">15:55:54</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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2
reference/av_property.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/availability.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/bug_drug_combinations.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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2
reference/count.html
View File

@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">2.1.1.9216</small>
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2
reference/custom_eucast_rules.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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2
reference/dosage.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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2
reference/eucast_rules.html
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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2
reference/example_isolates.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="">2.1.1.9216</small>
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2
reference/example_isolates_unclean.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="">2.1.1.9216</small>
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2
reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/first_isolate.html
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@ -9,7 +9,7 @@
<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="">2.1.1.9216</small>
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2
reference/g.test.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="">2.1.1.9216</small>
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108
reference/get_episode.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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@ -155,27 +155,27 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 12 40 46 27 46 46 47 1 47 13 7 37 27 5 14 48 13 22 30 18 27 21 6 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 6 38 13 5 11 15 9 41 47 42 27 18 4 44 26 2 30 42 10 4 23 46 25 34 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 37 24 15 19 4 16 5 16 1 43 38 40 25 4 11 29 1 17 29 3 47 8 38 6 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 5 20 36 35 43 30 47 39 41 42 43 32 12 4 10 33 11 8 12 31 10 32 28 45 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 33 15 22 12 31 27 11 45 38 19 3 29 4 42 41 41 13 36 23 33 38 46 31 45 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 24 9 18 10 6 11 41 1 12 38 26 11 36 1 41 32 14 7 37 22 26 16 44 14 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 44 4 45 4 2 39 20 43 9 42 29 11 6 36 25 30 23 8 14 4 28 11 14 20 40</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 23 6 11 16 29 27 9 8 15 45 31 35 44 35 46 5 39 44 24 17 12 31 32 36 34</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE TRUE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&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;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-31 151041 85 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&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;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-16 241328 78 M Outpatie… <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@ -209,19 +209,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 067927 2002-01-29 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 069276 2015-06-18 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 078381 2014-08-17 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 09B453 2010-03-21 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0DBF93 2015-10-12 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 118928 2004-02-01 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 119392 2010-11-01 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 122506 2007-08-10 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 146120 2011-09-23 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 151041 2003-01-31 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 067927 2002-02-14 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 067927 2002-02-14 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 0E2483 2007-06-21 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 151041 2006-02-10 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 155435 2014-06-18 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 167474 2008-02-15 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 174209 2011-10-03 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 175532 2012-10-11 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 187841 2012-09-30 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 197007 2012-07-17 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -235,19 +235,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2002-01-29 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2015-06-18 069276 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2014-08-17 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2010-03-21 09B453 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2015-10-12 0DBF93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2004-02-01 118928 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2010-11-01 119392 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2007-08-10 122506 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2011-09-23 146120 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2003-01-31 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [93]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2002-02-14 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2002-02-14 067927 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2007-06-21 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-02-10 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-06-18 155435 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2008-02-15 167474 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Outpatient 2011-10-03 174209 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2012-10-11 175532 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2012-09-30 187841 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2012-07-17 197007 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -263,9 +263,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 56 13 36 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 31 12 25 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 7 5 7 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 55 13 35 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 32 9 19 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 6 6 6</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -294,19 +294,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 969275 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A87231 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A84726 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F5F794 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 146120 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 501607 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>AGLC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 402950 <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 560323 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 4FC193 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D80438 <span style="color: #949494;">B_</span>CRYNB<span style="color: #949494;">_</span>STRT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 88B975 <span style="color: #949494;">B_</span>STRPT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 904485 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 167474 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 777154 <span style="color: #949494;">B_</span>CTRBC Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E58140 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E58549 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D65308 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 871020 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B13995 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> CB6026 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -7,7 +7,7 @@
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6
reference/kurtosis.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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</small>
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@ -92,9 +92,9 @@
<div class="section level2">
<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="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.97029</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.032783</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <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] -0.05238668</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.05102003</span>
</code></pre></div>
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2
reference/like.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/mdro.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">

73
reference/mean_amr_distance.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">
@ -111,30 +111,31 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R I I S R S S S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S I I I R R S I S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.621059 1.449138 -0.621059 -0.621059 -0.621059 1.449138 -0.621059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [8] -0.621059 -0.621059 1.449138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.8973666 -0.4743416 -0.4743416 -0.4743416</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 0.25 1 2 &gt;=16 8 1 1 0.025 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=128 0.125 0.01 64 64 8 0.002 1 &gt;=128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.9714967 -0.4147020 0.1369756 0.4128144 1.2403309 0.9644921</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1369756 0.1369756 -1.3310188 0.6886533</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.02853908 -0.44976893 -0.98844311 0.88070828 0.88070828 0.43721587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.33169561 -0.00627653 1.02853908 -1.47952641</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.9714967 -0.4147020 0.1369756 0.4128144 1.2403309 0.9644921</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1369756 0.1369756 -1.3310188 0.6886533</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.02853908 -0.44976893 -0.98844311 0.88070828 0.88070828 0.43721587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.33169561 -0.00627653 1.02853908 -1.47952641</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 15 15 50 41 10 21 44 42 10 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 39 35 46 27 13 50 30 49 41 20</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.8693350 -0.8693350 1.3196381 0.7567593 -1.1820455 -0.4940825</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9443855 0.8193014 -1.1820455 0.7567593</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.3216338 0.0000000 0.8844928 -0.6432675 -1.7689857 1.2061266</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4020422 1.1257182 0.4824506 -1.2061266</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -144,22 +145,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 26 &gt;=4 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 20 1 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 28 2 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 26 &lt;=0.25 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 23 2 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 31 2 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 29 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 27 &lt;=0.25 &gt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 22 0.5 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 23 &gt;=4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 26 &lt;=1 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 20 &gt;=4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 27 &gt;=4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 31 &gt;=4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 27 &gt;=4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 31 &lt;=1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 30 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 27 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 20 &gt;=4 0.5</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04047504 -0.25789134 -0.08826444 -0.63237868 -0.42488867 0.02453739</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.18267023 0.72772870 0.36605356 -0.85709171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12237407 -0.92897174 -0.07982527 0.24282355 0.22020411 0.34940813</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.12306945 0.80126097 0.09975463 -0.70395902</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -175,17 +176,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 28 2 0.25 -0.08826444 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A S 26 &gt;=4 0.25 -0.04047504 0.0477894</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F I 31 0.5 1 0.02453739 0.1128018</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 B S 20 1 &gt;=4 -0.25789134 0.1696269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 23 2 0.25 -0.42488867 0.3366242</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I R 27 &lt;=0.25 &gt;=4 0.36605356 0.4543180</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D S 26 &lt;=0.25 0.5 -0.63237868 0.5441142</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J I 22 0.5 0.25 -0.85709171 0.7688273</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H R 29 1 2 0.72772870 0.8159931</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G R 31 2 &gt;=4 1.18267023 1.2709347</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 20 &gt;=4 &gt;=16 -0.07982527 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G I 31 &lt;=1 8 -0.12306945 0.04324419</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I S 27 &gt;=4 4 0.09975463 0.17957990</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 A R 23 &gt;=4 1 0.12237407 0.20219934</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 31 &gt;=4 2 0.22020411 0.30002938</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 D R 27 &gt;=4 0.5 0.24282355 0.32264882</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F I 27 &gt;=4 &gt;=16 0.34940813 0.42923340</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J I 20 &gt;=4 0.5 -0.70395902 0.62413375</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 B I 26 &lt;=1 0.5 -0.92897174 0.84914647</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 H R 30 &gt;=4 4 0.80126097 0.88108624</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/microorganisms.groups.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/microorganisms.html
View File

@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/mo_matching_score.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/mo_property.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/mo_source.html
View File

@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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/pca.html
View File

@ -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="">2.1.1.9216</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9217</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">

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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 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -101,42 +101,43 @@
<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="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.005 0.125 1 0.002 1 0.125 32 0.01 0.5 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2 0.001 0.005 0.0625 0.001 0.001 2 256 128 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.002 1 0.002 32 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 2 0.25 8 4 &gt;=256 64 0.125 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 16 2 0.025 8 32 &lt;=0.001 4 2 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125 4 0.01 &gt;=256 0.25 0.25 1 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 40 42 43 46 45 40 48 50 23 9 25 36 16 6 43 36 41 50 40 47 25 34 37 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 8 6 21 6 34 30 30 42 26 10 41 26 22 46 19 16 38 34 12 50 42 45 42 44</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I S R R I I I I R R I I I S R S R S S S R R I S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R R S R I I R R R R R R I R S S S I I S S R R R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 16 2 0.025 8 32 0.001 4 2 128 0.125 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.01 &gt;=256 0.25 0.25 1 0.002 0.25 2 0.005 0.001 64 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 16 0.025 0.001 4 4 0.125 0.002 2 0.25 0.25 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.5 0.005 256 8 0.125 16 0.005 0.001 64 0.5 8 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.001</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=1 8 4 &lt;=1 &gt;=16 &gt;=16 &gt;=16 2 &gt;=16 2 &gt;=16 4 &gt;=16 &gt;=16 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 2 &gt;=16 &lt;=1 4 8 8 &gt;=16 4 8 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 8 2 &gt;=16 &lt;=0.25 &lt;=0.25 &gt;=16 1 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 8 &lt;=0.25 2 0.5 2 &lt;=0.25 1 4 1 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] &gt;=16 4 2 1 &lt;=0.25</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.125 0.125 0.25 1 1 0.0625 0.5 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4 0.125 0.25 0.25 0.0625 4 0.25 0.125 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4 0.5 0.0625 4 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 8 0.0625 0.0625 0.0625 4 &lt;=0.025 0.125 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 8 0.25 0.25 0.125 &lt;=0.025 0.25 &lt;=0.025 0.0625 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &lt;=0.025 8 4 4 &lt;=0.025 8 8 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 49 10 40 23 16 20 34 45 8 42 10 20 11 30 36 40 35 14 24 8 38 10 10 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 24 46 50 48 11 23 30 47 33 21 43 17 16 48 16 39 38 16 49 33 47 14 18 42</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 12 14 11 13 15 13 11 17 15 14 13 11 15 17 14 16 17 17 17 11 12 12 12 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 13 15 14 12 16 15 16 13 13 12 13 12 11 16 17 11 17 11 14 12 14 11 12 12</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 27 15 17 23 23 18 18 17 15 18 27 15 25 16 21 15 24 23 22 22 15 23 25 23 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 18 24 24 17 18 26 24 26 24 20 20 26 24 19 15 17 17 24 20 17 22 22 19 15</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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2
reference/resistance_predict.html
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@ -7,7 +7,7 @@
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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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@ -91,7 +91,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<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="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0199978</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01927257</span>
</code></pre></div>
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