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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Dataset with 420 antibiotics
#'
#' A dataset containing all antibiotics with a J0 code, with their DDD's. Properties were downloaded from the WHO, see Source.
#' @format A data.frame with 420 observations and 18 variables:
#' \describe{
#' \item{\code{atc}}{ATC code, like \code{J01CR02}}
#' \item{\code{molis}}{MOLIS code, like \code{amcl}}
#' \item{\code{umcg}}{UMCG code, like \code{AMCL}}
#' \item{\code{abbr}}{Abbreviation as used by many countries, to be used for \code{\link{guess_atc}}}
#' \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and enzyme inhibitor"}}
#' \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
#' \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
#' \item{\code{trade_name}}{Trade name as used by many countries, to be used for \code{\link{guess_atc}}}
#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
#' \item{\code{oral_units}}{Units of \code{ddd_units}}
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
#' \item{\code{atc_group1}}{ATC group, like \code{"Macrolides, lincosamides and streptogramins"}}
#' \item{\code{atc_group2}}{Subgroup of \code{atc_group1}, like \code{"Macrolides"}}
#' \item{\code{atc_group1_nl}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
#' \item{\code{atc_group2_nl}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
#' \item{\code{useful_gramnegative}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
#' \item{\code{useful_grampositive}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
#' }
#' @source - World Health Organization: \url{https://www.whocc.no/atc_ddd_index/} \cr - EUCAST - Expert rules intrinsic exceptional V3.1 \cr - MOLIS (LIS of Certe): \url{https://www.certe.nl} \cr - GLIMS (LIS of UMCG): \url{https://www.umcg.nl}
#' @seealso \code{\link{microorganisms}}
# abbr and trade_name created with:
# https://hs.unr.edu/Documents/dhs/chs/NVPHTC/antibiotic_refeference_guide.pdf
# antibiotics %>%
# mutate(abbr =
# case_when(
# official == 'Amikacin' ~ 'Ak|AN|AMI|AMK',
# official == 'Amoxicillin' ~ 'AMX|AMOX|AC',
# official == 'Amoxicillin and beta-lactamase inhibitor' ~ 'AUG|A/C|XL|AML',
# official == 'Ampicillin' ~ 'AM|AMP',
# official == 'Ampicillin and beta-lactamase inhibitor' ~ 'A/S|SAM|AMS|AB',
# official == 'Azithromycin' ~ 'Azi|AZM|AZ',
# official == 'Azlocillin' ~ 'AZ|AZL',
# official == 'Aztreonam' ~ 'Azt|ATM|AT|AZM',
# official == 'Carbenicillin' ~ 'Cb|BAR',
# official == 'Cefaclor' ~ 'Ccl|CEC|Cfr|FAC|CF',
# official == 'Cefadroxil' ~ 'CFR|FAD',
# official == 'Cefazolin' ~ 'Cfz|CZ|FAZ|KZ',
# official == 'Cefdinir' ~ 'Cdn|CDR|DIN|CD|CFD',
# official == 'Cefditoren' ~ 'CDN',
# official == 'Cefepime' ~ 'Cpe|FEP|PM|CPM',
# official == 'Cefixime' ~ 'Cfe|DCFM|FIX|IX',
# official == 'Cefoperazone' ~ 'Cfp|CPZ|PER|FOP|CP',
# official == 'Cefotaxime' ~ 'Cft|CTX|TAX|FOT|CT',
# official == 'Cefotetan' ~ 'Ctn|CTT|CTE|TANS|CN',
# official == 'Cefoxitin' ~ 'Cfx|FOX|CX|FX',
# official == 'Cefpodoxime' ~ 'Cpd|POD|PX',
# official == 'Cefprozil' ~ 'Cpz|CPR|FP',
# official == 'Ceftaroline' ~ 'CPT',
# official == 'Ceftazidime' ~ 'Caz|TAZ|TZ',
# official == 'Ceftibuten' ~ 'CTB|TIB|CB',
# official == 'Ceftizoxime' ~ 'Cz|ZOX|CZX|CZ|CTZ|TIZ',
# official == 'Ceftriaxone' ~ 'Cax|CRO|CTR|FRX|AXO|TX',
# official == 'Cefuroxime' ~ 'Crm|CXM|CFX|ROX|FUR|XM',
# official == 'Cephalexin' ~ 'CN|LX|CFL',
# official == 'Cephalothin' ~ 'Cf',
# official == 'Chloramphenicol' ~ 'C|CHL|CL',
# official == 'Ciprofloxacin' ~ 'Cp|CIP|CI',
# official == 'Clarithromycin' ~ 'Cla|CLR|CLM|CH',
# official == 'Clindamycin' ~ 'Cd|CC|CM|CLI|DA',
# official == 'Colistin' ~ 'CL|CS|CT',
# official == 'Daptomycin' ~ 'Dap',
# official == 'Doxycycline' ~ 'Dox',
# official == 'Doripenem' ~ 'DOR|Dor',
# official == 'Ertapenem' ~ 'Etp',
# official == 'Erythromycin' ~ 'E|ERY|EM',
# official == 'Fosfomycin' ~ 'FOS|FF|FO|FM',
# official == 'Flucloxacillin' ~ 'CLOX',
# official == 'Gentamicin' ~ 'Gm|CN|GEN',
# official == 'Imipenem' ~ 'Imp|IPM|IMI|IP',
# official == 'Kanamycin' ~ 'K|KAN|HLK|KM',
# official == 'Levofloxacin' ~ 'Lvx|LEV|LEVO|LE',
# official == 'Linezolid' ~ 'Lzd|LNZ|LZ',
# official == 'Lomefloxacin' ~ 'Lmf|LOM',
# official == 'Meropenem' ~ 'Mer|MEM|MERO|MRP|MP',
# official == 'Metronidazole' ~ 'MNZ',
# official == 'Mezlocillin' ~ 'Mz|MEZ',
# official == 'Minocycline' ~ 'Min|MI|MN|MNO|MC|MH',
# official == 'Moxifloxacin' ~ 'Mox|MXF',
# official == 'Mupirocin' ~ 'MUP',
# official == 'Nafcillin' ~ 'Naf|NF',
# official == 'Nalidixic acid' ~ 'NA|NAL',
# official == 'Nitrofurantoin' ~ 'Fd|F/M|FT|NIT|NI|F',
# official == 'Norfloxacin' ~ 'Nxn|NOR|NX',
# official == 'Ofloxacin' ~ 'Ofl|OFX|OF',
# official == 'Oxacillin' ~ 'Ox|OXS|OXA',
# official == 'Benzylpenicillin' ~ 'P|PEN|PV',
# official == 'Penicillins, combinations with other antibacterials' ~ 'P|PEN|PV',
# official == 'Piperacillin' ~ 'Pi|PIP|PP',
# official == 'Piperacillin and beta-lactamase inhibitor' ~ 'PT|TZP|PTZ|P/T|PTc',
# official == 'Polymyxin B' ~ 'PB',
# official == 'Quinupristin/dalfopristin' ~ 'Syn|Q/D|QDA|RP',
# official == 'Rifampin' ~ 'Rif|RA|RI|RD',
# official == 'Spectinomycin' ~ 'SPT|SPE|SC',
# official == 'Streptomycin' ~ 'S|STR',
# official == 'Teicoplanin' ~ 'Tei|TEC|TPN|TP|TPL',
# official == 'Telavancin' ~ 'TLV',
# official == 'Telithromcyin' ~ 'Tel',
# official == 'Tetracycline' ~ 'Te|TET|TC',
# official == 'Ticarcillin' ~ 'Ti|TIC|TC',
# official == 'Ticarcillin and beta-lactamase inhibitor' ~ 'Tim|T/C|TCC|TLc',
# official == 'Tigecycline' ~ 'TGC',
# official == 'Tobramycin' ~ 'To|NN|TM|TOB',
# official == 'Trimethoprim' ~ 'T|TMP|TR|W',
# official == 'Sulfamethoxazole and trimethoprim' ~ 'T/S|SXT|SxT|TS|COT',
# official == 'Vancomycin' ~ 'Va|VAN',
# TRUE ~ NA_character_),
#
# trade_name =
# case_when(
# official == 'Amikacin' ~ 'Amikin',
# official == 'Amoxicillin' ~ 'Amoxil|Dispermox|Larotid|Trimox',
# official == 'Amoxicillin and beta-lactamase inhibitor' ~ 'Augmentin',
# official == 'Ampicillin' ~ 'Pfizerpen-A|Principen',
# official == 'Ampicillin and beta-lactamase inhibitor' ~ 'Unasyn',
# official == 'Azithromycin' ~ 'Zithromax',
# official == 'Azlocillin' ~ 'Azlin',
# official == 'Aztreonam' ~ 'Azactam',
# official == 'Carbenicillin' ~ 'Geocillin',
# official == 'Cefaclor' ~ 'Ceclor',
# official == 'Cefadroxil' ~ 'Duricef',
# official == 'Cefazolin' ~ 'Ancef',
# official == 'Cefdinir' ~ 'Omnicef',
# official == 'Cefditoren' ~ 'Spectracef',
# official == 'Cefepime' ~ 'Maxipime',
# official == 'Cefixime' ~ 'Suprax',
# official == 'Cefoperazone' ~ 'Cefobid',
# official == 'Cefotaxime' ~ 'Claforan',
# official == 'Cefotetan' ~ 'Cefotan',
# official == 'Cefoxitin' ~ 'Mefoxin',
# official == 'Cefpodoxime' ~ 'Vantin',
# official == 'Cefprozil' ~ 'Cefzil',
# official == 'Ceftaroline' ~ 'Teflaro',
# official == 'Ceftazidime' ~ 'Fortaz|Tazicef|Tazidime',
# official == 'Ceftibuten' ~ 'Cedax',
# official == 'Ceftizoxime' ~ 'Cefizox',
# official == 'Ceftriaxone' ~ 'Rocephin',
# official == 'Cefuroxime' ~ 'Ceftin|Zinacef',
# official == 'Cephalexin' ~ 'Keflex|Panixine',
# official == 'Cephalothin' ~ 'Keflin',
# official == 'Chloramphenicol' ~ 'Chloromycetin',
# official == 'Ciprofloxacin' ~ 'Cipro|Ciloxan|Ciproxin',
# official == 'Clarithromycin' ~ 'Biaxin',
# official == 'Clindamycin' ~ 'Cleocin|Clinda-Derm|Clindagel|Clindesse|Clindets|Evoclin',
# official == 'Colistin' ~ 'Coly-Mycin',
# official == 'Daptomycin' ~ 'Cubicin',
# official == 'Doxycycline' ~ 'Doryx|Monodox|Vibramycin|Atridox|Oracea|Periostat|Vibra-Tabs',
# official == 'Doripenem' ~ 'Doribax',
# official == 'Ertapenem' ~ 'Invanz',
# official == 'Erythromycin' ~ 'Eryc|EryPed|Erythrocin|E-Base|E-Glades|E-Mycin|E.E.S.|Ery-Tab|Eryderm|Erygel|Erythra-derm|Eryzole|Pediamycin',
# official == 'Fosfomycin' ~ 'Monurol',
# official == 'Flucloxacillin' ~ 'Flopen|Floxapen|Fluclox|Sesamol|Softapen|Staphylex',
# official == 'Gentamicin' ~ 'Garamycin|Genoptic',
# official == 'Imipenem' ~ 'Primaxin',
# official == 'Kanamycin' ~ 'Kantrex',
# official == 'Levofloxacin' ~ 'Levaquin|Quixin',
# official == 'Linezolid' ~ 'Zyvox',
# official == 'Lomefloxacin' ~ 'Maxaquin',
# official == 'Meropenem' ~ 'Merrem',
# official == 'Metronidazole' ~ 'Flagyl|MetroGel|MetroCream|MetroLotion',
# official == 'Mezlocillin' ~ 'Mezlin',
# official == 'Minocycline' ~ 'Arestin|Solodyn',
# official == 'Moxifloxacin' ~ 'Avelox|Vigamox',
# official == 'Mupirocin' ~ 'Bactroban|Centany',
# official == 'Nafcillin' ~ 'Unipen',
# official == 'Nalidixic acid' ~ 'NegGram',
# official == 'Nitrofurantoin' ~ 'Furadantin|Macrobid|Macrodantin',
# official == 'Norfloxacin' ~ 'Noroxin',
# official == 'Ofloxacin' ~ 'Floxin|Ocuflox|Ophthalmic',
# official == 'Oxacillin' ~ 'Bactocill',
# official == 'Benzylpenicillin' ~ 'Permapen|Pfizerpen|Veetids',
# official == 'Penicillins, combinations with other antibacterials' ~ 'Permapen|Pfizerpen|Veetids',
# official == 'Piperacillin' ~ 'Pipracil',
# official == 'Piperacillin and beta-lactamase inhibitor' ~ 'Zosyn',
# official == 'Polymyxin B' ~ 'Poly-RX',
# official == 'Quinupristin/dalfopristin' ~ 'Synercid',
# official == 'Rifampin' ~ 'Rifadin|Rifamate|Rimactane',
# official == 'Spectinomycin' ~ 'Trobicin',
# official == 'Streptomycin' ~ 'Streptomycin Sulfate',
# official == 'Teicoplanin' ~ 'Targocid',
# official == 'Telavancin' ~ 'Vibativ',
# official == 'Telithromcyin' ~ 'Ketek',
# official == 'Tetracycline' ~ 'Sumycin|Bristacycline|Tetrex',
# official == 'Ticarcillin' ~ 'Ticar',
# official == 'Ticarcillin and beta-lactamase inhibitor' ~ 'Timentin',
# official == 'Tigecycline' ~ 'Tygacil',
# official == 'Tobramycin' ~ 'Tobi|Aktob|Tobre',
# official == 'Trimethoprim' ~ 'Primsol|Proloprim',
# official == 'Sulfamethoxazole and trimethoprim' ~ 'Bactrim|Septra|Sulfatrim',
# official == 'Vancomycin' ~ 'Vancocin|Vancomycin Hydrochloride',
# TRUE ~ NA_character_)
# )
# last two columns created with:
# antibiotics %>%
# mutate(useful_gramnegative =
# if_else(
# atc_group1 %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)' |
# atc_group2 %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)' |
# official %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)',
# FALSE,
# NA
# ),
# useful_grampositive =
# if_else(
# atc_group1 %like% '(aztreonam|temocillin|polymyxin|colistin|nalidixic)' |
# atc_group2 %like% '(aztreonam|temocillin|polymyxin|colistin|nalidixic)' |
# official %like% '(aztreonam|temocillin|polymyxin|colistin|nalidixic)',
# FALSE,
# NA
# )
# )
"antibiotics"
#' Dataset with ~2500 microorganisms
#'
#' A dataset containing 2464 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
#' @format A data.frame with 2464 observations and 12 variables:
#' \describe{
#' \item{\code{bactid}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode of microorganism}
#' \item{\code{family}}{Family name of microorganism}
#' \item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
#' \item{\code{species}}{Species name of microorganism, like \code{"coli"}}
#' \item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
#' \item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
#' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
#' \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
#' \item{\code{aerobic}}{Logical whether bacteria is aerobic}
#' \item{\code{type_nl}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
#' \item{\code{gramstain_nl}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
# new <- microorganisms %>% filter(genus == "Bacteroides") %>% .[1,]
# new[1, 'bactid'] <- "DIAPNU"
# new[1, 'bactsys'] <- "DIAPNU"
# new[1, 'family'] <- "Veillonellaceae"
# new[1, 'genus'] <- "Dialister"
# new[1, 'species'] <- "pneumosintes"
# new[1, 'subspecies'] <- NA
# new[1, 'fullname'] <- paste(new[1, 'genus'], new[1, 'species'])
# microorganisms <- microorganisms %>% bind_rows(new) %>% arrange(bactid)
#' @seealso \code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
"microorganisms"
#' Translation table for UMCG with ~1100 microorganisms
#'
#' A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$bactid} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{bactid}'s with \code{\link{guess_bactid}}.
#' @format A data.frame with 1090 observations and 2 variables:
#' \describe{
#' \item{\code{mocode}}{Code of microorganism according to UMCG MMB}
#' \item{\code{bactid}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl}
#' @seealso \code{\link{guess_bactid}} \code{\link{microorganisms}}
"microorganisms.umcg"
#' Dataset with 2000 blood culture isolates of septic patients
#'
#' An anonymised dataset containing 2000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, press F1.
#' @format A data.frame with 2000 observations and 49 variables:
#' \describe{
#' \item{\code{date}}{date of receipt at the laboratory}
#' \item{\code{hospital_id}}{ID of the hospital, from A to D}
#' \item{\code{ward_icu}}{logical to determine if ward is an intensive care unit}
#' \item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward}
#' \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
#' \item{\code{age}}{age of the patient}
#' \item{\code{sex}}{sex of the patient}
#' \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
#' \item{\code{bactid}}{ID of microorganism, see \code{\link{microorganisms}}}
#' \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
#' @examples
#' # ----------- #
#' # PREPARATION #
#' # ----------- #
#'
#' # Save this example dataset to an object, so we can edit it:
#' my_data <- septic_patients
#'
#' # load the dplyr package to make data science A LOT easier
#' library(dplyr)
#'
#' # Add first isolates to our dataset:
#' my_data <- my_data %>%
#' mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
#'
#' # -------- #
#' # ANALYSIS #
#' # -------- #
#'
#' # 1. Get the amoxicillin resistance percentages (p)
#' # and numbers (n) of E. coli, divided by hospital:
#'
#' my_data %>%
#' filter(bactid == guess_bactid("E. coli"),
#' first_isolates == TRUE) %>%
#' group_by(hospital_id) %>%
#' summarise(n = n_rsi(amox),
#' p = portion_IR(amox))
#'
#'
#' # 2. Get the amoxicillin/clavulanic acid resistance
#' # percentages of E. coli, trend over the years:
#'
#' my_data %>%
#' filter(bactid == guess_bactid("E. coli"),
#' first_isolates == TRUE) %>%
#' group_by(year = format(date, "%Y")) %>%
#' summarise(n = n_rsi(amcl),
#' p = portion_IR(amcl, minimum = 20))
"septic_patients"
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