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(v1.5.0.9041) SNOMED update

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dr. M.S. (Matthijs) Berends committed 2021-03-11 21:42:30 +01:00
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man/as.mo.Rd
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@@ -127,7 +127,9 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
\item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
\item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org}
\item List of Prokaryotic names with Standing in Nomenclature (March 2021), \doi{10.1099/ijsem.0.004332}
\item 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: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009}
}
}
@@ -155,7 +157,7 @@ where:
\item \ifelse{html}{\out{<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.}}{l_n is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}
}
The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella},\\\emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium},\emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium},\emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
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"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
man/eucast_rules.Rd
+3 -3
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@@ -47,9 +47,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".}
\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' 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} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
\item{ampc_cephalosporin_resistance}{a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' 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} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
@@ -89,7 +89,7 @@ To define antibiotics column names, leave as it is to determine it automatically
The following antibiotics are used for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CR01}), avoparcin (\code{AVO}, no ATC code), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01CA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01CE01}), cadazolid (\code{CDZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01DB05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01DB02}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01DC03}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, no ATC code), cefcapene pivoxil (\code{CCX}, no ATC code), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01DD16}), cefditoren pivoxil (\code{DIX}, no ATC code), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01DD10}), cefetamet pivoxil (\code{CPI}, no ATC code), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, no ATC code), cefotaxime/sulbactam (\code{CTS}, no ATC code), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DC07}), cefotiam hexetil (\code{CHE}, no ATC code), cefovecin (\code{FOV}, no ATC code), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01DC01}), cefoxitin screening (\code{FOX1}, no ATC code), cefpimizole (\code{CFZ}, no ATC code), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01DD13}), cefpodoxime proxetil (\code{CPX}, no ATC code), cefpodoxime/clavulanic Line truncated
Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CR01}), apalcillin (\code{APL}, no ATC code), aspoxicillin (\code{APX}, no ATC code), avibactam (\code{AVB}, no ATC code), avoparcin (\code{AVO}, no ATC code), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01CA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01CE01}), cadazolid (\code{CDZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01DB05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01DB02}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01DC03}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, no ATC code), cefcapene pivoxil (\code{CCX}, no ATC code), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01DD16}), cefditoren pivoxil (\code{DIX}, no ATC code), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01DD10}), cefetamet pivoxil (\code{CPI}, no ATC code), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, no ATC code), cefotaxime/sulbactam (\code{CTS}, no ATC code), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DC07}), cefotiam hexetil (\code{CHE}, no ATC code), cefovecin (\code{FOV}, no ATC code), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01DC01}), cefoxitin screening (\code{FOX1}, no ATC code), cefpimizole (\code{CFZ}, no ATC code), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?Line truncated
}
\section{Stable Lifecycle}{
man/filter_ab_class.Rd
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@@ -148,7 +148,7 @@ filter_tetracyclines(
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{arguments passed on to \code{\link[=filter_ab_class]{filter_ab_class()}}}
}
man/guess_ab_col.Rd
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@@ -18,7 +18,7 @@ guess_ab_col(
\item{verbose}{a logical to indicate whether additional info should be printed}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
}
\value{
A column name of \code{x}, or \code{NULL} when no result is found.
man/lifecycle.Rd
+2 -2
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@@ -2,9 +2,9 @@
% Please edit documentation in R/lifecycle.R
\name{lifecycle}
\alias{lifecycle}
\title{Lifecycles of Functions in the \code{amr} Package}
\title{Lifecycles of Functions in the \code{AMR} Package}
\description{
Functions in this \code{AMR} package are categorised using \href{https://www.Tidyverse.org/lifecycle}{the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle}.
Functions in this \code{AMR} package are categorised using \href{https://lifecycle.r-lib.org/articles/stages.html}{the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle}.
\if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
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.
man/mdro.Rd
+2 -2
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@@ -58,7 +58,7 @@ eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...)
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.}
@@ -157,7 +157,7 @@ To define antibiotics column names, leave as it is to determine it automatically
The following antibiotics are used for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CR01}), avoparcin (\code{AVO}, no ATC code), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01CA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01CE01}), cadazolid (\code{CDZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01DB05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01DB02}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01DC03}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, no ATC code), cefcapene pivoxil (\code{CCX}, no ATC code), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01DD16}), cefditoren pivoxil (\code{DIX}, no ATC code), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01DD10}), cefetamet pivoxil (\code{CPI}, no ATC code), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, no ATC code), cefotaxime/sulbactam (\code{CTS}, no ATC code), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DC07}), cefotiam hexetil (\code{CHE}, no ATC code), cefovecin (\code{FOV}, no ATC code), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01DC01}), cefoxitin screening (\code{FOX1}, no ATC code), cefpimizole (\code{CFZ}, no ATC code), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no}{J01DD13}), cefpodoxime proxetil (\code{CPX}, no ATC code), cefpodoxime/clavulanic Line truncated
Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CR01}), apalcillin (\code{APL}, no ATC code), aspoxicillin (\code{APX}, no ATC code), avibactam (\code{AVB}, no ATC code), avoparcin (\code{AVO}, no ATC code), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01CA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01CE01}), cadazolid (\code{CDZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01CA05}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01DB05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{J01DB02}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01DC03}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, no ATC code), cefcapene pivoxil (\code{CCX}, no ATC code), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01DD16}), cefditoren pivoxil (\code{DIX}, no ATC code), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01DE01}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01DD10}), cefetamet pivoxil (\code{CPI}, no ATC code), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, no ATC code), cefotaxime/sulbactam (\code{CTS}, no ATC code), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DC07}), cefotiam hexetil (\code{CHE}, no ATC code), cefovecin (\code{FOV}, no ATC code), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01DC01}), cefoxitin screening (\code{FOX1}, no ATC code), cefpimizole (\code{CFZ}, no ATC code), cefpiramide (\code{CPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://www.whocc.no/atc_ddd_index/?Line truncated
}
\section{Interpretation of R and S/I}{
man/microorganisms.Rd
+8 -3
View File
@@ -15,22 +15,27 @@ A \link{data.frame} with 70,026 observations and 16 variables:
\item \code{species_id}\cr ID of the species as used by the Catalogue of Life
\item \code{source}\cr Either "CoL", "LPSN" or "manually added" (see \emph{Source})
\item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
\item \code{snomed}\cr SNOMED code of the microorganism. Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}.
\item \code{snomed}\cr Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, according to the US Edition of SNOMED CT from 1 September 2020 (see \emph{Source}). Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}.
}
}
\source{
Catalogue of Life: 2019 Annual Checklist
Catalogue of Life: 2019 Annual Checklist as currently implemented in this \code{AMR} package:
\itemize{
\item Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org}
}
List of Prokaryotic names with Standing in Nomenclature: March 2021
List of Prokaryotic names with Standing in Nomenclature (March 2021) as currently implemented in this \code{AMR} package:
\itemize{
\item 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{10.1099/ijsem.0.004332}
\item 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{10.1099/ijsem.0.002786}
\item Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; \doi{10.1093/nar/gkt1111}
\item 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{10.1099/00207713-47-2-590}
}
US Edition of SNOMED CT from 1 September 2020 as currently implemented in this \code{AMR} package:
\itemize{
\item 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: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009}
}
}
\usage{
microorganisms
man/mo_matching_score.Rd
+1 -1
View File
@@ -30,7 +30,7 @@ where:
\item \ifelse{html}{\out{<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.}}{l_n is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}
}
The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella},\\\emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium},\emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium},\emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
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"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
man/mo_property.Rd
+9 -4
View File
@@ -105,7 +105,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
\item An \link{integer} in case of \code{\link[=mo_year]{mo_year()}}
\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
\item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
\item A \link{double} in case of \code{\link[=mo_snomed]{mo_snomed()}}
\item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
\item A \link{character} in all other cases
}
}
@@ -133,6 +133,8 @@ Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_r
All output \link[=translate]{will be translated} where possible.
The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See the \link{microorganisms} data set for more info.
}
\section{Stable Lifecycle}{
@@ -158,7 +160,7 @@ where:
\item \ifelse{html}{\out{<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.}}{l_n is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.}
}
The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella},\\\emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium},\emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. \strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Alternaria}, \emph{Anaerosalibacter}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobacterium}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Blastocystis}, \emph{Branhamella}, \emph{Calymmatobacterium}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Chaetomium}, \emph{Chryseobacterium}, \emph{Chryseomonas}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Hendersonula}, \emph{Hypomyces}, \emph{Koserella}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Nectria}, \emph{Ochroconis}, \emph{Oidiodendron}, \emph{Phoma}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium},\emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Stomatococcus}, \emph{Treponema}, \emph{Trichoderma}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Tritirachium} or \emph{Ureaplasma}. \strong{Group 3} consists of all other microorganisms.
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"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
}
@@ -178,7 +180,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} \strong{Emergence of coagulase-negative staphylococci} 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
\item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
\item Catalogue of Life: 2019 Annual Checklist, \url{http://www.catalogueoflife.org}
\item List of Prokaryotic names with Standing in Nomenclature (March 2021), \doi{10.1099/ijsem.0.004332}
\item 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: \url{https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009}
}
}
@@ -287,7 +291,8 @@ if (require("dplyr")) {
# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("E. coli")
# get a list with the taxonomy, the authors, Gram-stain and URL to the online database
# get a list with the taxonomy, the authors, Gram-stain,
# SNOMED codes, and URL to the online database
mo_info("E. coli")
}
}