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Conduct AMR Analysis
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Set User- Or Team-specific Package Settings
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Conduct Principal Component Analysis for AMR
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Get Taxonomy of a Microorganism
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AMR & dplyr/tidyverse
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Join <a href="microorganisms.html">microorganisms</a> to a Data Set</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/join_microorganisms.R" class="external-link"><code>R/join_microorganisms.R</code></a></small>
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<div class="d-none name"><code>join.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Join the data set <a href="microorganisms.html">microorganisms</a> easily to an existing data set or to a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">inner_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">right_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">full_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">semi_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">anti_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>existing data set to join, or <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector. In case of a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector, the resulting <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> will contain a column 'x' with these values.</p></dd>
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<dt>by</dt>
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<dd><p>a variable to join by - if left empty will search for a column with class <code><a href="as.mo.html">mo</a></code> (created with <code><a href="as.mo.html">as.mo()</a></code>) or will be <code>"mo"</code> if that column name exists in <code>x</code>, could otherwise be a column name of <code>x</code> with values that exist in <code>microorganisms$mo</code> (such as <code>by = "bacteria_id"</code>), or another column in <a href="microorganisms.html">microorganisms</a> (but then it should be named, like <code>by = c("bacteria_id" = "fullname")</code>)</p></dd>
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<dt>suffix</dt>
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<dd><p>if there are non-joined duplicate variables in <code>x</code> and <code>y</code>, these suffixes will be added to the output to disambiguate them. Should be a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector of length 2.</p></dd>
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<dt>...</dt>
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<dd><p>ignored, only in place to allow future extensions</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></p>
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p><strong>Note:</strong> As opposed to the <code>join()</code> functions of <code>dplyr</code>, <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix.</p>
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<p>If the <code>dplyr</code> package is installed, their join functions will be used. Otherwise, the much slower <code><a href="https://Rdatatable.gitlab.io/data.table/reference/merge.html" class="external-link">merge()</a></code> and <code><a href="https://rdrr.io/r/base/interaction.html" class="external-link">interaction()</a></code> functions from base <span style="R">R</span> will be used.</p>
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</div>
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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 × 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 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 × 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 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>
|
||
<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>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_renamed_to <chr>, prevalence <dbl>, 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>
|
||
<span class="r-in"><span> from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-01"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-07"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> by <span class="op">=</span> <span class="fl">1</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> bacteria <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="st">"S. aureus"</span>, <span class="st">"MRSA"</span>, <span class="st">"MSSA"</span>, <span class="st">"STAAUR"</span>,</span></span>
|
||
<span class="r-in"><span> <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span></span></span>
|
||
<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-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" "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" "oxygen_tolerance" "source" </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [17] "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [21] "gbif_parent" "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>
|
||
<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">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></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="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" </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" "oxygen_tolerance" "source" </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [61] "lpsn" "lpsn_parent" "lpsn_renamed_to" "gbif" </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [65] "gbif_parent" "gbif_renamed_to" "prevalence" "snomed" </span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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<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: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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