P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

(v0.9.0.9019) website update

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-02-01 15:09:36 +01:00
parent f152ab9a48
commit 4e1c16c5a5
24 changed files with 70132 additions and 101 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR
Version: 0.9.0.9018
Date: 2020-01-31
Version: 0.9.0.9019
Date: 2020-02-01
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
NEWS.md
View File

@ -1,5 +1,5 @@
# AMR 0.9.0.9018
## <small>Last updated: 31-Jan-2020</small>
# AMR 0.9.0.9019
## <small>Last updated: 01-Feb-2020</small>
### New
* Support for LOINC and SNOMED codes

11
R/data.R
View File

@ -52,6 +52,12 @@
#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
#'
#' Synonyms (i.e. trade names) are derived from the Compound ID (`cid`) and consequently only available where a CID is available.
#'
#' ### Direct download
#' These data sets are available as 'flat files' for use even without R - you can find the files here:
#'
#' * <https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R>
#' * <https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R>
#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
#'
#' WHONET 2019 software: <http://www.whonet.org/software.html>
@ -88,6 +94,11 @@
#' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
#' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not in the Catalogue of Life
#' - 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
#'
#' ### Direct download
#' This data set is available as 'flat file' for use even without R - you can find the file here:
#'
#' * <https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R>
#' @section About the records from DSMZ (see source):
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
#'

453
data-raw/antibiotics.txt Normal file
View File

@ -0,0 +1,453 @@
"ab" "atc" "cid" "name" "group" "atc_group1" "atc_group2" "oral_ddd" "oral_units" "iv_ddd" "iv_units"
"AMA" "J04AA01" 4649 "4-aminosalicylic acid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" 12 "g"
"FCT" "D01AE21" 3366 "5-fluorocytosine" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use"
"ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides"
"ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides"
"ALS" "J04BA03" 8954 "Aldesulfone sodium" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" 0.33 "g"
"AMK" "J01GB06" 37768 "Amikacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 1 "g"
"AKF" "Amikacin/fosfomycin" "Aminoglycosides"
"AMX" "J01CA04" 33613 "Amoxicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 1 "g" 1 "g"
"AMC" "J01CR02" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" 1 "g" 3 "g"
"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins"
"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" 35 "mg"
"AMP" "J01CA01" 6249 "Ampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 2 "g" 2 "g"
"SAM" "J01CR01" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" 6 "g"
"AMR" 73341 "Amprolium" "Other antibacterials"
"ANI" "J02AX06" 166548 "Anidulafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" 0.1 "g"
"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins"
"APR" 3081545 "Apramycin" "Aminoglycosides"
"ARB" 68682 "Arbekacin" "Aminoglycosides"
"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins"
"AST" 5284517 "Astromicin" "Aminoglycosides"
"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins"
"AVI" 71674 "Avilamycin" "Other antibacterials"
"AVO" 16131159 "Avoparcin" "Glycopeptides"
"AZD" "J01CE04" 15574941 "Azidocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 1.5 "g"
"AZM" "J01FA10" 447043 "Azithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.3 "g" 0.5 "g"
"AZL" "J01CA09" 6479523 "Azlocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 12 "g"
"ATM" "J01DF01" 5742832 "Aztreonam" "Beta-lactams/penicillins" "Other beta-lactam antibacterials" "Monobactams" 4 "g"
"AZA" "Aztreonam/avibactam" "Beta-lactams/penicillins"
"BAM" "J01CA06" 441397 "Bacampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 1.2 "g"
"BAC" "R02AB04" 78358334 "Bacitracin zinc" "Other antibacterials"
"BDQ" 5388906 "Bedaquiline" "Other antibacterials"
"BEK" 439318 "Bekanamycin" "Aminoglycosides"
"BNB" "J01CE08" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 3.6 "g"
"BNP" "J01CE10" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 2 "g"
"BES" 10178705 "Besifloxacin" "Quinolones"
"BIA" 71339 "Biapenem" "Carbapenems"
"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials"
"BDP" "J01EA02" 68760 "Brodimoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" 0.2 "g"
"BUT" 47472 "Butoconazole" "Antifungals/antimycotics"
"CDZ" "J01DD09" 44242317 "Cadazolid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 2 "g"
"CLA" "J04AA03" "Calcium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives"
"CAP" "J04AB30" 135565060 "Capreomycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" 1 "g"
"CRB" "J01CA03" 20824 "Carbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 12 "g"
"CRN" "J01CA05" 93184 "Carindacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 4 "g"
"CAR" 6540466 "Carumonam" "Other antibacterials"
"CAS" "J02AX04" 2826718 "Caspofungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" 50 "mg"
"CAC" "J01DB10" 91562 "Cefacetrile" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins"
"CEC" "J01DC04" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 1 "g"
"CFR" "J01DB05" 47965 "Cefadroxil" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 2 "g"
"RID" "J01DB02" 5773 "Cefaloridine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 3 "g"
"MAN" "J01DC03" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 6 "g"
"CTZ" "J01DB07" 6410758 "Cefatrizine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 1 "g"
"CZD" "J01DB06" 71736 "Cefazedone" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 3 "g"
"CZO" "J01DB04" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 3 "g"
"CFB" 127527 "Cefbuperazone" "Other antibacterials"
"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)"
"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)"
"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 0.6 "g"
"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 0.4 "g"
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)"
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" 2 "g"
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)"
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)"
"FPZ" "Cefepime/zidebactam" "Other antibacterials"
"CAT" "J01DD10" 5487888 "Cefetamet" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 1 "g"
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)"
"CCL" 71719688 "Cefetecol (Cefcatacol)" "Cephalosporins (4th gen.)"
"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)"
"FDC" 77843966 "Cefiderocol" "Other antibacterials"
"CFM" "J01DD08" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 0.4 "g"
"CMX" "J01DD05" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 2 "g"
"CMZ" "J01DC09" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 4 "g"
"CNX" 71141 "Cefminox" "Other antibacterials"
"DIZ" "J01DD09" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 2 "g"
"CID" "J01DC06" 43594 "Cefonicid" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 1 "g"
"CFP" "J01DD12" 44187 "Cefoperazone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"CSL" "J01DD62" "Cefoperazone/sulbactam" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"CND" "J01DC11" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 4 "g"
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)"
"CTX" "J01DD01" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)"
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)"
"CTT" "J01DC05" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 4 "g"
"CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 1.2 "g" 4 "g"
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)"
"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 6 "g"
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)"
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)"
"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 2 "g"
"CPO" "J01DE02" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" 4 "g"
"CPD" "J01DD13" 6335986 "Cefpodoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 0.4 "g"
"CPX" 6526396 "Cefpodoxime proxetil" "Cephalosporins (3rd gen.)"
"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)"
"CPR" "J01DC10" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 1 "g"
"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.)"
"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins"
"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)"
"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)"
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)"
"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"CZA" "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)"
"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins"
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)"
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)"
"CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 3 "g"
"CTB" "J01DD14" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 0.4 "g"
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)"
"CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)"
"BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)"
"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins"
"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins"
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)"
"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 2 "g"
"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 0.5 "g" 3 "g"
"CXA" 6321416 "Cefuroxime axetil" "Cephalosporins (2nd gen.)"
"CFM2" "J01RA03" "Cefuroxime/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials"
"ZON" 6336505 "Cefuzonam" "Other antibacterials"
"LEX" "J01DB01" 27447 "Cephalexin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 2 "g"
"CEP" "J01DB03" 6024 "Cephalothin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 4 "g"
"HAP" "J01DB08" 30699 "Cephapirin" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 4 "g"
"CED" "J01DB09" 38103 "Cephradine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" 2 "g" 2 "g"
"CTO" 71402 "Cetocycline" "Tetracyclines"
"CHL" "J01BA01" 5959 "Chloramphenicol" "Amphenicols" "Amphenicols" "Amphenicols" 3 "g" 3 "g"
"CTE" "J01AA03" 54675777 "Chlortetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 1 "g"
"CIC" 19003 "Ciclacillin" "Beta-lactams/penicillins"
"CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" 1 "g"
"CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 1 "g" 0.5 "g"
"CLR" "J01FA09" 84029 "Clarithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.5 "g" 1 "g"
"CLA1" 5280980 "Clavulanic acid" "Other antibacterials"
"CLX" 60063 "Clinafloxacin" "Quinolones"
"CLI" "J01FF01" 446598 "Clindamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" 1.2 "g" 1.8 "g"
"CLF" "J04BA01" 2794 "Clofazimine" "Antimycobacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" 0.1 "g"
"CLF1" "J01XX03" 2799 "Clofoctol" "Other antibacterials" "Other antibacterials" "Other antibacterials"
"CLM" "J01CE07" 71807 "Clometocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 1 "g"
"CLM1" "J01AA11" 54680675 "Clomocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 1 "g"
"CTR" "G01AF02" 2812 "Clotrimazole" "Antifungals/antimycotics"
"CLO" "J01CF02" 6098 "Cloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" 2 "g" 2 "g"
"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" 3 "MU"
"COP" "Colistin/polysorbate" "Other antibacterials"
"CYC" "J04AB01" 6234 "Cycloserine" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" 0.75 "g"
"DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials"
"DAN" 71335 "Danofloxacin" "Quinolones"
"DPS" "J04BA02" 2955 "Dapsone" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" 50 "mg"
"DAP" "J01XX09" 16134395 "Daptomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" 0.28 "g"
"DFX" 487101 "Delafloxacin" "Quinolones"
"DLM" "J04AK06" 6480466 "Delamanid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis"
"DEM" "J01AA01" 54680690 "Demeclocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.6 "g"
"DKB" "J01GB09" 470999 "Dibekacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 0.14 "g"
"DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" 2 "g" 2 "g"
"DIF" 56206 "Difloxacin" "Quinolones"
"DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.5 "g"
"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems"
"DOX" "J01AA02" 54671203 "Doxycycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.1 "g" 0.1 "g"
"ECO" "J01XDXX" 3198 "Econazole" "Antifungals/antimycotics"
"ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.8 "g"
"ENR" 71188 "Enrofloxacin" "Quinolones"
"ENV" 135565326 "Enviomycin (Tuberactinomycin)" "Antimycobacterials"
"EPE" "Eperozolid" "Other antibacterials"
"EPC" "J01CA07" 71392 "Epicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 2 "g" 2 "g"
"EPP" 68916 "Epiroprim" "Other antibacterials"
"ERV" "J01AA13" 54726192 "Eravacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines"
"ETP" "J01DH03" 150610 "Ertapenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" 1 "g"
"ERY" "J01FA01" 12560 "Erythromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 2 "g" 1 "g"
"ETH" "J04AK02" 14052 "Ethambutol" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" 1.2 "g" 1.2 "g"
"ETI" "J04AM03" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis"
"ETI1" "J04AD03" 2761171 "Ethionamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" 0.75 "g"
"ETO" 6034 "Ethopabate" "Other antibacterials"
"FAR" "J01DI03" 65894 "Faropenem" "Other antibacterials"
"FDX" 10034073 "Fidaxomicin" "Other antibacterials"
"FIN" 11567473 "Finafloxacin" "Quinolones"
"FLA" 46783781 "Flavomycin" "Other antibacterials"
"FLE" "J01MA08" 3357 "Fleroxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.4 "g" 0.4 "g"
"FLO" 65864 "Flomoxef" "Other antibacterials"
"FLR" 114811 "Florfenicol" "Other antibacterials"
"FLC" "J01CF05" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" 2 "g" 2 "g"
"FLU" "J02AC01" 3365 "Fluconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" 0.2 "g" 0.2 "g"
"FLM" "J01MB07" 3374 "Flumequine" "Quinolones" "Quinolone antibacterials" "Other quinolones" 1.2 "g"
"FLR1" "J01FA14" 71260 "Flurithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.75 "g"
"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics"
"FOS" "J01XX01" 446987 "Fosfomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" 3 "g" 8 "g"
"FMD" 572 "Fosmidomycin" "Other antibacterials"
"FRM" 8378 "Framycetin" "Aminoglycosides"
"FRZ" 5323714 "Furazolidone" "Other antibacterials"
"FUS" "J01XC01" 3000226 "Fusidic acid" "Other antibacterials" "Other antibacterials" "Steroid antibacterials" 1.5 "g" 1.5 "g"
"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides"
"GRN" 124093 "Garenoxacin" "Quinolones"
"GAT" "J01MA16" 5379 "Gatifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.4 "g" 0.4 "g"
"GEM" "J01MA15" 9571107 "Gemifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones"
"GEN" "J01GB03" 3467 "Gentamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 0.24 "g"
"GEH" "Gentamicin-high" "Aminoglycosides"
"GEP" 25101874 "Gepotidacin" "Other antibacterials"
"GRX" "J01MA11" 72474 "Grepafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.4 "g"
"GRI" 441140 "Griseofulvin" "Antifungals/antimycotics"
"HAB" 175989 "Habekacin" "Aminoglycosides"
"HCH" "J02AA02" 11979956 "Hachimycin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics"
"HET" "J01CA18" 443387 "Hetacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 2 "g"
"HYG" 56928061 "Hygromycin" "Aminoglycosides"
"ICL" 213043 "Iclaprim" "Other antibacterials"
"IPM" "J01DH51" 104838 "Imipenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" 2 "g"
"IPE" "Imipenem/EDTA" "Carbapenems"
"IMR" "Imipenem/relebactam" "Carbapenems"
"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics"
"ISE" "J01GB11" 3037209 "Isepamicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 0.4 "g"
"ISO" "D01AC05" 3760 "Isoconazole" "Antifungals/antimycotics" "Antimycotics for topic use" "Triazole derivatives"
"INH" "J04AC01" 3767 "Isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Hydrazides" 0.3 "g" 0.3 "g"
"ITR" "J02AC02" 3793 "Itraconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" 0.2 "g" 0.2 "g"
"JOS" "J01FA07" 5282165 "Josamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 2 "g"
"KAN" "J01GB04" 6032 "Kanamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 1 "g"
"KAH" "Kanamycin-high" "Aminoglycosides"
"KAC" "Kanamycin/cephalexin" "Aminoglycosides"
"KET" "J02AB02" 456201 "Ketoconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" 0.2 "g"
"KIT" "Kitasamycin (Leucomycin)" "Macrolides/lincosamides"
"LAS" 5360807 "Lasalocid" "Other antibacterials"
"LTM" "J01DD06" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" 4 "g"
"LMU" 25185057 "Lefamulin" "Other antibacterials"
"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins"
"LVX" "J01MA12" 149096 "Levofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.5 "g" 0.5 "g"
"LND" 9850038 "Levonadifloxacin" "Quinolones"
"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials"
"LIN" "J01FF02" 3000540 "Lincomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" 1.8 "g" 1.8 "g"
"LNZ" "J01XX08" 441401 "Linezolid" "Other antibacterials" "Other antibacterials" "Other antibacterials" 1.2 "g" 1.2 "g"
"LFE" "Linoprist-flopristin" "Other antibacterials"
"LOM" "J01MA07" 3948 "Lomefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones"
"LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" 0.6 "g"
"LYM" "J01AA04" 54707177 "Lymecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.6 "g" 0.6 "g"
"MNA" "J01XX06" 1292 "Mandelic acid" "Other antibacterials" "Other antibacterials" "Other antibacterials" 12 "g"
"MAR" 60651 "Marbofloxacin" "Quinolones"
"MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 1.2 "g"
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides"
"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" 2 "g"
"MNC" "Meropenem/nacubactam" "Carbapenems"
"MEV" "J01DH52" "Meropenem/vaborbactam" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems"
"MES" 176886 "Mesulfamide" "Other antibacterials"
"MTC" "J01AA05" 54675785 "Metacycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.6 "g"
"MTM" "J01CA14" 6713928 "Metampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 1.5 "g" 1.5 "g"
"MTH" "J01XX05" 4101 "Methenamine" "Other antibacterials" "Other antibacterials" "Other antibacterials" 3 "g"
"MET" "J01CF03" 6087 "Methicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" 4 "g"
"MTP" 68590 "Metioprim" "Other antibacterials"
"MXT" 3047729 "Metioxate" "Quinolones"
"MTR" "J01XD01" 4173 "Metronidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" 1.5 "g"
"MEZ" "J01CA10" 656511 "Mezlocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 6 "g"
"MSU" "Mezlocillin/sulbactam" "Beta-lactams/penicillins"
"MIF" "J02AX05" 477468 "Micafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" 0.1 "g"
"MCZ" "J02AB01" 4189 "Miconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Imidazole derivatives" 1 "g"
"MCR" 3037206 "Micronomicin" "Aminoglycosides"
"MID" "J01FA03" 5282169 "Midecamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 1 "g"
"MIL" 37614 "Miloxacin" "Quinolones"
"MNO" "J01AA08" 54675783 "Minocycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.2 "g" 0.2 "g"
"MCM" "J01FA11" 5282188 "Miocamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 1.2 "g"
"MON" 23667299 "Monensin sodium" "Other antibacterials"
"MRN" "J04AK04" 70374 "Morinamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis"
"MFX" "J01MA14" 152946 "Moxifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.4 "g" 0.4 "g"
"MUP" "R01AX06" 446596 "Mupirocin" "Other antibacterials"
"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins"
"NAD" 4410 "Nadifloxacin" "Quinolones"
"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins"
"ZWK" 117587595 "Nafithromycin" "Macrolides/lincosamides"
"NAL" "J01MB02" 4421 "Nalidixic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" 4 "g"
"NAR" 65452 "Narasin" "Other antibacterials"
"NEO" "J01GB05" 8378 "Neomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 1 "g"
"NET" "J01GB07" 441306 "Netilmicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 0.35 "g" 0.35 "g"
"NIC" 9507 "Nicarbazin" "Other antibacterials"
"NIF" 71946 "Nifuroquine" "Quinolones"
"NFR" "J01XE02" 9571062 "Nifurtoinol" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" 0.16 "g"
"NTZ" 41684 "Nitazoxanide" "Other antibacterials"
"NIT" "J01XE01" 6604200 "Nitrofurantoin" "Other antibacterials" "Other antibacterials" "Nitrofuran derivatives" 0.2 "g"
"NIZ" 5447130 "Nitrofurazone" "Other antibacterials"
"NTR" "J01XX07" 19910 "Nitroxoline" "Quinolones" "Other antibacterials" "Other antibacterials" 1 "g"
"NOR" "J01MA06" 4539 "Norfloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.8 "g"
"NVA" 10419027 "Norvancomycin" "Glycopeptides"
"NOV" "QJ01XX95" 54675769 "Novobiocin" "Other antibacterials"
"NYS" "G01AA01" 6433272 "Nystatin" "Antifungals/antimycotics"
"OFX" "J01MA01" 4583 "Ofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.4 "g" 0.4 "g"
"OLE" "J01FA05" 72493 "Oleandomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 1 "g"
"OMC" 54697325 "Omadacycline" "Tetracyclines"
"OPT" 87880 "Optochin" "Other antibacterials"
"ORB" 60605 "Orbifloxacin" "Quinolones"
"ORI" "J01XA05" 16136912 "Oritavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials"
"ORS" "Ormetroprim/sulfamethoxazole" "Other antibacterials"
"ORN" "J01XD03" 28061 "Ornidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" 1 "g"
"OXA" "J01CF04" 6196 "Oxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" 2 "g" 2 "g"
"OXO" "J01MB05" 4628 "Oxolinic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" 1 "g"
"OXY" "J01AA06" 54675779 "Oxytetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 1 "g" 1 "g"
"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials"
"PAN" 72015 "Panipenem" "Carbapenems"
"PAR" 165580 "Paromomycin" "Other antibacterials"
"PAZ" "J01MA18" 65957 "Pazufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 1 "g"
"PEF" "J01MA03" 51081 "Pefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.8 "g" 0.8 "g"
"PNM" "J01CE06" 10250769 "Penamecillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 1.05 "g"
"PEN" "J01CE01" 5904 "Penicillin G" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials"
"PNV" "J01CE01" 6869 "Penicillin V" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 3.6 "g"
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins"
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins"
"PNM1" "J01AA10" 54686187 "Penimepicycline" "Tetracyclines" "Tetracyclines" "Tetracyclines"
"PIM" 65453 "Pentisomicin" "Aminoglycosides"
"PTZ" 55250256 "Pentizidone" "Other antibacterials"
"PEX" 16132253 "Pexiganan" "Other antibacterials"
"PHE" "J01CE05" 272833 "Phenethicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 1 "g"
"PHN" "J01CE02" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 2 "g"
"PMR" 5284447 "Pimaricin (Natamycin)" "Antifungals/antimycotics"
"PPA" "J01MB04" 4831 "Pipemidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" 0.8 "g"
"PIP" "J01CA12" 43672 "Piperacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 14 "g"
"PIS" "Piperacillin/sulbactam" "Beta-lactams/penicillins"
"TZP" "J01CR05" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" 14 "g"
"PRC" 71978 "Piridicillin" "Beta-lactams/penicillins"
"PRL" 157385 "Pirlimycin" "Other antibacterials"
"PIR" "J01MB03" 4855 "Piromidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" 2 "g"
"PVM" "J01CA02" 33478 "Pivampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 1.05 "g"
"PME" "J01CA08" 115163 "Pivmecillinam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 0.6 "g"
"PLZ" 42613186 "Plazomicin" "Aminoglycosides"
"PLB" "J01XB02" 49800004 "Polymyxin B" "Polymyxins" "Other antibacterials" "Polymyxins" 0.15 "g"
"POP" "Polymyxin B/polysorbate 80" "Polymyxins"
"POS" "J02AC04" 468595 "Posaconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" 0.3 "g" 0.3 "g"
"PRA" 9802884 "Pradofloxacin" "Quinolones"
"PRX" 71455 "Premafloxacin" "Quinolones"
"PRM" 6446787 "Primycin" "Macrolides/lincosamides"
"PRI" "J01FG01" 11979535 "Pristinamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Streptogramins" 2 "g"
"PRB" "J01CE09" 5903 "Procaine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 0.6 "g"
"PRP" "J01CE03" 92879 "Propicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" 0.9 "g"
"PKA" 9872451 "Propikacin" "Aminoglycosides"
"PTH" "J04AD01" 666418 "Prothionamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" 0.75 "g"
"PRU" "J01MA17" 65947 "Prulifloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.6 "g"
"PZA" "J04AK01" 1046 "Pyrazinamide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" 1.5 "g"
"QDA" "J01FG02" 11979418 "Quinupristin/dalfopristin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Streptogramins" 1.5 "g"
"RAC" 56052 "Ractopamine" "Other antibacterials"
"RAM" 16132338 "Ramoplanin" "Glycopeptides"
"RZM" 10993211 "Razupenem" "Carbapenems"
"RTP" "A07AA11" 6918462 "Retapamulin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" 0.6 "g"
"RBC" "J02AC05" 44631912 "Ribociclib" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives"
"RST" "J01GB10" 33042 "Ribostamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 1 "g"
"RID1" 16659285 "Ridinilazole" "Other antibacterials"
"RIB" "J04AB04" 135398743 "Rifabutin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" 0.15 "g"
"RIF" "J04AB02" 135398735 "Rifampicin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" 0.6 "g" 0.6 "g"
"RFI" "J04AM02" "Rifampicin/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis"
"RPEI" "J04AM06" "Rifampicin/pyrazinamide/ethambutol/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis"
"RPI" "J04AM05" "Rifampicin/pyrazinamide/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis"
"RFM" "J04AB03" 6324616 "Rifamycin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" 0.6 "g"
"RFP" "J04AB05" 135403821 "Rifapentine" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" 0.11 "g"
"RFX" "A07AA11" 6436173 "Rifaximin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" 0.6 "g"
"RIT" 65633 "Ritipenem" "Carbapenems"
"RIA" 163692 "Ritipenem acoxil" "Carbapenems"
"ROK" "J01FA12" 5282211 "Rokitamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.8 "g"
"RLT" "J01AA09" 54682938 "Rolitetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.35 "g"
"ROS" "J01MB01" 287180 "Rosoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" 0.3 "g"
"RXT" "J01FA06" "Roxithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.3 "g"
"RFL" "J01MA10" 58258 "Rufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.2 "g"
"SAL" 3085092 "Salinomycin" "Other antibacterials"
"SAR" 56208 "Sarafloxacin" "Quinolones"
"SRX" 9933415 "Sarmoxicillin" "Beta-lactams/penicillins"
"SEC" 71815 "Secnidazole" "Other antibacterials"
"SMF" "J04AK05" "Simvastatin/fenofibrate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis"
"SIS" "J01GB08" 36119 "Sisomicin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 0.24 "g"
"SIT" 461399 "Sitafloxacin" "Quinolones"
"SDA" "J04AA02" 2724368 "Sodium aminosalicylate" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" 14 "g" 14 "g"
"SOL" 25242512 "Solithromycin" "Macrolides/lincosamides"
"SPX" "J01MA09" 60464 "Sparfloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.2 "g"
"SPT" "J01XX04" 15541 "Spectinomycin" "Other antibacterials" "Other antibacterials" "Other antibacterials" 3 "g"
"SPI" "J01FA02" 6419898 "Spiramycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 3 "g"
"SPM" "J01RA04" "Spiramycin/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials"
"STR" "J01GA02" "Streptoduocin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" 1 "g"
"STR1" "J01GA01" 19649 "Streptomycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Streptomycins" 1 "g"
"STH" "Streptomycin-high" "Aminoglycosides"
"STI" "J04AM01" "Streptomycin/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis"
"SUL" "J01CG01" 130313 "Sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" 1 "g"
"SBC" "J01CA16" 20055036 "Sulbenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 15 "g"
"SUC" 5318 "Sulconazole" "Antifungals/antimycotics"
"SUP" 6634 "Sulfachlorpyridazine" "Other antibacterials"
"SDI" "J01EC02" 5215 "Sulfadiazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" 0.6 "g"
"SLT" "J01EE06" 122284 "Sulfadiazine/tetroxoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"SLT1" "J01EE02" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"SUD" "J01ED01" 5323 "Sulfadimethoxine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 0.5 "g"
"SDM" "J01EB03" 5327 "Sulfadimidine" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" 4 "g"
"SLT2" "J01EE05" "Sulfadimidine/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"SLF" "J01EB05" 5344 "Sulfafurazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" 4 "g" 4 "g"
"SLF1" "J01EB01" 5343 "Sulfaisodimidine" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" 4 "g" 4 "g"
"SLF2" "J01ED02" 9047 "Sulfalene" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 0.1 "g"
"SZO" "J01ED09" 187764 "Sulfamazone" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 1.5 "g"
"SLF3" "J01ED07" 5325 "Sulfamerazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 3 "g"
"SLT3" "J01EE07" "Sulfamerazine/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"SUM" 5327 "Sulfamethazine" "Other antibacterials"
"SLF4" "J01EB02" 5328 "Sulfamethizole" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" 4 "g"
"SMX" "J01EC01" 5329 "Sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" 2 "g"
"SLF5" "J01ED05" 5330 "Sulfamethoxypyridazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 0.5 "g"
"SLF6" "J01ED03" 19596 "Sulfametomidine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides"
"SLF7" "J01ED04" 5326 "Sulfametoxydiazine" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 0.5 "g"
"SLT4" "J01EE03" "Sulfametrole/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"SLF8" "J01EC03" 12894 "Sulfamoxole" "Trimethoprims" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" 1 "g" 1 "g"
"SLT5" "J01EE04" "Sulfamoxole/trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"SLF9" "J01EB06" 5333 "Sulfanilamide" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides"
"SLF10" "J01ED06" 68933 "Sulfaperin" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 0.5 "g"
"SLF11" "J01ED08" 5335 "Sulfaphenazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" 1 "g"
"SLF12" "J01EB04" 5336 "Sulfapyridine" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" 1 "g"
"SNA" 60582 "Sulfasuccinamide" "Other antibacterials"
"SUT" "J01EB07" 5340 "Sulfathiazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides"
"SLF13" "J01EB08" 3000579 "Sulfathiourea" "Trimethoprims" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" 6 "g"
"SOX" 5344 "Sulfisoxazole" "Other antibacterials"
"SSS" 86225 "Sulfonamides" "Other antibacterials"
"SLP" 9950244 "Sulopenem" "Other antibacterials"
"SLT6" "J01CR04" 444022 "Sultamicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" 1.5 "g"
"SUR" 46700778 "Surotomycin" "Other antibacterials"
"TAL" "J01CA15" 71447 "Talampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 2 "g"
"TLP" 163307 "Talmetoprim" "Other antibacterials"
"TAZ" "J01CG02" 123630 "Tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors"
"TBP" 9800194 "Tebipenem" "Carbapenems"
"TZD" "J01XX11" 11234049 "Tedizolid" "Other antibacterials" "Other antibacterials" "Other antibacterials"
"TEC" "J01XA02" 16131923 "Teicoplanin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" 0.4 "g"
"TCM" "Teicoplanin-macromethod" "Glycopeptides"
"TLV" "J01XA03" 3081362 "Telavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials"
"TLT" "J01FA15" 3002190 "Telithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 0.8 "g"
"TMX" "J01MA05" 60021 "Temafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.8 "g"
"TEM" "J01CA17" 171758 "Temocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 2 "g"
"TRB" "D01BA02" 1549008 "Terbinafine" "Antifungals/antimycotics" "Antifungals for systemic use" "Antifungals for systemic use" 0.25 "g"
"TRC" 441383 "Terconazole" "Antifungals/antimycotics"
"TRZ" "J04AK03" 65720 "Terizidone" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis"
"TCY" "J01AA07" 54675776 "Tetracycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 1 "g" 1 "g"
"TET" 65450 "Tetroxoprim" "Other antibacterials"
"THA" 9568512 "Thiacetazone" "Antimycobacterials"
"THI" "J01BA02" 27200 "Thiamphenicol" "Amphenicols" "Amphenicols" "Amphenicols" 1.5 "g" 1.5 "g"
"THI1" "J04AM04" "Thioacetazone/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis"
"TIA" 656958 "Tiamulin" "Other antibacterials"
"TIC" "J01CA13" 36921 "Ticarcillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" 15 "g"
"TCC" "J01CR03" 6437075 "Ticarcillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" 15 "g"
"TGC" "J01AA12" 54686904 "Tigecycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" 0.1 "g"
"TBQ" 65592 "Tilbroquinol" "Quinolones"
"TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides"
"TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides"
"TIN" "J01XD02" 5479 "Tinidazole" "Other antibacterials" "Other antibacterials" "Imidazole derivatives" 1.5 "g"
"TCR" "J04AD02" 3001386 "Tiocarlide" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" 7 "g"
"TDC" 10247721 "Tiodonium chloride" "Other antibacterials"
"TXC" 65788 "Tioxacin" "Quinolones"
"TIZ" 394397 "Tizoxanide" "Other antibacterials"
"TOB" "J01GB01" 36294 "Tobramycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" 0.24 "g"
"TFX" 5517 "Tosufloxacin" "Quinolones"
"TMP" "J01EA01" 5578 "Trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" 0.4 "g" 0.4 "g"
"SXT" "J01EE01" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives"
"TRL" "J01FA08" 202225 "Troleandomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" 1 "g"
"TRO" 55886 "Trospectomycin" "Other antibacterials"
"TVA" "J01MA13" 62959 "Trovafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" 0.2 "g" 0.2 "g"
"TUL" 9832301 "Tulathromycin" "Macrolides/lincosamides"
"TYL" 5280440 "Tylosin" "Macrolides/lincosamides"
"TYL1" "A07AA11" 6441094 "Tylvalosin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" 0.6 "g"
"PRU1" 124225 "Ulifloxacin (Prulifloxacin)" "Other antibacterials"
"VAN" "J01XA01" 14969 "Vancomycin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" 2 "g"
"VAM" "Vancomycin-macromethod" "Glycopeptides"
"VIO" 135398671 "Viomycin" "Antimycobacterials"
"VIR" 11979535 "Virginiamycine" "Other antibacterials"
"VOR" "J02AC03" 71616 "Voriconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" 0.4 "g" 0.4 "g"
"XBR" "J01XX02" 72144 "Xibornol" "Other antibacterials" "Other antibacterials" "Other antibacterials"
"ZID" 77846445 "Zidebactam" "Other antibacterials"

103
data-raw/antivirals.txt Normal file
View File

@ -0,0 +1,103 @@
"atc" "cid" "name" "atc_group" "oral_ddd" "oral_units" "iv_ddd" "iv_units"
"J05AF06" 441300 "abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.6 "g"
"J05AB01" 135398513 "aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 4 "g" 4 "g"
"J05AF08" 60871 "adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" 10 "mg"
"J05AE05" 65016 "amprenavir" "Protease inhibitors" 1.2 "g"
"J05AP06" 16076883 "asunaprevir" "Antivirals for treatment of HCV infections"
"J05AE08" 148192 "atazanavir" "Protease inhibitors" 0.3 "g"
"J05AR15" 86583336 "atazanavir and cobicistat" "Antivirals for treatment of HIV infections, combinations"
"J05AR23" "atazanavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" 0.3 "g"
"J05AP03" 10324367 "boceprevir" "Antivirals for treatment of HCV infections" 2.4 "g"
"J05AB15" 446727 "brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 0.125 "g"
"J05AB12" 60613 "cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 25 "mg"
"J05AF12" 73115 "clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 30 "mg"
"J05AP07" 25154714 "daclatasvir" "Antivirals for treatment of HCV infections" 60 "mg"
"J05AE10" 213039 "darunavir" "Protease inhibitors" 1.2 "g"
"J05AR14" "darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations"
"J05AP09" 56640146 "dasabuvir" "Antivirals for treatment of HCV infections" 0.5 "g"
"J05AP52" "dasabuvir, ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections"
"J05AG02" 5625 "delavirdine" "Non-nucleoside reverse transcriptase inhibitors" 1.2 "g"
"J05AF02" 135398739 "didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.4 "g"
"J05AX12" 54726191 "dolutegravir" "Other antivirals" 50 "mg"
"J05AR21" 131801472 "dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations"
"J05AG06" 58460047 "doravirine" "Non-nucleoside reverse transcriptase inhibitors"
"J05AG03" 64139 "efavirenz" "Non-nucleoside reverse transcriptase inhibitors" 0.6 "g"
"J05AP54" 91669168 "elbasvir and grazoprevir" "Antivirals for treatment of HCV infections"
"J05AX11" 5277135 "elvitegravir" "Other antivirals"
"J05AF09" 60877 "emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.2 "g"
"J05AR17" 90469070 "emtricitabine and tenofovir alafenamide" "Antivirals for treatment of HIV infections, combinations"
"J05AR20" "emtricitabine, tenofovir alafenamide and bictegravir" "Antivirals for treatment of HIV infections, combinations"
"J05AR19" "emtricitabine, tenofovir alafenamide and rilpivirine" "Antivirals for treatment of HIV infections, combinations"
"J05AR22" "emtricitabine, tenofovir alafenamide, darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations"
"J05AR18" "emtricitabine, tenofovir alafenamide, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations"
"J05AR06" "emtricitabine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations"
"J05AR08" "emtricitabine, tenofovir disoproxil and rilpivirine" "Antivirals for treatment of HIV infections, combinations"
"J05AR09" "emtricitabine, tenofovir disoproxil, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations"
"J05AX07" 16130199 "enfuvirtide" "Other antivirals" 0.18 "g"
"J05AX17" 10089466 "enisamium iodide" "Other antivirals" 1.5 "g"
"J05AF10" 135398508 "entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.5 "mg"
"J05AG04" 193962 "etravirine" "Non-nucleoside reverse transcriptase inhibitors" 0.4 "g"
"J05AP04" 42601552 "faldaprevir" "Antivirals for treatment of HCV infections"
"J05AB09" 3324 "famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 0.75 "g"
"J05AE07" 131536 "fosamprenavir" "Protease inhibitors" 1.4 "g"
"J05AD01" 3415 "foscarnet" "Phosphonic acid derivatives" 6.5 "g"
"J05AD02" 546 "fosfonet" "Phosphonic acid derivatives"
"J05AB06" 135398740 "ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 3 "g" 0.5 "g"
"J05AP57" "glecaprevir and pibrentasvir" "Antivirals for treatment of HCV infections"
"J05AX23" "ibalizumab" "Other antivirals"
"J05AB02" 5905 "idoxuridine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors"
"J05AE02" 5362440 "indinavir" "Protease inhibitors" 2.4 "g"
"J05AX05" 135449284 "inosine pranobex" "Other antivirals" 3 "g"
"J05AF05" 60825 "lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.3 "g"
"J05AR02" "lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations"
"J05AR16" 73386700 "lamivudine and raltegravir" "Antivirals for treatment of HIV infections, combinations"
"J05AR12" "lamivudine and tenofovir disoproxil" "Antivirals for treatment of HIV infections, combinations"
"J05AR13" "lamivudine, abacavir and dolutegravir" "Antivirals for treatment of HIV infections, combinations"
"J05AR24" "lamivudine, tenofovir disoproxil and doravirine" "Antivirals for treatment of HIV infections, combinations"
"J05AR11" "lamivudine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations"
"J05AX18" 45138674 "letermovir" "Other antivirals" 0.48 "g" 0.48 "g"
"J05AR10" 11979606 "lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" 0.8 "g"
"J05AX02" 24839946 "lysozyme" "Other antivirals"
"J05AX09" 3002977 "maraviroc" "Other antivirals" 0.6 "g"
"J05AX10" 471161 "maribavir" "Other antivirals"
"J05AA01" 667492 "metisazone" "Thiosemicarbazones"
"J05AX01" 71655 "moroxydine" "Other antivirals" 0.3 "g"
"J05AE04" 64143 "nelfinavir" "Protease inhibitors" 2.25 "g"
"J05AG01" 4463 "nevirapine" "Non-nucleoside reverse transcriptase inhibitors" 0.4 "g"
"J05AP53" "ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections"
"J05AH02" 65028 "oseltamivir" "Neuraminidase inhibitors" 0.15 "g"
"J05AB13" 135398748 "penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors"
"J05AX21" 9942657 "pentanedioic acid imidazolyl ethanamide" "Other antivirals" 90 "mg"
"J05AH03" 154234 "peramivir" "Neuraminidase inhibitors"
"J05AX06" 1684 "pleconaril" "Other antivirals"
"J05AX08" 54671008 "raltegravir" "Other antivirals" 0.8 "g"
"J05AP01" 37542 "ribavirin" "Antivirals for treatment of HCV infections" 1 "g"
"J05AG05" 6451164 "rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" 25 "mg"
"J05AC02" 5071 "rimantadine" "Cyclic amines" 0.2 "g"
"J05AE03" 392622 "ritonavir" "Protease inhibitors" 1.2 "g"
"J05AE01" 441243 "saquinavir" "Protease inhibitors" 1.8 "g"
"J05AP05" 24873435 "simeprevir" "Antivirals for treatment of HCV infections" 0.15 "g"
"J05AP08" 45375808 "sofosbuvir" "Antivirals for treatment of HCV infections" 0.4 "g"
"J05AP51" 72734365 "sofosbuvir and ledipasvir" "Antivirals for treatment of HCV infections"
"J05AP55" 91885554 "sofosbuvir and velpatasvir" "Antivirals for treatment of HCV infections"
"J05AP56" "sofosbuvir, velpatasvir and voxilaprevir" "Antivirals for treatment of HCV infections"
"J05AF04" 18283 "stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 80 "mg"
"J05AR07" 15979285 "stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations"
"J05AP02" 3010818 "telaprevir" "Antivirals for treatment of HCV infections" 2.25 "g"
"J05AF11" 159269 "telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.6 "g"
"J05AF13" 9574768 "tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" 25 "mg"
"J05AF07" 5481350 "tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.245 "g"
"J05AR03" "tenofovir disoproxil and emtricitabine" "Antivirals for treatment of HIV infections, combinations"
"J05AX19" 5475 "tilorone" "Other antivirals" 0.125 "g"
"J05AE09" 54682461 "tipranavir" "Protease inhibitors" 1 "g"
"J05AC03" 64377 "tromantadine" "Cyclic amines"
"J05AX13" 131411 "umifenovir" "Other antivirals" 0.8 "g"
"J05AB11" 135398742 "valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 3 "g"
"J05AB14" 135413535 "valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" 0.9 "g"
"J05AB03" 21704 "vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors"
"J05AF03" 24066 "zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 2.25 "mg"
"J05AH01" 60855 "zanamivir" "Neuraminidase inhibitors"
"J05AF01" 35370 "zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" 0.6 "g" 0.6 "g"
"J05AR01" "zidovudine and lamivudine" "Antivirals for treatment of HIV infections, combinations"
"J05AR04" "zidovudine, lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations"
"J05AR05" "zidovudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations"

24
data-raw/internals.R
View File

@ -69,15 +69,15 @@ rm(eucast_rules_file)
rm(translations_file)
rm(microorganisms.translation)
# Clean mo history ----
usethis::ui_done(paste0("Resetting {usethis::ui_value('mo_history.csv')}"))
tryCatch(
write.csv(x = data.frame(x = character(0),
mo = character(0),
uncertainty_level = integer(0),
package_version = character(0),
stringsAsFactors = FALSE),
row.names = FALSE,
file = "inst/mo_history/mo_history.csv"),
warning = function(w) cat("Warning:", w$message, "\n"),
error = function(e) cat("Error:", e$message, "\n"))
# Save to raw data to repository ----
library(dplyr, warn.conflicts = FALSE, quietly = TRUE)
usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
devtools::load_all(quiet = TRUE)
write.table(AMR::rsi_translation,
"data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
write.table(microorganisms %>% select(-snomed),
"data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
write.table(antibiotics %>% select(-c(abbreviations, synonyms, loinc)),
"data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
write.table(antivirals %>% select(-synonyms),
"data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)

69448
data-raw/microorganisms.txt Normal file
View File

File diff suppressed because it is too large Load Diff

3
data-raw/reproduction_of_rsi_translation.R
View File

@ -44,9 +44,6 @@ rsi_translation <- bind_rows(tbl_mic, tbl_disk) %>%
mutate(mo = as.mo(mo),
ab = as.ab(ab))
# save to data-raw
write.table(rsi_translation, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
# save to package
usethis::use_data(rsi_translation, overwrite = TRUE)
rm(rsi_translation)

2
docs/404.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

111
docs/articles/benchmarks.html
View File

@ -41,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 January 2020</h4>
<h4 class="date">01 February 2020</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -222,20 +222,20 @@
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 9.1 9.4 15.0 9.7 10.0 38.0</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 33.0 34.0 43.0 36.0 58.0 68.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 33.0 35.0 52.0 39.0 56.0 130.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 9.0 9.5 13.0 9.9 11.0 36.0</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.8 9.3 12.0 9.9 10.0 32.0</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 9.9 10.0 11.0 11.0 11.0 13.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 10.0 11.0 20.0 12.0 36.0 42.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.4 4.7 4.9 5.0 5.1 5.3</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 640.0 660.0 710.0 680.0 720.0 890.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 360.0 370.0 390.0 380.0 410.0 460.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.9 9.4 9.6 9.5 9.9 10.0</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 21.0 22.0 28.0 24.0 27.0 50.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 20.0 21.0 33.0 22.0 45.0 63.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 19.0 20.0 26.0 21.0 27.0 45.0</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.3 8.3 11.0 8.8 9.4 34.0</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 37.0 46.0 76.0 62.0 70.0 160.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 37.0 38.0 48.0 44.0 61.0 65.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 8.3 8.4 8.9 8.6 9.2 10.0</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.2 8.2 8.5 8.5 8.6 9.3</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 14.0 14.0 23.0 15.0 37.0 46.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 14.0 14.0 18.0 14.0 15.0 46.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.9 4.9 5.4 5.1 5.4 7.7</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 630.0 660.0 700.0 690.0 700.0 830.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 330.0 380.0 380.0 380.0 390.0 440.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.3 8.4 14.0 8.9 12.0 37.0</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 23.0 25.0 35.0 31.0 49.0 53.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 24.0 25.0 65.0 26.0 51.0 270.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 160.0 170.0</span></a>
<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co"># neval</span></a>
<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co"># 10</span></a>
@ -251,9 +251,9 @@
<a class="sourceLine" id="cb2-46" data-line-number="46"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-48" data-line-number="48"><span class="co"># 10</span></a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">M.semesiae &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),</a>
@ -262,24 +262,21 @@
<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1406.000 1502.000 1535.000 1531.000 1607.000</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1492.000 1535.000 1575.000 1581.000 1613.000</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 11.060 11.130 14.330 11.460 12.450</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 10.810 10.860 18.920 11.270 35.510</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 5.155 5.427 8.507 5.601 6.023</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1444.000 1496.000 1539.00 1530.000 1573.000</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1451.000 1478.000 1521.00 1505.000 1555.000</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 14.140 14.370 17.22 14.790 14.970</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 14.460 14.690 20.25 14.850 15.800</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 5.014 5.383 11.53 5.566 5.831</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># max neval</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1616.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1631.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 37.45 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 39.12 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 32.03 10</span></a></code></pre></div>
<p>That takes 6.5 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1628.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1658.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 39.56 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 42.11 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 38.03 10</span></a></code></pre></div>
<p>That takes 5.6 times as much time on average. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-8-1.png" width="900"></p>
<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds, because the <code><a href="../reference/as.mo.html">as.mo()</a></code> function <strong>learns from its own output to speed up determinations for next times</strong>.</p>
<p>In below figure, this effect was disabled to show the difference with the boxplot above:</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-9-1.png" width="900"></p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
@ -311,8 +308,8 @@
<a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 570 630 657 650 674 777 100</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.65 seconds (649 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 568 612 633 626 649 774 100</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.63 seconds (626 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -325,10 +322,10 @@
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.730 6.830 7.540 7.000 8.340 8.98 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 11.600 11.700 15.500 11.900 13.200 44.90 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.781 0.796 0.892 0.823 0.987 1.15 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.310 6.380 6.720 6.46 6.740 8.79 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 13.500 13.800 18.200 14.60 15.000 52.20 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.815 0.839 0.886 0.86 0.899 1.13 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -341,15 +338,15 @@
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.464 0.483 0.491 0.485 0.503 0.533 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.504 0.515 0.533 0.528 0.534 0.612 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.762 0.771 0.794 0.795 0.815 0.820 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.498 0.503 0.529 0.530 0.541 0.584 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.478 0.481 0.494 0.495 0.498 0.534 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.471 0.477 0.484 0.481 0.490 0.517 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.468 0.474 0.483 0.480 0.482 0.530 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.464 0.476 0.503 0.482 0.492 0.705 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.485 0.510 0.514 0.515 0.529 0.535 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.492 0.510 0.538 0.535 0.565 0.588 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.665 0.679 0.794 0.804 0.883 0.932 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.512 0.530 0.547 0.547 0.562 0.584 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.467 0.504 0.507 0.512 0.515 0.520 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.472 0.492 0.511 0.515 0.524 0.557 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.473 0.476 0.497 0.497 0.515 0.523 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.470 0.499 0.507 0.507 0.524 0.553 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor">
@ -375,13 +372,13 @@
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 21.72 22.92 27.04 23.44 24.14 62.83 100</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 23.14 24.37 28.32 24.79 25.84 57.85 100</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 28.85 30.61 35.40 31.25 32.79 64.85 100</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 23.17 24.51 28.62 24.85 25.51 65.76 100</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 23.04 24.25 30.77 24.82 27.58 58.95 100</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 22.88 24.37 27.90 24.94 25.53 61.63 100</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 23.16 24.54 29.65 24.90 25.59 156.50 100</span></a></code></pre></div>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 23.40 25.17 29.92 25.55 26.50 62.94 100</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 24.69 26.72 31.90 27.14 29.34 159.90 100</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 31.03 32.69 40.33 33.21 39.65 73.05 100</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 25.22 26.61 32.78 27.11 31.04 61.09 100</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 24.68 26.52 30.28 26.99 27.93 61.03 100</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 24.97 26.48 29.79 26.86 27.88 59.57 100</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 25.19 26.65 33.03 27.15 28.42 161.00 100</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

BIN
docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 94 KiB

After

Width:  |  Height:  |  Size: 94 KiB

BIN
docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 74 KiB

After

Width:  |  Height:  |  Size: 75 KiB

2
docs/articles/index.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

2
docs/authors.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

2
docs/index.html
View File

@ -45,7 +45,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

13
docs/news/index.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>
@ -231,13 +231,13 @@
</div>
<div id="amr-0-9-0-9017" class="section level1">
<div id="amr-0-9-0-9019" class="section level1">
<h1 class="page-header">
<a href="#amr-0-9-0-9017" class="anchor"></a>AMR 0.9.0.9017<small> Unreleased </small>
<a href="#amr-0-9-0-9019" class="anchor"></a>AMR 0.9.0.9019<small> Unreleased </small>
</h1>
<div id="last-updated-27-jan-2020" class="section level2">
<div id="last-updated-01-feb-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-27-jan-2020" class="anchor"></a><small>Last updated: 27-Jan-2020</small>
<a href="#last-updated-01-feb-2020" class="anchor"></a><small>Last updated: 01-Feb-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -272,6 +272,7 @@
<h3 class="hasAnchor">
<a href="#changes" class="anchor"></a>Changes</h3>
<ul>
<li>The <code><a href="../reference/as.mo.html">as.mo()</a></code> function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function <code>clear_mo_history()</code> was removed.</li>
<li>Bugfix for some WHONET microorganism codes that were not interpreted correctly when using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Speed improvement for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally), especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K penumoniae</em>
@ -1459,7 +1460,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-9-0-9017">0.9.0.9017</a></li>
<li><a href="#amr-0-9-0-9019">0.9.0.9019</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>

12
docs/reference/antibiotics.html
View File

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>
@ -286,7 +286,15 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p>
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3>Direct download</h3>
<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R</a></p></li>
</ul>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>

2
docs/reference/as.mo.html
View File

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>

9
docs/reference/microorganisms.html
View File

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
</span>
</div>
@ -269,6 +269,13 @@
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not in the Catalogue of Life</p></li>
<li><p>12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
</ul>
<h3>Direct download</h3>
<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R</a></p></li>
</ul>
<h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the records from DSMZ (see source)</h2>

8
man/antibiotics.Rd
View File

@ -56,6 +56,14 @@ Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{
Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}.
Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and consequently only available where a CID is available.
\subsection{Direct download}{
These data sets are available as 'flat files' for use even without R - you can find the files here:
\itemize{
\item \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R}
\item \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R}
}
}
}
\section{WHOCC}{

7
man/microorganisms.Rd
View File

@ -39,6 +39,13 @@ Manually added were:
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life
\item 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
}
\subsection{Direct download}{
This data set is available as 'flat file' for use even without R - you can find the file here:
\itemize{
\item \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R}
}
}
}
\section{About the records from DSMZ (see source)}{

9
vignettes/benchmarks.Rmd
View File

@ -161,9 +161,6 @@ So transforming 500,000 values (!!) of `r n_distinct(x)` unique values only take
What about precalculated results? If the input is an already precalculated result of a helper function like `mo_name()`, it almost doesn't take any time at all (see 'C' below):
```{r, echo = FALSE}
clear_mo_history()
```
```{r}
run_it <- microbenchmark(A = mo_name("B_STPHY_AURS"),
B = mo_name("S. aureus"),
@ -174,9 +171,6 @@ print(run_it, unit = "ms", signif = 3)
So going from `mo_name("Staphylococcus aureus")` to `"Staphylococcus aureus"` takes `r format(round(run_it %>% filter(expr == "C") %>% pull(time) %>% median() / 1e9, 4), scientific = FALSE)` seconds - it doesn't even start calculating *if the result would be the same as the expected resulting value*. That goes for all helper functions:
```{r, echo = FALSE}
clear_mo_history()
```
```{r}
run_it <- microbenchmark(A = mo_species("aureus"),
B = mo_genus("Staphylococcus"),
@ -196,9 +190,6 @@ Of course, when running `mo_phylum("Firmicutes")` the function has zero knowledg
When the system language is non-English and supported by this `AMR` package, some functions will have a translated result. This almost does't take extra time:
```{r, echo = FALSE}
clear_mo_history()
```
```{r}
mo_name("CoNS", language = "en") # or just mo_name("CoNS") on an English system