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(v1.5.0.9041) SNOMED update
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@@ -82,7 +82,7 @@
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
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</div>
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<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>10.1016/j.cmi.2019.02.028</a></p></li>
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<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href='https://doi.org/10.1080/14787210.2020.1730813'>10.1080/14787210.2020.1730813</a></p></li>
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<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <a href='https://doi.org/10.1084/jem.57.4.571'>10.1084/jem.57.4.571</a></p></li>
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<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
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<li><p>Catalogue of Life: 2019 Annual Checklist, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
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<li><p>List of Prokaryotic names with Standing in Nomenclature (March 2021), doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
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<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href='https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009'>https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
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</ol>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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@@ -397,7 +399,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
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</ul>
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<p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>,\<em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>,<em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
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<p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>,<em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
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<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
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<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
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@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
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</span>
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</div>
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@@ -292,11 +292,11 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<th>ampc_cephalosporin_resistance</th>
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<td><p>a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of <code>NA</code> for this argument will remove results for these agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em> and <em>Serratia</em>.</p></td>
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<td><p>a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of <code>NA</code> (the default) for this argument will remove results for these three agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em> and <em>Serratia</em>.</p></td>
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<th>only_rsi_columns</th>
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<td><p>a logical to indicate whether only antibiotic columns must be detected that were <a href='[rsi]'>transformed to class <code><rsi></code></a> on beforehand (defaults to <code>FALSE</code>)</p></td>
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<td><p>a logical to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
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<th>...</th>
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@@ -349,7 +349,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
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<p>The following antibiotics are used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
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<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01DB04</a>), cefcapene (<code>CCP</code>, no ATC code), cefcapene pivoxil (<code>CCX</code>, no ATC code), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01DD16</a>), cefditoren pivoxil (<code>DIX</code>, no ATC code), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01DD10</a>), cefetamet pivoxil (<code>CPI</code>, no ATC code), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01DD01</a>), cefotaxime/clavulanic acid (<code>CTC</code>, no ATC code), cefotaxime/sulbactam (<code>CTS</code>, no ATC code), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no'>J01DC07</a>), cefotiam hexetil (<code>CHE</code>, no ATC code), cefoveciLine truncated
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<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CR01</a>), apalcillin (<code>APL</code>, no ATC code), aspoxicillin (<code>APX</code>, no ATC code), avibactam (<code>AVB</code>, no ATC code), avoparcin (<code>AVO</code>, no ATC code), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no'>J01CE04</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01DB04</a>), cefcapene (<code>CCP</code>, no ATC code), cefcapene pivoxil (<code>CCX</code>, no ATC code), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01DD16</a>), cefditoren pivoxil (<code>DIX</code>, no ATC code), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01DD10</a>), cefetamet pivoxil (<code>CPI</code>, no ATC code), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01DD01</a>), cefotaxime/clavulanic acid (<code>CTC</code>, no ATC code), cefotaxime/sulbactam (<code>CTS</code>, no ATC code), cefotetan (<code>CTT</code>, <a href='https://wLine truncated
|
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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<th>only_rsi_columns</th>
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<td><p>a logical to indicate whether only columns must be included that were <a href='[rsi]'>transformed to class <code><rsi></code></a> on beforehand (defaults to <code>FALSE</code>)</p></td>
|
||||
<td><p>a logical to indicate whether only columns must be included that were transformed to class <code><rsi></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
|
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|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
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|
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|
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<th>only_rsi_columns</th>
|
||||
<td><p>a logical to indicate whether only antibiotic columns must be detected that were <a href='[rsi]'>transformed to class <code><rsi></code></a> on beforehand (defaults to <code>FALSE</code>)</p></td>
|
||||
<td><p>a logical to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
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||||
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|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
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|
||||
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
|
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|
||||
<td><p>Lifecycles of Functions in the <code>amr</code> Package</p></td>
|
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<td><p>Lifecycles of Functions in the <code>AMR</code> Package</p></td>
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<title>Lifecycles of Functions in the AMR Package — lifecycle • AMR (for R)</title>
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<meta property="og:description" content="Functions in this AMR package are categorised using the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle.
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This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions." />
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|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
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<div class="row">
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<div class="col-md-9 contents">
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<div class="page-header">
|
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<h1>Lifecycles of Functions in the <code>amr</code> Package</h1>
|
||||
<h1>Lifecycles of Functions in the <code>AMR</code> Package</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/lifecycle.R'><code>R/lifecycle.R</code></a></small>
|
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|
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<div class="ref-description">
|
||||
<p>Functions in this <code>AMR</code> package are categorised using <a href='https://www.Tidyverse.org/lifecycle'>the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle</a>.</p>
|
||||
<p>Functions in this <code>AMR</code> package are categorised using <a href='https://lifecycle.r-lib.org/articles/stages.html'>the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle</a>.</p>
|
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<p><img src='figures/lifecycle_tidyverse.svg' height=200px style=margin-bottom:5px /> <br />
|
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This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.</p>
|
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||||
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||||
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|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
|
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|
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</tr>
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<tr>
|
||||
<th>only_rsi_columns</th>
|
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<td><p>a logical to indicate whether only antibiotic columns must be detected that were <a href='[rsi]'>transformed to class <code><rsi></code></a> on beforehand (defaults to <code>FALSE</code>)</p></td>
|
||||
<td><p>a logical to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
|
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<th>...</th>
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@@ -394,7 +394,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
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<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
|
||||
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
|
||||
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01DB04</a>), cefcapene (<code>CCP</code>, no ATC code), cefcapene pivoxil (<code>CCX</code>, no ATC code), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01DD16</a>), cefditoren pivoxil (<code>DIX</code>, no ATC code), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01DD10</a>), cefetamet pivoxil (<code>CPI</code>, no ATC code), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01DD01</a>), cefotaxime/clavulanic acid (<code>CTC</code>, no ATC code), cefotaxime/sulbactam (<code>CTS</code>, no ATC code), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no'>J01DC07</a>), cefotiam hexetil (<code>CHE</code>, no ATC code), cefoveciLine truncated
|
||||
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01CR01</a>), apalcillin (<code>APL</code>, no ATC code), aspoxicillin (<code>APX</code>, no ATC code), avibactam (<code>AVB</code>, no ATC code), avoparcin (<code>AVO</code>, no ATC code), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no'>J01CE04</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01DB04</a>), cefcapene (<code>CCP</code>, no ATC code), cefcapene pivoxil (<code>CCX</code>, no ATC code), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01DD16</a>), cefditoren pivoxil (<code>DIX</code>, no ATC code), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01DD10</a>), cefetamet pivoxil (<code>CPI</code>, no ATC code), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01DD01</a>), cefotaxime/clavulanic acid (<code>CTC</code>, no ATC code), cefotaxime/sulbactam (<code>CTS</code>, no ATC code), cefotetan (<code>CTT</code>, <a href='https://wLine truncated
|
||||
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
|
||||
|
||||
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -256,20 +256,24 @@
|
||||
<li><p><code>species_id</code><br /> ID of the species as used by the Catalogue of Life</p></li>
|
||||
<li><p><code>source</code><br /> Either "CoL", "LPSN" or "manually added" (see <em>Source</em>)</p></li>
|
||||
<li><p><code>prevalence</code><br /> Prevalence of the microorganism, see <code><a href='as.mo.html'>as.mo()</a></code></p></li>
|
||||
<li><p><code>snomed</code><br /> SNOMED code of the microorganism. Use <code><a href='mo_property.html'>mo_snomed()</a></code> to retrieve it quickly, see <code><a href='mo_property.html'>mo_property()</a></code>.</p></li>
|
||||
<li><p><code>snomed</code><br /> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, according to the US Edition of SNOMED CT from 1 September 2020 (see <em>Source</em>). Use <code><a href='mo_property.html'>mo_snomed()</a></code> to retrieve it quickly, see <code><a href='mo_property.html'>mo_property()</a></code>.</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>Catalogue of Life: 2019 Annual Checklist</p><ul>
|
||||
<p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul>
|
||||
<li><p>Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
|
||||
</ul>
|
||||
|
||||
<p>List of Prokaryotic names with Standing in Nomenclature: March 2021</p><ul>
|
||||
<p>List of Prokaryotic names with Standing in Nomenclature (March 2021) as currently implemented in this <code>AMR</code> package:</p><ul>
|
||||
<li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
|
||||
<li><p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: <a href='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p></li>
|
||||
<li><p>Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; doi: <a href='https://doi.org/10.1093/nar/gkt1111'>10.1093/nar/gkt1111</a></p></li>
|
||||
<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: <a href='https://doi.org/10.1099/00207713-47-2-590'>10.1099/00207713-47-2-590</a></p></li>
|
||||
</ul>
|
||||
|
||||
<p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul>
|
||||
<li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href='https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009'>https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -272,7 +272,7 @@
|
||||
<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
|
||||
</ul>
|
||||
|
||||
<p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>,\<em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>,<em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
|
||||
<p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>,<em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
|
||||
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -334,7 +334,7 @@
|
||||
<li><p>An <a href='https://rdrr.io/r/base/integer.html'>integer</a> in case of <code>mo_year()</code></p></li>
|
||||
<li><p>A <a href='https://rdrr.io/r/base/list.html'>list</a> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
|
||||
<li><p>A named <a href='https://rdrr.io/r/base/character.html'>character</a> in case of <code>mo_url()</code></p></li>
|
||||
<li><p>A <a href='https://rdrr.io/r/base/double.html'>double</a> in case of <code>mo_snomed()</code></p></li>
|
||||
<li><p>A <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> in case of <code>mo_snomed()</code></p></li>
|
||||
<li><p>A <a href='https://rdrr.io/r/base/character.html'>character</a> in all other cases</p></li>
|
||||
</ul>
|
||||
|
||||
@@ -353,6 +353,7 @@
|
||||
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
|
||||
<p>All output <a href='translate.html'>will be translated</a> where possible.</p>
|
||||
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
||||
<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See the <a href='microorganisms.html'>microorganisms</a> data set for more info.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
|
||||
|
||||
|
||||
@@ -375,7 +376,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<li><p><i>k<sub>n</sub></i> is the taxonomic kingdom of <i>n</i>, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.</p></li>
|
||||
</ul>
|
||||
|
||||
<p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>,\<em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>,<em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
|
||||
<p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>,<em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
|
||||
@@ -393,7 +394,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<li><p>Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect; doi: <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>10.1016/j.cmi.2019.02.028</a></p></li>
|
||||
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href='https://doi.org/10.1080/14787210.2020.1730813'>10.1080/14787210.2020.1730813</a></p></li>
|
||||
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <a href='https://doi.org/10.1084/jem.57.4.571'>10.1084/jem.57.4.571</a></p></li>
|
||||
<li><p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p></li>
|
||||
<li><p>Catalogue of Life: 2019 Annual Checklist, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
|
||||
<li><p>List of Prokaryotic names with Standing in Nomenclature (March 2021), doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
|
||||
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href='https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009'>https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
|
||||
</ol>
|
||||
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
@@ -505,7 +508,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
|
||||
<span class='fu'>mo_taxonomy</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># get a list with the taxonomy, the authors, Gram-stain and URL to the online database</span>
|
||||
<span class='co'># get a list with the taxonomy, the authors, Gram-stain,</span>
|
||||
<span class='co'># SNOMED codes, and URL to the online database</span>
|
||||
<span class='fu'>mo_info</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
|
||||
Reference in new issue
Block a user