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(v0.8.0.9004) added MDR guideline by Magiorakos et al.

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dr. M.S. (Matthijs) Berends
2019-10-26 21:56:41 +02:00
parent c01dc8a5b7
commit d2e8249edd
20 changed files with 605 additions and 118 deletions
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17
R/eucast_rules.R
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@ -47,6 +47,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
#' \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
#' \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
#' \strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
#' \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
#' \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
#' \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
@ -55,17 +56,20 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
#' \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
#' \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
#' \strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
#' \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
#' \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
#' \strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
#' \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
#' \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
#' \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
#' \strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
#' \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
#' \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
#' \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
#' \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
#' \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
#' \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
#' \strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
#' \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
#' \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
#' \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
@ -75,6 +79,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
#' \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
#' \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
#' \strong{GEH}: gentamicin-high (no ATC code),
#' \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
#' \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
#' \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
@ -91,10 +96,10 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
#' \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
#' \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
#' \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
#' \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
#' \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
#' \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}),
#' \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
#' \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
#' \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
@ -103,13 +108,15 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
#' \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
#' \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
#' \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
#' \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
#' \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
#' \strong{STH}: streptomycin-high (no ATC code),
#' \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
#' \strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
#' \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
#' \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
#' \strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
#' \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
#' \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
#' \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),