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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9002</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9003</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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@@ -52,8 +52,7 @@
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<div class="section-desc"><p>Please find the introduction to (and some general information about) our package here.</p></div>
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</div><div class="section level2">
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<dl></dl></div><div class="section level2">
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<div class="section-desc"><p>These functions are meant to get taxonomically valid properties of microorganisms from any input, but also properties derived from taxonomy, such as the Gram stain (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) , or <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganisms, and use <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add your own custom microorganisms to this package.</p></div>
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</div><div class="section level2">
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<dl></dl></div><div class="section level2">
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</dt>
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<dd>Transform Arbitrary Input to Valid Microbial Taxonomy</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_pathogenicity()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_oxygen_tolerance()</a></code> <code><a href="mo_property.html">mo_is_anaerobic()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_mycobank()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_current()</a></code> <code><a href="mo_property.html">mo_group_members()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>
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</dt>
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<dd>Get Properties of a Microorganism</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> <code><a href="add_custom_microorganisms.html">clear_custom_microorganisms()</a></code>
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</dt>
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<dd>Add Custom Microorganisms</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code>
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<div class="section-desc"><p>Use these functions to get valid properties of antimicrobials from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p></div>
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</div><div class="section level2">
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<dl></dl></div><div class="section level2">
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</dt>
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<dd>Transform Input to an Antibiotic ID</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_ddd_units()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> <code><a href="ab_property.html">set_ab_names()</a></code>
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</dt>
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<dd>Get Properties of an Antibiotic</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="ab_from_text.html">ab_from_text()</a></code>
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</dt>
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<dd>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> <code><a href="atc_online.html">atc_online_ddd_units()</a></code>
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</dt>
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<dd>Get ATC Properties from WHOCC Website</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> <code><a href="add_custom_antimicrobials.html">clear_custom_antimicrobials()</a></code>
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@@ -145,8 +149,7 @@
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<div class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></div>
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</div><div class="section level2">
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<dl></dl></div><div class="section level2">
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</dt>
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<dd>Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">rescale_mic()</a></code> <code><a href="as.mic.html">mic_p50()</a></code> <code><a href="as.mic.html">mic_p90()</a></code> <code><a href="as.mic.html">droplevels(<i><mic></i>)</a></code>
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</dt>
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<dd>Transform Input to Minimum Inhibitory Concentrations (MIC)</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">NA_disk_</a></code> <code><a href="as.disk.html">is.disk()</a></code>
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</dt>
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<dd>Transform Input to Disk Diffusion Diameters</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_dosage()</a></code>
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</dt>
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<dd>Apply EUCAST Rules</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>
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<div class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram (WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antimicrobial_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></div>
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</div><div class="section level2">
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<dl></dl></div><div class="section level2">
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</dt>
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<dd>Generate Traditional, Combination, Syndromic, or WISCA Antibiograms</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">sir_confidence_interval()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">sir_df()</a></code>
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</dt>
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<dd>Calculate Antimicrobial Resistance</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_sir()</a></code> <code><a href="count.html">count_df()</a></code>
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</dt>
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<dd>Count Available Isolates</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code>
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</dt>
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<dd>Determine Clinical or Epidemic Episodes</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code>
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</dt>
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<dd>Determine First Isolates</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> <code><a href="key_antimicrobials.html">all_antimicrobials()</a></code> <code><a href="key_antimicrobials.html">antimicrobials_equal()</a></code>
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</dt>
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<dd>(Key) Antimicrobials for First Weighted Isolates</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code>
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</dt>
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<dd>Determine Multidrug-Resistant Organisms (MDRO)</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="custom_mdro_guideline.html">custom_mdro_guideline()</a></code> <code><a href="custom_mdro_guideline.html">c(<i><custom_mdro_guideline></i>)</a></code>
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</dt>
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<dd>Define Custom MDRO Guideline</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i><bug_drug_combinations></i>)</a></code>
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</dt>
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<dd>Determine Bug-Drug Combinations</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
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</dt>
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<dd>Antimicrobial Selectors</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="top_n_microorganisms.html">top_n_microorganisms()</a></code>
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</dt>
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<dd>Filter Top <em>n</em> Microorganisms</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="mean_amr_distance.html">mean_amr_distance()</a></code> <code><a href="mean_amr_distance.html">amr_distance_from_row()</a></code>
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</dt>
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<dd>Calculate the Mean AMR Distance</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">sir_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_sir_predict()</a></code> <code><a href="resistance_predict.html">autoplot(<i><resistance_predict></i>)</a></code>
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</dt>
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<dd>Predict Antimicrobial Resistance</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="guess_ab_col.html">guess_ab_col()</a></code>
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<div class="section-desc"><p>Use these functions for the plotting part. The <code>scale_*_mic()</code> functions extend the ggplot2 package to allow plotting of MIC values, even within a manually set range. If using <code><a href="../reference/plot.html">plot()</a></code> (base R) or <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> (ggplot2) on MIC values or disk diffusion values, the user can set the interpretation guideline to give the bars the right SIR colours. The <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function is a short wrapper for users not much accustomed to ggplot2 yet. The <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function is a specific function to plot so-called biplots for PCA (principal component analysis).</p></div>
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</div><div class="section level2">
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<dl></dl></div><div class="section level2">
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</dt>
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<dd>Plotting Helpers for AMR Data Analysis</dd>
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</dl><dl><dt>
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<dt>
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<code><a href="ggplot_sir.html">ggplot_sir()</a></code> <code><a href="ggplot_sir.html">geom_sir()</a></code>
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</dt>
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<dd>AMR Plots with <code>ggplot2</code></dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="ggplot_pca.html">ggplot_pca()</a></code>
|
||||
|
||||
@@ -310,8 +330,7 @@
|
||||
|
||||
<div class="section-desc"><p>The AMR package is customisable, by providing settings that can be set per user or per team. For example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported language can be set for the whole team (system-language independent) for antibiotic names in a foreign language.</p></div>
|
||||
|
||||
|
||||
</div><div class="section level2">
|
||||
<dl></dl></div><div class="section level2">
|
||||
|
||||
|
||||
|
||||
@@ -327,8 +346,7 @@
|
||||
|
||||
<div class="section-desc"><p>This package also provides extensive support for antiviral agents, even though it is not the primary scope of this package. Working with data containing information about antiviral drugs was never easier. Use these functions to get valid properties of antiviral drugs from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/av_from_text.html">av_from_text()</a></code>.</p></div>
|
||||
|
||||
|
||||
</div><div class="section level2">
|
||||
<dl></dl></div><div class="section level2">
|
||||
|
||||
|
||||
|
||||
@@ -339,13 +357,15 @@
|
||||
|
||||
</dt>
|
||||
<dd>Transform Input to an Antiviral Drug ID</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="av_property.html">av_name()</a></code> <code><a href="av_property.html">av_cid()</a></code> <code><a href="av_property.html">av_synonyms()</a></code> <code><a href="av_property.html">av_tradenames()</a></code> <code><a href="av_property.html">av_group()</a></code> <code><a href="av_property.html">av_atc()</a></code> <code><a href="av_property.html">av_loinc()</a></code> <code><a href="av_property.html">av_ddd()</a></code> <code><a href="av_property.html">av_ddd_units()</a></code> <code><a href="av_property.html">av_info()</a></code> <code><a href="av_property.html">av_url()</a></code> <code><a href="av_property.html">av_property()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Get Properties of an Antiviral Drug</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="av_from_text.html">av_from_text()</a></code>
|
||||
|
||||
@@ -356,8 +376,7 @@
|
||||
|
||||
<div class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></div>
|
||||
|
||||
|
||||
</div><div class="section level2">
|
||||
<dl></dl></div><div class="section level2">
|
||||
|
||||
|
||||
|
||||
@@ -368,61 +387,71 @@
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with 78 679 Taxonomic Records of Microorganisms</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antibiotics</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Sets with 616 Antimicrobial Drugs</dd>
|
||||
</dl><dl><dt>
|
||||
<dd>Data Sets with 618 Antimicrobial Drugs</dd>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with Clinical Breakpoints for SIR Interpretation</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="example_isolates.html">example_isolates</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with 2 000 Example Isolates</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with 6 036 Common Microorganism Codes</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="microorganisms.groups.html">microorganisms.groups</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with 534 Microorganisms In Species Groups</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="intrinsic_resistant.html">intrinsic_resistant</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set Denoting Bacterial Intrinsic Resistance</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="dosage.html">dosage</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with Treatment Dosages as Defined by EUCAST</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="WHOCC.html">WHOCC</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="example_isolates_unclean.html">example_isolates_unclean</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Data Set with Unclean Data</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="WHONET.html">WHONET</a></code>
|
||||
|
||||
@@ -433,8 +462,7 @@
|
||||
|
||||
<div class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></div>
|
||||
|
||||
|
||||
</div><div class="section level2">
|
||||
<dl></dl></div><div class="section level2">
|
||||
|
||||
|
||||
|
||||
@@ -445,61 +473,71 @@
|
||||
|
||||
</dt>
|
||||
<dd>Split Ages into Age Groups</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="age.html">age()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Age in Years of Individuals</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="export_ncbi_biosample.html">export_ncbi_biosample()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Export Data Set as NCBI BioSample Antibiogram</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="availability.html">availability()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Check Availability of Columns</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="translate.html">get_AMR_locale()</a></code> <code><a href="translate.html">set_AMR_locale()</a></code> <code><a href="translate.html">reset_AMR_locale()</a></code> <code><a href="translate.html">translate_AMR()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Translate Strings from the AMR Package</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code> <code><a href="italicise_taxonomy.html">italicize_taxonomy()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Italicise Taxonomic Families, Genera, Species, Subspecies</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Join microorganisms to a Data Set</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%unlike%`</a></code> <code><a href="like.html">`%like_case%`</a></code> <code><a href="like.html">`%unlike_case%`</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Vectorised Pattern Matching with Keyboard Shortcut</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="mo_matching_score.html">mo_matching_score()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Calculate the Matching Score for Microorganisms</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="pca.html">pca()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Principal Component Analysis (for AMR)</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="random.html">random_mic()</a></code> <code><a href="random.html">random_disk()</a></code> <code><a href="random.html">random_sir()</a></code>
|
||||
|
||||
@@ -510,8 +548,7 @@
|
||||
|
||||
<div class="section-desc"><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p></div>
|
||||
|
||||
|
||||
</div><div class="section level2">
|
||||
<dl></dl></div><div class="section level2">
|
||||
|
||||
|
||||
|
||||
@@ -522,13 +559,15 @@
|
||||
|
||||
</dt>
|
||||
<dd><em>G</em>-test for Count Data</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="kurtosis.html">kurtosis()</a></code>
|
||||
|
||||
</dt>
|
||||
<dd>Kurtosis of the Sample</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<dt>
|
||||
|
||||
<code><a href="skewness.html">skewness()</a></code>
|
||||
|
||||
@@ -539,8 +578,7 @@
|
||||
|
||||
<div class="section-desc"><p>These objects are deprecated, meaning that they will still work but show a warning that they will be removed in a future version.</p></div>
|
||||
|
||||
|
||||
</div><div class="section level2">
|
||||
<dl></dl></div><div class="section level2">
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user