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945 lines
46 KiB
R
Executable File
945 lines
46 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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# global variables
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EUCAST_VERSION_BREAKPOINTS <- "10.0, 2020"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' Apply EUCAST rules
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#'
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#' @description
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#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
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#'
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#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
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#' @inheritSection lifecycle Maturing lifecycle
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#' @param x data with antibiotic columns, like e.g. `AMX` and `AMC`
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#' @param info print progress
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#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using e.g. `options(AMR.eucast_rules = "all")`.
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#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.
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#' @param ... column name of an antibiotic, please see section *Antibiotics* below
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#' @inheritParams first_isolate
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#' @details
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#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
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#' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
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#'
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#' Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:
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#'
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#' 1. A drug **with** enzyme inhibitor will be set to S if the drug **without** enzyme inhibitor is S
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#' 2. A drug **without** enzyme inhibitor will be set to R if the drug **with** enzyme inhibitor is R
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#'
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#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
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#'
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#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
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#'
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#' @section Antibiotics:
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#' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
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#'
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#' The following antibiotics are used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format '**antimicrobial ID**: name ([ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted by name:
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#'
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#' **AMK**: amikacin ([J01GB06](https://www.whocc.no/atc_ddd_index/?code=J01GB06)),
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#' **AMX**: amoxicillin ([J01CA04](https://www.whocc.no/atc_ddd_index/?code=J01CA04)),
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#' **AMC**: amoxicillin/clavulanic acid ([J01CR02](https://www.whocc.no/atc_ddd_index/?code=J01CR02)),
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#' **AMP**: ampicillin ([J01CA01](https://www.whocc.no/atc_ddd_index/?code=J01CA01)),
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#' **SAM**: ampicillin/sulbactam ([J01CR01](https://www.whocc.no/atc_ddd_index/?code=J01CR01)),
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#' **AZM**: azithromycin ([J01FA10](https://www.whocc.no/atc_ddd_index/?code=J01FA10)),
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#' **AZL**: azlocillin ([J01CA09](https://www.whocc.no/atc_ddd_index/?code=J01CA09)),
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#' **ATM**: aztreonam ([J01DF01](https://www.whocc.no/atc_ddd_index/?code=J01DF01)),
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#' **CAP**: capreomycin ([J04AB30](https://www.whocc.no/atc_ddd_index/?code=J04AB30)),
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#' **RID**: cefaloridine ([J01DB02](https://www.whocc.no/atc_ddd_index/?code=J01DB02)),
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#' **CZO**: cefazolin ([J01DB04](https://www.whocc.no/atc_ddd_index/?code=J01DB04)),
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#' **FEP**: cefepime ([J01DE01](https://www.whocc.no/atc_ddd_index/?code=J01DE01)),
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#' **CTX**: cefotaxime ([J01DD01](https://www.whocc.no/atc_ddd_index/?code=J01DD01)),
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#' **CTT**: cefotetan ([J01DC05](https://www.whocc.no/atc_ddd_index/?code=J01DC05)),
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#' **FOX**: cefoxitin ([J01DC01](https://www.whocc.no/atc_ddd_index/?code=J01DC01)),
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#' **CPT**: ceftaroline ([J01DI02](https://www.whocc.no/atc_ddd_index/?code=J01DI02)),
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#' **CAZ**: ceftazidime ([J01DD02](https://www.whocc.no/atc_ddd_index/?code=J01DD02)),
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#' **CRO**: ceftriaxone ([J01DD04](https://www.whocc.no/atc_ddd_index/?code=J01DD04)),
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#' **CXM**: cefuroxime ([J01DC02](https://www.whocc.no/atc_ddd_index/?code=J01DC02)),
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#' **CED**: cephradine ([J01DB09](https://www.whocc.no/atc_ddd_index/?code=J01DB09)),
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#' **CHL**: chloramphenicol ([J01BA01](https://www.whocc.no/atc_ddd_index/?code=J01BA01)),
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#' **CIP**: ciprofloxacin ([J01MA02](https://www.whocc.no/atc_ddd_index/?code=J01MA02)),
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#' **CLR**: clarithromycin ([J01FA09](https://www.whocc.no/atc_ddd_index/?code=J01FA09)),
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#' **CLI**: clindamycin ([J01FF01](https://www.whocc.no/atc_ddd_index/?code=J01FF01)),
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#' **COL**: colistin ([J01XB01](https://www.whocc.no/atc_ddd_index/?code=J01XB01)),
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#' **DAP**: daptomycin ([J01XX09](https://www.whocc.no/atc_ddd_index/?code=J01XX09)),
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#' **DOR**: doripenem ([J01DH04](https://www.whocc.no/atc_ddd_index/?code=J01DH04)),
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#' **DOX**: doxycycline ([J01AA02](https://www.whocc.no/atc_ddd_index/?code=J01AA02)),
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#' **ETP**: ertapenem ([J01DH03](https://www.whocc.no/atc_ddd_index/?code=J01DH03)),
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#' **ERY**: erythromycin ([J01FA01](https://www.whocc.no/atc_ddd_index/?code=J01FA01)),
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#' **ETH**: ethambutol ([J04AK02](https://www.whocc.no/atc_ddd_index/?code=J04AK02)),
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#' **FLC**: flucloxacillin ([J01CF05](https://www.whocc.no/atc_ddd_index/?code=J01CF05)),
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#' **FOS**: fosfomycin ([J01XX01](https://www.whocc.no/atc_ddd_index/?code=J01XX01)),
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#' **FUS**: fusidic acid ([J01XC01](https://www.whocc.no/atc_ddd_index/?code=J01XC01)),
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#' **GAT**: gatifloxacin ([J01MA16](https://www.whocc.no/atc_ddd_index/?code=J01MA16)),
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#' **GEN**: gentamicin ([J01GB03](https://www.whocc.no/atc_ddd_index/?code=J01GB03)),
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#' **GEH**: gentamicin-high (no ATC code),
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#' **IPM**: imipenem ([J01DH51](https://www.whocc.no/atc_ddd_index/?code=J01DH51)),
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#' **INH**: isoniazid ([J04AC01](https://www.whocc.no/atc_ddd_index/?code=J04AC01)),
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#' **KAN**: kanamycin ([J01GB04](https://www.whocc.no/atc_ddd_index/?code=J01GB04)),
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#' **LVX**: levofloxacin ([J01MA12](https://www.whocc.no/atc_ddd_index/?code=J01MA12)),
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#' **LIN**: lincomycin ([J01FF02](https://www.whocc.no/atc_ddd_index/?code=J01FF02)),
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#' **LNZ**: linezolid ([J01XX08](https://www.whocc.no/atc_ddd_index/?code=J01XX08)),
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#' **MEM**: meropenem ([J01DH02](https://www.whocc.no/atc_ddd_index/?code=J01DH02)),
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#' **MTR**: metronidazole ([J01XD01](https://www.whocc.no/atc_ddd_index/?code=J01XD01)),
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#' **MEZ**: mezlocillin ([J01CA10](https://www.whocc.no/atc_ddd_index/?code=J01CA10)),
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#' **MNO**: minocycline ([J01AA08](https://www.whocc.no/atc_ddd_index/?code=J01AA08)),
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#' **MFX**: moxifloxacin ([J01MA14](https://www.whocc.no/atc_ddd_index/?code=J01MA14)),
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#' **NAL**: nalidixic acid ([J01MB02](https://www.whocc.no/atc_ddd_index/?code=J01MB02)),
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#' **NEO**: neomycin ([J01GB05](https://www.whocc.no/atc_ddd_index/?code=J01GB05)),
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#' **NET**: netilmicin ([J01GB07](https://www.whocc.no/atc_ddd_index/?code=J01GB07)),
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#' **NIT**: nitrofurantoin ([J01XE01](https://www.whocc.no/atc_ddd_index/?code=J01XE01)),
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#' **NOR**: norfloxacin ([J01MA06](https://www.whocc.no/atc_ddd_index/?code=J01MA06)),
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#' **NOV**: novobiocin ([QJ01XX95](https://www.whocc.no/atc_ddd_index/?code=QJ01XX95)),
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#' **OFX**: ofloxacin ([J01MA01](https://www.whocc.no/atc_ddd_index/?code=J01MA01)),
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#' **OXA**: oxacillin ([J01CF04](https://www.whocc.no/atc_ddd_index/?code=J01CF04)),
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#' **PEN**: penicillin G ([J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01)),
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#' **PIP**: piperacillin ([J01CA12](https://www.whocc.no/atc_ddd_index/?code=J01CA12)),
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#' **TZP**: piperacillin/tazobactam ([J01CR05](https://www.whocc.no/atc_ddd_index/?code=J01CR05)),
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#' **PLB**: polymyxin B ([J01XB02](https://www.whocc.no/atc_ddd_index/?code=J01XB02)),
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#' **PRI**: pristinamycin ([J01FG01](https://www.whocc.no/atc_ddd_index/?code=J01FG01)),
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#' **PZA**: pyrazinamide ([J04AK01](https://www.whocc.no/atc_ddd_index/?code=J04AK01)),
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#' **QDA**: quinupristin/dalfopristin ([J01FG02](https://www.whocc.no/atc_ddd_index/?code=J01FG02)),
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#' **RIB**: rifabutin ([J04AB04](https://www.whocc.no/atc_ddd_index/?code=J04AB04)),
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#' **RIF**: rifampicin ([J04AB02](https://www.whocc.no/atc_ddd_index/?code=J04AB02)),
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#' **RFP**: rifapentine ([J04AB05](https://www.whocc.no/atc_ddd_index/?code=J04AB05)),
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#' **RXT**: roxithromycin ([J01FA06](https://www.whocc.no/atc_ddd_index/?code=J01FA06)),
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#' **SIS**: sisomicin ([J01GB08](https://www.whocc.no/atc_ddd_index/?code=J01GB08)),
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#' **STH**: streptomycin-high (no ATC code),
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#' **TEC**: teicoplanin ([J01XA02](https://www.whocc.no/atc_ddd_index/?code=J01XA02)),
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#' **TLV**: telavancin ([J01XA03](https://www.whocc.no/atc_ddd_index/?code=J01XA03)),
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#' **TCY**: tetracycline ([J01AA07](https://www.whocc.no/atc_ddd_index/?code=J01AA07)),
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#' **TIC**: ticarcillin ([J01CA13](https://www.whocc.no/atc_ddd_index/?code=J01CA13)),
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#' **TCC**: ticarcillin/clavulanic acid ([J01CR03](https://www.whocc.no/atc_ddd_index/?code=J01CR03)),
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#' **TGC**: tigecycline ([J01AA12](https://www.whocc.no/atc_ddd_index/?code=J01AA12)),
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#' **TOB**: tobramycin ([J01GB01](https://www.whocc.no/atc_ddd_index/?code=J01GB01)),
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#' **TMP**: trimethoprim ([J01EA01](https://www.whocc.no/atc_ddd_index/?code=J01EA01)),
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#' **SXT**: trimethoprim/sulfamethoxazole ([J01EE01](https://www.whocc.no/atc_ddd_index/?code=J01EE01)),
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#' **VAN**: vancomycin ([J01XA01](https://www.whocc.no/atc_ddd_index/?code=J01XA01)).
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#' @aliases EUCAST
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#' @rdname eucast_rules
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#' @export
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#' @return The input of `x`, possibly with edited values of antibiotics. Or, if `verbose = TRUE`, a [`data.frame`] with all original and new values of the affected bug-drug combinations.
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#' @source
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#' - EUCAST Expert Rules. Version 2.0, 2012. \cr
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#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60. \cr
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#' <https://doi.org/10.1111/j.1469-0691.2011.03703.x>
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#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
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#' <http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf>
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#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
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#' <http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx>
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#' @inheritSection AMR Reference data publicly available
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' \donttest{
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#' a <- data.frame(mo = c("Staphylococcus aureus",
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#' "Enterococcus faecalis",
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#' "Escherichia coli",
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#' "Klebsiella pneumoniae",
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#' "Pseudomonas aeruginosa"),
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#' VAN = "-", # Vancomycin
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#' AMX = "-", # Amoxicillin
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#' COL = "-", # Colistin
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#' CAZ = "-", # Ceftazidime
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#' CXM = "-", # Cefuroxime
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#' PEN = "S", # Penicillin G
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#' FOX = "S", # Cefoxitin
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#' stringsAsFactors = FALSE)
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#'
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#' a
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#' # mo VAN AMX COL CAZ CXM PEN FOX
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#' # 1 Staphylococcus aureus - - - - - S S
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#' # 2 Enterococcus faecalis - - - - - S S
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#' # 3 Escherichia coli - - - - - S S
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#' # 4 Klebsiella pneumoniae - - - - - S S
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#' # 5 Pseudomonas aeruginosa - - - - - S S
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#'
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#'
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#' # apply EUCAST rules: 18 results are forced as R or S
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#' b <- eucast_rules(a)
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#'
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#' b
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#' # mo VAN AMX COL CAZ CXM PEN FOX
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#' # 1 Staphylococcus aureus - S R R S S S
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#' # 2 Enterococcus faecalis - - R R R S R
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#' # 3 Escherichia coli R - - - - R S
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#' # 4 Klebsiella pneumoniae R R - - - R S
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#' # 5 Pseudomonas aeruginosa R R - - R R R
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#'
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#'
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#' # do not apply EUCAST rules, but rather get a data.frame
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#' # with 18 rows, containing all details about the transformations:
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#' c <- eucast_rules(a, verbose = TRUE)
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#' }
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eucast_rules <- function(x,
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col_mo = NULL,
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info = interactive(),
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rules = getOption("AMR.eucast_rules", default = c("breakpoints", "expert")),
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verbose = FALSE,
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...) {
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check_dataset_integrity()
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if (verbose == TRUE & interactive()) {
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txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
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"\n\nThis may overwrite your existing data if you use e.g.:",
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"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
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if ("rstudioapi" %in% rownames(utils::installed.packages())) {
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showQuestion <- import_fn("showQuestion", "rstudioapi")
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q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt)
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} else {
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q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
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}
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if (q_continue %in% c(FALSE, 2)) {
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message("Cancelled, returning original data")
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return(x)
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}
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}
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stop_ifnot(is.data.frame(x), "`x` must be a data frame")
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# try to find columns based on type
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# -- mo
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(x = x, type = "mo")
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}
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stop_if(is.null(col_mo), "`col_mo` must be set")
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stop_ifnot(all(rules %in% c("breakpoints", "expert", "other", "all")),
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'`rules` must be one or more of: "breakpoints", "expert", "other", "all".')
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decimal.mark <- getOption("OutDec")
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big.mark <- ifelse(decimal.mark != ",", ",", ".")
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formatnr <- function(x, big = big.mark, dec = decimal.mark) {
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trimws(format(x, big.mark = big, decimal.mark = dec))
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}
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warned <- FALSE
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warn_lacking_rsi_class <- FALSE
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txt_error <- function() {
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if (info == TRUE) cat("", font_red_bg(font_white(" ERROR ")), "\n\n")
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}
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txt_warning <- function() {
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if (warned == FALSE) {
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if (info == TRUE) cat("", font_yellow_bg(font_black(" WARNING ")))
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}
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warned <<- TRUE
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}
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txt_ok <- function(no_added, no_changed) {
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if (warned == FALSE) {
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if (no_added + no_changed == 0) {
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cat(font_subtle(" (no changes)\n"))
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} else {
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# opening
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cat(font_grey(" ("))
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# additions
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if (no_added > 0) {
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if (no_added == 1) {
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cat(font_green("1 value added"))
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} else {
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cat(font_green(formatnr(no_added), "values added"))
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}
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}
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# separator
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if (no_added > 0 & no_changed > 0) {
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cat(font_grey(", "))
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}
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# changes
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if (no_changed > 0) {
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if (no_changed == 1) {
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cat(font_blue("1 value changed"))
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} else {
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cat(font_blue(formatnr(no_changed), "values changed"))
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}
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}
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# closing
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cat(font_grey(")\n"))
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}
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warned <<- FALSE
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}
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}
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cols_ab <- get_column_abx(x = x,
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soft_dependencies = c("AMC",
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"AMK",
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"AMX",
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"AMP",
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"AZM",
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"AZL",
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"ATM",
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"RID",
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"FEP",
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"CTX",
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"FOX",
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"CED",
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"CAZ",
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"CRO",
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"CXM",
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"CHL",
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"CIP",
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"CLR",
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"CLI",
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"FLC",
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"COL",
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"CZO",
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"DAP",
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"DOX",
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"ETP",
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"ERY",
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"FOS",
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"FUS",
|
|
"GEN",
|
|
"IPM",
|
|
"KAN",
|
|
"LVX",
|
|
"LIN",
|
|
"LNZ",
|
|
"MEM",
|
|
"MEZ",
|
|
"MNO",
|
|
"MFX",
|
|
"NAL",
|
|
"NEO",
|
|
"NET",
|
|
"NIT",
|
|
"NOR",
|
|
"NOV",
|
|
"OFX",
|
|
"OXA",
|
|
"PEN",
|
|
"PIP",
|
|
"TZP",
|
|
"PLB",
|
|
"PRI",
|
|
"QDA",
|
|
"RIF",
|
|
"RXT",
|
|
"SIS",
|
|
"TEC",
|
|
"TCY",
|
|
"TIC",
|
|
"TGC",
|
|
"TOB",
|
|
"TMP",
|
|
"SXT",
|
|
"VAN"),
|
|
hard_dependencies = NULL,
|
|
verbose = verbose,
|
|
...)
|
|
|
|
# data preparation ----
|
|
message(font_blue("NOTE: Preparing data..."), appendLF = FALSE)
|
|
|
|
AMC <- cols_ab["AMC"]
|
|
AMK <- cols_ab["AMK"]
|
|
AMP <- cols_ab["AMP"]
|
|
AMX <- cols_ab["AMX"]
|
|
ATM <- cols_ab["ATM"]
|
|
AZL <- cols_ab["AZL"]
|
|
AZM <- cols_ab["AZM"]
|
|
CAZ <- cols_ab["CAZ"]
|
|
CED <- cols_ab["CED"]
|
|
CHL <- cols_ab["CHL"]
|
|
CIP <- cols_ab["CIP"]
|
|
CLI <- cols_ab["CLI"]
|
|
CLR <- cols_ab["CLR"]
|
|
COL <- cols_ab["COL"]
|
|
CRO <- cols_ab["CRO"]
|
|
CTX <- cols_ab["CTX"]
|
|
CXM <- cols_ab["CXM"]
|
|
CZO <- cols_ab["CZO"]
|
|
DAP <- cols_ab["DAP"]
|
|
DOX <- cols_ab["DOX"]
|
|
ERY <- cols_ab["ERY"]
|
|
ETP <- cols_ab["ETP"]
|
|
FEP <- cols_ab["FEP"]
|
|
FLC <- cols_ab["FLC"]
|
|
FOS <- cols_ab["FOS"]
|
|
FOX <- cols_ab["FOX"]
|
|
FUS <- cols_ab["FUS"]
|
|
GEN <- cols_ab["GEN"]
|
|
IPM <- cols_ab["IPM"]
|
|
KAN <- cols_ab["KAN"]
|
|
LIN <- cols_ab["LIN"]
|
|
LNZ <- cols_ab["LNZ"]
|
|
LVX <- cols_ab["LVX"]
|
|
MEM <- cols_ab["MEM"]
|
|
MEZ <- cols_ab["MEZ"]
|
|
MFX <- cols_ab["MFX"]
|
|
MNO <- cols_ab["MNO"]
|
|
NAL <- cols_ab["NAL"]
|
|
NEO <- cols_ab["NEO"]
|
|
NET <- cols_ab["NET"]
|
|
NIT <- cols_ab["NIT"]
|
|
NOR <- cols_ab["NOR"]
|
|
NOV <- cols_ab["NOV"]
|
|
OFX <- cols_ab["OFX"]
|
|
OXA <- cols_ab["OXA"]
|
|
PEN <- cols_ab["PEN"]
|
|
PIP <- cols_ab["PIP"]
|
|
PLB <- cols_ab["PLB"]
|
|
PRI <- cols_ab["PRI"]
|
|
QDA <- cols_ab["QDA"]
|
|
RID <- cols_ab["RID"]
|
|
RIF <- cols_ab["RIF"]
|
|
RXT <- cols_ab["RXT"]
|
|
SAM <- cols_ab["SAM"]
|
|
SIS <- cols_ab["SIS"]
|
|
SXT <- cols_ab["SXT"]
|
|
TCY <- cols_ab["TCY"]
|
|
TEC <- cols_ab["TEC"]
|
|
TGC <- cols_ab["TGC"]
|
|
TIC <- cols_ab["TIC"]
|
|
TMP <- cols_ab["TMP"]
|
|
TOB <- cols_ab["TOB"]
|
|
TZP <- cols_ab["TZP"]
|
|
VAN <- cols_ab["VAN"]
|
|
|
|
ab_missing <- function(ab) {
|
|
all(ab %in% c(NULL, NA))
|
|
}
|
|
|
|
verbose_info <- data.frame(row = integer(0),
|
|
col = character(0),
|
|
mo_fullname = character(0),
|
|
old = as.rsi(character(0)),
|
|
new = as.rsi(character(0)),
|
|
rule = character(0),
|
|
rule_group = character(0),
|
|
rule_name = character(0),
|
|
stringsAsFactors = FALSE)
|
|
|
|
# helper function for editing the table ----
|
|
edit_rsi <- function(to, rule, rows, cols) {
|
|
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
|
|
if (length(rows) > 0 & length(cols) > 0) {
|
|
before_df <- x_original
|
|
if (any(!sapply(x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) {
|
|
warn_lacking_rsi_class <<- TRUE
|
|
}
|
|
tryCatch(
|
|
# insert into original table
|
|
x_original[rows, cols] <<- to,
|
|
warning = function(w) {
|
|
if (w$message %like% "invalid factor level") {
|
|
xyz <- sapply(cols, function(col) {
|
|
x_original[, col] <<- factor(x = as.character(pull(x_original, col)), levels = c(to, levels(pull(x_original, col))))
|
|
x[, col] <<- factor(x = as.character(pull(x, col)), levels = c(to, levels(pull(x, col))))
|
|
invisible()
|
|
})
|
|
x_original[rows, cols] <<- to
|
|
warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = "`, `"), "` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.", call. = FALSE)
|
|
txt_warning()
|
|
warned <<- FALSE
|
|
} else {
|
|
warning(w$message, call. = FALSE)
|
|
txt_warning()
|
|
cat("\n") # txt_warning() does not append a "\n" on itself
|
|
}
|
|
},
|
|
error = function(e) {
|
|
txt_error()
|
|
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
|
|
ifelse(length(rows) > 10, "...", ""),
|
|
" while writing value '", to,
|
|
"' to column(s) `", paste(cols, collapse = "`, `"),
|
|
"`:\n", e$message),
|
|
call. = FALSE)
|
|
}
|
|
)
|
|
|
|
tryCatch(
|
|
x[rows, cols] <<- x_original[rows, cols],
|
|
error = function(e) {
|
|
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
|
|
"... while writing value '", to,
|
|
"' to column(s) `", paste(cols, collapse = "`, `"),
|
|
"`:\n", e$message), call. = FALSE)
|
|
}
|
|
)
|
|
|
|
# before_df might not be a data.frame, but a tibble or data.table instead
|
|
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows, ]
|
|
track_changes <- list(added = 0,
|
|
changed = 0)
|
|
for (i in seq_len(length(cols))) {
|
|
verbose_new <- data.frame(row = rows,
|
|
col = cols[i],
|
|
mo_fullname = x[rows, "fullname"],
|
|
old = as.rsi(as.character(old[, cols[i]]), warn = FALSE),
|
|
new = as.rsi(as.character(x[rows, cols[i]])),
|
|
rule = font_stripstyle(rule[1]),
|
|
rule_group = font_stripstyle(rule[2]),
|
|
rule_name = font_stripstyle(rule[3]),
|
|
stringsAsFactors = FALSE)
|
|
colnames(verbose_new) <- c("row", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name")
|
|
verbose_new <- verbose_new %>% filter(old != new | is.na(old))
|
|
# save changes to data set 'verbose_info'
|
|
verbose_info <<- rbind(verbose_info, verbose_new)
|
|
# count adds and changes
|
|
track_changes$added <- track_changes$added + verbose_new %>% filter(is.na(old)) %>% nrow()
|
|
track_changes$changed <- track_changes$changed + verbose_new %>% filter(!is.na(old)) %>% nrow()
|
|
}
|
|
# after the applied changes: return list with counts of added and changed
|
|
return(track_changes)
|
|
}
|
|
# no changes were applied: return number of (new) changes: none.
|
|
return(list(added = 0,
|
|
changed = 0))
|
|
}
|
|
|
|
|
|
old_cols <- colnames(x)
|
|
old_attributes <- attributes(x)
|
|
x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc.
|
|
# create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination)
|
|
x$`.rowid` <- sapply(as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]))), function(x) {
|
|
x[is.na(x)] <- "."
|
|
paste0(x, collapse = "")
|
|
})
|
|
|
|
# save original table, with the new .rowid column
|
|
x_original.bak <- x
|
|
# keep only unique rows for MO and ABx
|
|
x <- x %>% distinct(`.rowid`, .keep_all = TRUE)
|
|
x_original <- x
|
|
|
|
# join to microorganisms data set
|
|
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
|
x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE])
|
|
x <- x %>%
|
|
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
|
|
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
|
|
x$genus_species <- paste(x$genus, x$species)
|
|
message(font_blue("OK."))
|
|
|
|
if (ab_missing(AMP) & !ab_missing(AMX)) {
|
|
# ampicillin column is missing, but amoxicillin is available
|
|
message(font_blue(paste0("NOTE: Using column `", font_bold(AMX), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
|
|
AMP <- AMX
|
|
}
|
|
|
|
# nolint start
|
|
# antibiotic classes ----
|
|
aminoglycosides <- c(TOB, GEN, KAN, NEO, NET, SIS)
|
|
tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart
|
|
polymyxins <- c(PLB, COL)
|
|
macrolides <- c(ERY, AZM, RXT, CLR) # since EUCAST v3.1 clinda is set apart
|
|
glycopeptides <- c(VAN, TEC)
|
|
streptogramins <- c(QDA, PRI) # should officially also be quinupristin/dalfopristin
|
|
aminopenicillins <- c(AMP, AMX)
|
|
cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
|
|
cephalosporins_except_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)]
|
|
carbapenems <- c(ETP, IPM, MEM)
|
|
ureidopenicillins <- c(PIP, TZP, AZL, MEZ)
|
|
all_betalactams <- c(aminopenicillins, cephalosporins, carbapenems, ureidopenicillins, AMC, OXA, FLC, PEN)
|
|
fluoroquinolones <- c(OFX, CIP, NOR, LVX, MFX)
|
|
# nolint end
|
|
|
|
# help function to get available antibiotic column names ------------------
|
|
get_antibiotic_columns <- function(x, df) {
|
|
x <- trimws(unlist(strsplit(x, ",", fixed = TRUE)))
|
|
y <- character(0)
|
|
for (i in seq_len(length(x))) {
|
|
if (is.function(get(x[i]))) {
|
|
stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.")
|
|
}
|
|
y <- c(y, tryCatch(get(x[i]), error = function(e) ""))
|
|
}
|
|
y[y != "" & y %in% colnames(df)]
|
|
}
|
|
get_antibiotic_names <- function(x) {
|
|
x <- x %>%
|
|
strsplit(",") %>%
|
|
unlist() %>%
|
|
trimws() %>%
|
|
sapply(function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
|
|
sort() %>%
|
|
paste(collapse = ", ")
|
|
x <- gsub("_", " ", x, fixed = TRUE)
|
|
x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
|
|
x
|
|
}
|
|
format_antibiotic_names <- function(ab_names, ab_results) {
|
|
ab_names <- trimws(unlist(strsplit(ab_names, ",")))
|
|
ab_results <- trimws(unlist(strsplit(ab_results, ",")))
|
|
if (length(ab_results) == 1) {
|
|
if (length(ab_names) == 1) {
|
|
# like FOX S
|
|
x <- paste(ab_names, "is")
|
|
} else if (length(ab_names) == 2) {
|
|
# like PEN,FOX S
|
|
x <- paste(paste0(ab_names, collapse = " and "), "are both")
|
|
} else {
|
|
# like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment)
|
|
x <- paste(paste0(ab_names, collapse = " and "), "are all")
|
|
}
|
|
return(paste0(x, " '", ab_results, "'"))
|
|
} else {
|
|
if (length(ab_names) == 2) {
|
|
# like PEN,FOX S,R
|
|
paste0(ab_names[1], " is '", ab_results[1], "' and ",
|
|
ab_names[2], " is '", ab_results[2], "'")
|
|
} else {
|
|
# like PEN,FOX,GEN S,R,R (although dependency on > 2 ABx does not exist at the moment)
|
|
paste0(ab_names[1], " is '", ab_results[1], "' and ",
|
|
ab_names[2], " is '", ab_results[2], "' and ",
|
|
ab_names[3], " is '", ab_results[3], "'")
|
|
}
|
|
}
|
|
}
|
|
|
|
as.rsi_no_warning <- function(x) suppressWarnings(as.rsi(x))
|
|
no_added <- 0
|
|
no_changed <- 0
|
|
|
|
# Other rules: enzyme inhibitors ------------------------------------------
|
|
if (any(c("all", "other") %in% rules)) {
|
|
if (info == TRUE) {
|
|
cat(font_bold(paste0("\nRules by this AMR package (",
|
|
font_red(paste0("v", utils::packageVersion("AMR"), ", ",
|
|
format(utils::packageDate("AMR"), "%Y"))), "), see ?eucast_rules\n")))
|
|
}
|
|
|
|
ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]
|
|
ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$name)
|
|
ab_enzyme$base_ab <- as.ab(ab_enzyme$base_name)
|
|
for (i in seq_len(nrow(ab_enzyme))) {
|
|
if (all(c(ab_enzyme[i, ]$ab, ab_enzyme[i, ]$base_ab) %in% names(cols_ab), na.rm = TRUE)) {
|
|
ab_name_base <- ab_name(cols_ab[ab_enzyme[i, ]$base_ab], language = NULL, tolower = TRUE)
|
|
ab_name_enzyme <- ab_name(cols_ab[ab_enzyme[i, ]$ab], language = NULL, tolower = TRUE)
|
|
|
|
# Set base to R where base + enzyme inhibitor is R
|
|
rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
|
|
ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
|
|
if (info == TRUE) {
|
|
cat(rule_current)
|
|
}
|
|
run_changes <- edit_rsi(to = "R",
|
|
rule = c(rule_current, "Other rules", ""),
|
|
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$ab]]) == "R"),
|
|
cols = cols_ab[ab_enzyme[i, ]$base_ab])
|
|
no_added <- no_added + run_changes$added
|
|
no_changed <- no_changed + run_changes$changed
|
|
# Print number of new changes
|
|
if (info == TRUE) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(no_added = no_added, no_changed = no_changed)
|
|
# and reset counters
|
|
no_added <- 0
|
|
no_changed <- 0
|
|
}
|
|
|
|
# Set base + enzyme inhibitor to S where base is S
|
|
rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
|
|
ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
|
|
if (info == TRUE) {
|
|
cat(rule_current)
|
|
}
|
|
run_changes <- edit_rsi(to = "S",
|
|
rule = c(rule_current, "Other rules", ""),
|
|
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$base_ab]]) == "S"),
|
|
cols = cols_ab[ab_enzyme[i, ]$ab])
|
|
no_added <- no_added + run_changes$added
|
|
no_changed <- no_changed + run_changes$changed
|
|
# Print number of new changes
|
|
if (info == TRUE) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(no_added = no_added, no_changed = no_changed)
|
|
# and reset counters
|
|
no_added <- 0
|
|
no_changed <- 0
|
|
}
|
|
}
|
|
}
|
|
|
|
} else {
|
|
if (info == TRUE) {
|
|
cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n"))
|
|
}
|
|
}
|
|
|
|
# Official EUCAST rules ---------------------------------------------------
|
|
eucast_notification_shown <- FALSE
|
|
if (!is.null(list(...)$eucast_rules_df)) {
|
|
# this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
|
|
eucast_rules_df <- list(...)$eucast_rules_df
|
|
} else {
|
|
# otherwise internal data file, created in data-raw/internals.R
|
|
eucast_rules_df <- eucast_rules_file
|
|
}
|
|
for (i in seq_len(nrow(eucast_rules_df))) {
|
|
|
|
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"]
|
|
rule_current <- eucast_rules_df[i, "reference.rule"]
|
|
rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule"]
|
|
rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group"]
|
|
rule_group_current <- eucast_rules_df[i, "reference.rule_group"]
|
|
if (is.na(eucast_rules_df[i, 4])) {
|
|
rule_text <- paste0("always report as '", eucast_rules_df[i, 7], "': ", get_antibiotic_names(eucast_rules_df[i, 6]))
|
|
} else {
|
|
rule_text <- paste0("report as '", eucast_rules_df[i, 7], "' when ",
|
|
format_antibiotic_names(ab_names = get_antibiotic_names(eucast_rules_df[i, 4]),
|
|
ab_results = eucast_rules_df[i, 5]), ": ",
|
|
get_antibiotic_names(eucast_rules_df[i, 6]))
|
|
}
|
|
if (i == 1) {
|
|
rule_previous <- ""
|
|
rule_group_previous <- ""
|
|
}
|
|
if (i == nrow(eucast_rules_df)) {
|
|
rule_next <- ""
|
|
}
|
|
|
|
# don't apply rules if user doesn't want to apply them
|
|
if (rule_group_current %like% "breakpoint" & !any(c("all", "breakpoints") %in% rules)) {
|
|
next
|
|
}
|
|
if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) {
|
|
next
|
|
}
|
|
|
|
if (info == TRUE & !rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
|
|
cat(paste0("\n", font_grey(strrep("-", options()$width - 1)),
|
|
"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
|
|
"\n", font_blue("http://eucast.org/"), "\n"))
|
|
eucast_notification_shown <- TRUE
|
|
}
|
|
|
|
if (info == TRUE) {
|
|
# Print rule (group) ------------------------------------------------------
|
|
if (rule_group_current != rule_group_previous) {
|
|
# is new rule group, one of Breakpoints, Expert Rules and Other
|
|
cat(font_bold(
|
|
ifelse(
|
|
rule_group_current %like% "breakpoint",
|
|
paste0("\nEUCAST Clinical Breakpoints (",
|
|
font_red(paste0("v", EUCAST_VERSION_BREAKPOINTS)), ")\n"),
|
|
ifelse(
|
|
rule_group_current %like% "expert",
|
|
paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (",
|
|
font_red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"),
|
|
""))))
|
|
}
|
|
# Print rule -------------------------------------------------------------
|
|
if (rule_current != rule_previous) {
|
|
# is new rule within group, print its name
|
|
if (rule_current %in% c(microorganisms$family,
|
|
microorganisms$fullname)) {
|
|
cat(font_italic(rule_current))
|
|
} else {
|
|
cat(rule_current)
|
|
}
|
|
warned <- FALSE
|
|
}
|
|
}
|
|
|
|
# Get rule from file ------------------------------------------------------
|
|
col_mo_property <- eucast_rules_df[i, 1]
|
|
like_is_one_of <- eucast_rules_df[i, 2]
|
|
|
|
# be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
|
|
if (eucast_rules_df[i, 3] %like% "coagulase") {
|
|
all_staph <- microorganisms[which(microorganisms$genus == "Staphylococcus"), ]
|
|
all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL))
|
|
if (eucast_rules_df[i, 3] %like% "coagulase") {
|
|
eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "negative"),
|
|
"fullname",
|
|
drop = TRUE],
|
|
collapse = "|"),
|
|
")$")
|
|
} else {
|
|
eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "positive"),
|
|
"fullname",
|
|
drop = TRUE],
|
|
collapse = "|"),
|
|
")$")
|
|
}
|
|
like_is_one_of <- "like"
|
|
}
|
|
|
|
if (like_is_one_of == "is") {
|
|
# so e.g. 'Enterococcus' will turn into '^Enterococcus$'
|
|
mo_value <- paste0("^", eucast_rules_df[i, 3], "$")
|
|
} else if (like_is_one_of == "one_of") {
|
|
# so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$'
|
|
mo_value <- paste0("^(",
|
|
paste(trimws(unlist(strsplit(eucast_rules_df[i, 3], ",", fixed = TRUE))),
|
|
collapse = "|"),
|
|
")$")
|
|
} else if (like_is_one_of == "like") {
|
|
mo_value <- eucast_rules_df[i, 3]
|
|
} else {
|
|
stop("invalid value for column 'like.is.one_of'", call. = FALSE)
|
|
}
|
|
|
|
source_antibiotics <- eucast_rules_df[i, 4]
|
|
source_value <- trimws(unlist(strsplit(eucast_rules_df[i, 5], ",", fixed = TRUE)))
|
|
target_antibiotics <- eucast_rules_df[i, 6]
|
|
target_value <- eucast_rules_df[i, 7]
|
|
|
|
if (is.na(source_antibiotics)) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value),
|
|
error = function(e) integer(0))
|
|
} else {
|
|
source_antibiotics <- get_antibiotic_columns(source_antibiotics, x)
|
|
if (length(source_value) == 1 & length(source_antibiotics) > 1) {
|
|
source_value <- rep(source_value, length(source_antibiotics))
|
|
}
|
|
if (length(source_antibiotics) == 0) {
|
|
rows <- integer(0)
|
|
} else if (length(source_antibiotics) == 1) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
|
|
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
|
|
error = function(e) integer(0))
|
|
} else if (length(source_antibiotics) == 2) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
|
|
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
|
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
|
|
error = function(e) integer(0))
|
|
} else if (length(source_antibiotics) == 3) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
|
|
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
|
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
|
|
& as.rsi_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
|
|
error = function(e) integer(0))
|
|
} else {
|
|
stop("only 3 antibiotics supported for source_antibiotics ", call. = FALSE)
|
|
}
|
|
}
|
|
|
|
cols <- get_antibiotic_columns(target_antibiotics, x)
|
|
|
|
# Apply rule on data ------------------------------------------------------
|
|
# this will return the unique number of changes
|
|
run_changes <- edit_rsi(to = target_value,
|
|
rule = c(rule_text, rule_group_current, rule_current),
|
|
rows = rows,
|
|
cols = cols)
|
|
no_added <- no_added + run_changes$added
|
|
no_changed <- no_changed + run_changes$changed
|
|
|
|
# Print number of new changes ---------------------------------------------
|
|
if (info == TRUE & rule_next != rule_current) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(no_added = no_added, no_changed = no_changed)
|
|
# and reset counters
|
|
no_added <- 0
|
|
no_changed <- 0
|
|
}
|
|
}
|
|
|
|
# Print overview ----------------------------------------------------------
|
|
if (info == TRUE) {
|
|
if (verbose == TRUE) {
|
|
wouldve <- "would have "
|
|
} else {
|
|
wouldve <- ""
|
|
}
|
|
|
|
verbose_info <- verbose_info %>%
|
|
arrange(row, rule_group, rule_name, col)
|
|
|
|
cat(paste0("\n", font_grey(strrep("-", options()$width - 1)), "\n"))
|
|
cat(font_bold(paste("The rules", paste0(wouldve, "affected"),
|
|
formatnr(n_distinct(verbose_info$row)),
|
|
"out of", formatnr(nrow(x_original)),
|
|
"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
|
|
|
|
n_added <- verbose_info %>% filter(is.na(old)) %>% nrow()
|
|
n_changed <- verbose_info %>% filter(!is.na(old)) %>% nrow()
|
|
|
|
# print added values ----
|
|
if (n_added == 0) {
|
|
colour <- cat # is function
|
|
} else {
|
|
colour <- font_green # is function
|
|
}
|
|
cat(colour(paste0("=> ", wouldve, "added ",
|
|
font_bold(formatnr(verbose_info %>%
|
|
filter(is.na(old)) %>%
|
|
nrow()), "test results"),
|
|
"\n")))
|
|
if (n_added > 0) {
|
|
added_summary <- verbose_info %>%
|
|
filter(is.na(old)) %>%
|
|
group_by(new) %>%
|
|
summarise(n = n())
|
|
cat(paste(" -",
|
|
paste0(formatnr(added_summary$n), " test result", ifelse(added_summary$n > 1, "s", ""),
|
|
" added as ", added_summary$new), collapse = "\n"))
|
|
}
|
|
|
|
# print changed values ----
|
|
if (n_changed == 0) {
|
|
colour <- cat # is function
|
|
} else {
|
|
colour <- font_blue # is function
|
|
}
|
|
if (n_added + n_changed > 0) {
|
|
cat("\n")
|
|
}
|
|
cat(colour(paste0("=> ", wouldve, "changed ",
|
|
font_bold(formatnr(verbose_info %>%
|
|
filter(!is.na(old)) %>%
|
|
nrow()), "test results"),
|
|
"\n")))
|
|
if (n_changed > 0) {
|
|
changed_summary <- verbose_info %>%
|
|
filter(!is.na(old)) %>%
|
|
group_by(old, new) %>%
|
|
summarise(n = n())
|
|
cat(paste(" -",
|
|
paste0(formatnr(changed_summary$n), " test result", ifelse(changed_summary$n > 1, "s", ""), " changed from ",
|
|
changed_summary$old, " to ", changed_summary$new), collapse = "\n"))
|
|
cat("\n")
|
|
}
|
|
cat(paste0(font_grey(strrep("-", options()$width - 1)), "\n"))
|
|
|
|
if (verbose == FALSE & nrow(verbose_info) > 0) {
|
|
cat(paste("\nUse", font_bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n"))
|
|
} else if (verbose == TRUE) {
|
|
cat(paste0("\nUsed 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data.\n\n"))
|
|
}
|
|
}
|
|
|
|
if (isTRUE(warn_lacking_rsi_class)) {
|
|
warning("Not all columns with antimicrobial results are of class <rsi>.\n",
|
|
"Transform eligible columns to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)",
|
|
call. = FALSE)
|
|
}
|
|
|
|
# Return data set ---------------------------------------------------------
|
|
if (verbose == TRUE) {
|
|
rownames(verbose_info) <- NULL
|
|
verbose_info
|
|
} else {
|
|
# reset original attributes
|
|
x_original <- x_original[, c(col_mo, cols_ab, ".rowid"), drop = FALSE]
|
|
x_original.bak <- x_original.bak[, setdiff(colnames(x_original.bak), c(col_mo, cols_ab)), drop = FALSE]
|
|
x_original.bak <- x_original.bak %>%
|
|
left_join(x_original, by = ".rowid")
|
|
x_original.bak <- x_original.bak[, old_cols, drop = FALSE]
|
|
attributes(x_original.bak) <- old_attributes
|
|
x_original.bak
|
|
}
|
|
}
|