mirror of https://github.com/msberends/AMR.git
78 lines
5.2 KiB
R
78 lines
5.2 KiB
R
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Dataset with 420 antibiotics
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#'
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#' A dataset containing all antibiotics with a J0 code, with their DDD's.
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#' @format A data.frame with 420 observations and 12 variables:
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#' \describe{
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#' \item{\code{atc}}{ATC code, like \code{J01CR02}}
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#' \item{\code{molis}}{MOLIS code, like \code{amcl}}
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#' \item{\code{umcg}}{UMCG code, like \code{AMCL}}
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#' \item{\code{official}}{Official name by the WHO, like \code{"amoxicillin and enzyme inhibitor"}}
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#' \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
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#' \item{\code{trivial}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
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#' \item{\code{oral_ddd}}{Daily Defined Dose (DDD) according to the WHO, oral treatment}
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#' \item{\code{oral_units}}{Units of \code{ddd_units}}
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#' \item{\code{iv_ddd}}{Daily Defined Dose (DDD) according to the WHO, bij parenteral treatment}
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#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
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#' \item{\code{atc_group1}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
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#' \item{\code{atc_group2}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
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#' }
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#' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl} \cr \cr World Health Organization - \url{https://www.whocc.no/atc_ddd_index/}
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#' @seealso \code{\link{bactlist}}
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# todo:
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# ablist <- ablist %>% mutate(useful_gramnegative = if_else(atc_group2 == 'Tetracyclines', FALSE, TRUE))
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# ablist <- ablist %>% mutate(useful_gramnegative = if_else(atc_group2 %like% 'Glycopept', FALSE, useful_gramnegative))
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# Tbl1 Enterobacteriaceae are also intrinsically resistant to benzylpenicillin, glycopeptides, fusidic acid, macrolides (with some exceptions1), lincosamides, streptogramins, rifampicin, daptomycin and linezolid.
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# Tbl2 Non-fermentative Gram-negative bacteria are also generally intrinsically resistant to benzylpenicillin, first and second generation cephalosporins, glycopeptides, fusidic acid, macrolides, lincosamides, streptogramins, rifampicin, daptomycin and linezolid
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# Tbl3 Gram-negative bacteria other than Enterobacteriaceae and non-fermentative Gram-negative bacteria listed are also intrinsically resistant to glycopeptides, lincosamides, daptomycin and linezolid.
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"ablist"
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#' Dataset with ~2500 microorganisms
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#'
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#' A dataset containing all microorganisms of MOLIS. MO codes of the UMCG can be looked up using \code{\link{bactlist.umcg}}.
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#' @format A data.frame with 2507 observations and 10 variables:
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#' \describe{
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#' \item{\code{bactid}}{ID of microorganism}
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#' \item{\code{bactsys}}{Bactsyscode of microorganism}
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#' \item{\code{family}}{Family name of microorganism}
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#' \item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
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#' \item{\code{species}}{Species name of microorganism, like \code{"coli"}}
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#' \item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
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#' \item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
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#' \item{\code{type}}{Type of microorganism, like \code{"Bacterie"} en \code{"Schimmel/gist"} (these are Dutch)}
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#' \item{\code{gramstain}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
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#' \item{\code{aerobic}}{Type aerobe/anaerobe of bacteria}
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#' }
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#' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
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#' @seealso \code{\link{ablist}} \code{\link{bactlist.umcg}}
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"bactlist"
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#' Translation table for UMCG with ~1100 microorganisms
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#'
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#' A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{bactlist}$bactid}, using \code{\link{left_join_bactlist}}.
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#' @format A data.frame with 1090 observations and 2 variables:
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#' \describe{
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#' \item{\code{mocode}}{Code of microorganism according to UMCG MMB}
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#' \item{\code{bactid}}{Code of microorganism in \code{\link{bactlist}}}
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#' }
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#' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl}
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#' @seealso \code{\link{bactlist}}
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"bactlist.umcg"
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