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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -196,21 +196,23 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 23</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus species</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, source <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 13 more variables: subspecies <chr>, rank <chr>, ref <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
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<span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="st">"B_KLBSL_PNMN"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 23</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus species</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, source <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 13 more variables: subspecies <chr>, rank <chr>, ref <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">df</span> <span class="op"><-</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>
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<span class="r-in"><span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span></span></span>
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@ -229,12 +231,12 @@
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">df_joined</span> <span class="op"><-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria" "fullname" "status" </span>
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<span class="r-out co"><span class="r-pr">#></span> [5] "kingdom" "phylum" "class" "order" </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] "family" "genus" "species" "subspecies" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "rank" "ref" "source" "lpsn" </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] "gbif_renamed_to" "prevalence" "snomed" </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria" "fullname" "status" </span>
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<span class="r-out co"><span class="r-pr">#></span> [5] "kingdom" "phylum" "class" "order" </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] "family" "genus" "species" "subspecies" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "rank" "ref" "oxygen_tolerance" "source" </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] "gbif_parent" "gbif_renamed_to" "prevalence" "snomed" </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<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>
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@ -243,23 +245,23 @@
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Joining, by = "mo"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" </span>
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<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "NIT" "FOS" </span>
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<span class="r-out co"><span class="r-pr">#></span> [29] "LNZ" "CIP" "MFX" "VAN" </span>
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<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
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<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
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<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
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<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "RIF" "fullname" "status" </span>
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<span class="r-out co"><span class="r-pr">#></span> [49] "kingdom" "phylum" "class" "order" </span>
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<span class="r-out co"><span class="r-pr">#></span> [53] "family" "genus" "species" "subspecies" </span>
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<span class="r-out co"><span class="r-pr">#></span> [57] "rank" "ref" "source" "lpsn" </span>
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<span class="r-out co"><span class="r-pr">#></span> [61] "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" </span>
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<span class="r-out co"><span class="r-pr">#></span> [65] "gbif_renamed_to" "prevalence" "snomed" </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" </span>
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<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "NIT" "FOS" </span>
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<span class="r-out co"><span class="r-pr">#></span> [29] "LNZ" "CIP" "MFX" "VAN" </span>
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<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
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<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
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<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
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<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "RIF" "fullname" "status" </span>
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<span class="r-out co"><span class="r-pr">#></span> [49] "kingdom" "phylum" "class" "order" </span>
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<span class="r-out co"><span class="r-pr">#></span> [53] "family" "genus" "species" "subspecies" </span>
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<span class="r-out co"><span class="r-pr">#></span> [57] "rank" "ref" "oxygen_tolerance" "source" </span>
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<span class="r-out co"><span class="r-pr">#></span> [61] "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" </span>
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<span class="r-out co"><span class="r-pr">#></span> [65] "gbif_parent" "gbif_renamed_to" "prevalence" "snomed" </span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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