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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
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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-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "K. pneumoniae" (assuming</span>
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<span class="r-msg co"><span class="r-pr">#></span> Klebsiella pneumoniae). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 6 more variables: rank <chr>, ref <chr>, species_id <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, prevalence <dbl>, snomed <list>, and abbreviated variable</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># name ¹subspecies</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus species</span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 12 more variables: subspecies <chr>, rank <chr>, ref <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># 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 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
|
||||
<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 Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 6 more variables: rank <chr>, ref <chr>, species_id <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, prevalence <dbl>, snomed <list>, and abbreviated variable</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># name ¹subspecies</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus species</span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 12 more variables: subspecies <chr>, rank <chr>, ref <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># snomed <list></span></span>
|
||||
<span class="r-in"><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/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<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>
|
||||
@ -211,18 +211,17 @@
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||||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli) and "S. aureus" (assuming Staphylococcus aureus). Run</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> `mo_uncertainties()` to review these uncertainties.</span>
|
||||
<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</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria" "fullname" "kingdom" "phylum" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] "class" "order" "family" "genus" "species" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] "subspecies" "rank" "ref" "species_id" "source" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] "prevalence" "snomed" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria" "fullname" "status" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "kingdom" "phylum" "class" "order" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "family" "genus" "species" "subspecies" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "rank" "ref" "source" "lpsn" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "gbif_renamed_to" "prevalence" "snomed" </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="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>
|
||||
@ -231,19 +230,23 @@
|
||||
<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>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Joining, by = "mo"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" "ward" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] "mo" "PEN" "OXA" "FLC" "AMX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] "AMC" "AMP" "TZP" "CZO" "FEP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] "CXM" "FOX" "CTX" "CAZ" "CRO" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" "TMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] "SXT" "NIT" "FOS" "LNZ" "CIP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [31] "MFX" "VAN" "TEC" "TCY" "TGC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [36] "DOX" "ERY" "CLI" "AZM" "IPM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" "MUP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [46] "RIF" "fullname" "kingdom" "phylum" "class" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] "order" "family" "genus" "species" "subspecies"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [56] "rank" "ref" "species_id" "source" "prevalence"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] "snomed" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "NIT" "FOS" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "LNZ" "CIP" "MFX" "VAN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "RIF" "fullname" "status" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] "kingdom" "phylum" "class" "order" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [53] "family" "genus" "species" "subspecies" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [57] "rank" "ref" "source" "lpsn" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] "lpsn_parent" "lpsn_renamed_to" "gbif" "gbif_parent" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [65] "gbif_renamed_to" "prevalence" "snomed" </span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
@ -256,7 +259,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown-footer-right">
|
||||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
|
||||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
Reference in New Issue
Block a user