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(v1.3.0.9012) data sets vignette update

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dr. M.S. (Matthijs) Berends 3 years ago
parent 50b953b141
commit 4f72b3bfc4
58 changed files with 282 additions and 216 deletions
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.github/workflows/check.yaml vendored
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pull_request:
branches:
- master
schedule:
# run a schedule everyday at 3 AM.
# this is to check that all dependencies are still available (see R/zzz.R)
- cron: '0 3 * * *'
name: R-code-check

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@ -63,5 +63,5 @@ jobs:
shell: Rscript {0}
- name: Test coverage
run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R"))
run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R"), quiet = FALSE)
shell: Rscript {0}

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- master
pull_request:
branches:
- premaster
- master
name: lintr

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DESCRIPTION
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Package: AMR
Version: 1.3.0.9011
Version: 1.3.0.9012
Date: 2020-08-29
Title: Antimicrobial Resistance Analysis
Authors@R: c(

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NEWS.md
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# AMR 1.3.0.9011
# AMR 1.3.0.9012
## <small>Last updated: 29 August 2020</small>
### New
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* Function `mo_shortname()` now returns the genus for input where the species is unknown
* BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
* Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: `tibble` printing support for classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`. When using `tibble`s containing antimicrobial columns (class `<rsi>`), "S" will print in green, "I" will print in yellow and "R" will print in red. Microbial IDs (class `<mo>`) will emphasise on the genus and species, not on the kingdom.
* Names of antiviral agents in data set `antivirals` now have a starting capital letter, like it is the case in the `antibiotics` data set
# AMR 1.3.0

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"atc" "cid" "name" "atc_group" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units"
"J05AF06" 441300 "abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Abacavir\", \"Abacavir sulfate\", \"Ziagen\")" 0.6 "g"
"J05AB01" 135398513 "aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Acicloftal\", \"Aciclovier\", \"Aciclovir\", \"Aciclovirum\", \"Activir\", \"AcycloFoam\", \"Acycloguanosine\", \"Acyclovir\", \"Acyclovir Lauriad\", \"ACYCLOVIR SODIUM\", \"Avirax\", \"Cargosil\", \"Cyclovir\", \"Genvir\", \"Gerpevir\", \"Hascovir\", \"Herpevir\", \"Maynar\", \"Poviral\", \"Sitavig\", \"Sitavir\", \"Vipral\", \"Virolex\", \"Viropump\", \"Virorax\", \"Zovirax\", \"Zovirax topical\", \"Zyclir\")" 4 "g" 4 "g"
"J05AF08" 60871 "adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Adefovir di ester\", \"Adefovir dipivoxil\", \"Adefovir Dipivoxil\", \"Adefovir dipivoxyl\", \"Adefovir pivoxil\", \"Adefovirdipivoxl\", \"Bisadenine\", \"BISADENINE\", \"BisPMEA\", \"Hepsera\", \"Preveon\", \"YouHeDing\")" 10 "mg"
"J05AE05" 65016 "amprenavir" "Protease inhibitors" "c(\"Agenerase\", \"Amprenavir\", \"Amprenavirum\", \"Prozei\", \"Vertex\")" 1.2 "g"
"J05AP06" 16076883 "asunaprevir" "Antivirals for treatment of HCV infections" "c(\"Asunaprevir\", \"Sunvepra\")"
"J05AE08" 148192 "atazanavir" "Protease inhibitors" "c(\"Atazanavir\", \"Atazanavir Base\", \"Latazanavir\", \"Reyataz\", \"Zrivada\")" 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" "c(\"Bocepravir\", \"Boceprevir\", \"Victrelis\")" 2.4 "g"
"J05AB15" 446727 "brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Bridic\", \"Brivox\", \"Brivudin\", \"Brivudina\", \"Brivudine\", \"Brivudinum\", \"BrVdUrd\", \"Helpin\", \"Zerpex\", \"Zostex\")" 0.125 "g"
"J05AB12" 60613 "cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cidofovir\", \"Cidofovir anhydrous\", \"Cidofovir gel\", \"Cidofovirum\", \"Forvade\", \"Vistide\")" 25 "mg"
"J05AF12" 73115 "clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Clevudine\", \"Levovir\", \"Revovir\")" 30 "mg"
"J05AP07" 25154714 "daclatasvir" "Antivirals for treatment of HCV infections" "c(\"Daclatasvir\", \"Daklinza\")" 60 "mg"
"J05AE10" 213039 "darunavir" "Protease inhibitors" "c(\"Darunavir\", \"Darunavirum\", \"Prezista\", \"Prezista Naive\")" 1.2 "g"
"J05AR14" "darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
"J05AP09" 56640146 "dasabuvir" "Antivirals for treatment of HCV infections" "Dasabuvir" 0.5 "g"
"J05AP52" "dasabuvir, ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
"J05AG02" 5625 "delavirdine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"BHAP der\", \"Delavirdin\", \"Delavirdina\", \"Delavirdine\", \"Delavirdinum\", \"PIPERAZINE\", \"Rescriptor\")" 1.2 "g"
"J05AF02" 135398739 "didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Didanosina\", \"Didanosine\", \"Didanosinum\", \"Dideoxyinosine\", \"DIDEOXYINOSINE\", \"Hypoxanthine ddN\", \"Videx\", \"Videx EC\")" 0.4 "g"
"J05AX12" 54726191 "dolutegravir" "Other antivirals" "c(\"Dolutegravir\", \"Dolutegravir Sodium\", \"Soltegravir\", \"Tivicay\")" 50 "mg"
"J05AR21" 131801472 "dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AG06" 58460047 "doravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Doravirine\", \"Pifeltro\")"
"J05AG03" 64139 "efavirenz" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Efavirenz\", \"Efavirenzum\", \"Eravirenz\", \"Stocrin\", \"Strocin\", \"Sustiva\")" 0.6 "g"
"J05AP54" 91669168 "elbasvir and grazoprevir" "Antivirals for treatment of HCV infections" ""
"J05AX11" 5277135 "elvitegravir" "Other antivirals" "c(\"Elvitegravir\", \"Vitekta\")"
"J05AF09" 60877 "emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Coviracil\", \"Emtricitabin\", \"Emtricitabina\", \"Emtricitabine\", \"Emtricitabinum\", \"Emtritabine\", \"Emtriva\", \"Racivir\")" 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" "c(\"Enfurvitide\", \"Enfuvirtide\", \"Fuzeon\", \"Pentafuside\")" 0.18 "g"
"J05AX17" 10089466 "enisamium iodide" "Other antivirals" "Enisamium iodide" 1.5 "g"
"J05AF10" 135398508 "entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Baraclude\", \"Entecavir\", \"Entecavir anhydrous\", \"Entecavirum\")" 0.5 "mg"
"J05AG04" 193962 "etravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"DAPY deriv\", \"Etravine\", \"Etravirine\", \"Intelence\")" 0.4 "g"
"J05AP04" 42601552 "faldaprevir" "Antivirals for treatment of HCV infections" "Faldaprevir"
"J05AB09" 3324 "famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Famciclovir\", \"Famciclovirum\", \"Famvir\", \"Oravir\")" 0.75 "g"
"J05AE07" 131536 "fosamprenavir" "Protease inhibitors" "c(\"Amprenavir phosphate\", \"Fosamprenavir\", \"Lexiva\", \"Telzir\")" 1.4 "g"
"J05AD01" 3415 "foscarnet" "Phosphonic acid derivatives" "c(\"Forscarnet\", \"Forscarnet sodium\", \"Foscarmet\", \"Foscarnet\", \"Phosphonoformate\", \"Phosphonoformic acid\")" 6.5 "g"
"J05AD02" 546 "fosfonet" "Phosphonic acid derivatives" "c(\"Fosfonet\", \"Fosfonet sodium\", \"Fosfonet Sodium\", \"Fosfonoacetate\", \"Fosfonoacetic acid\", \"Phosphonacetate\", \"Phosphonacetic acid\")"
"J05AB06" 135398740 "ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Citovirax\", \"Cymevan\", \"Cymeven\", \"Cymevene\", \"Cytovene\", \"Cytovene IV\", \"Ganciclovir\", \"Ganciclovirum\", \"Gancyclovir\", \"Hydroxyacyclovir\", \"Virgan\", \"Vitrasert\", \"Zirgan\")" 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" "c(\"Antizona\", \"Dendrid\", \"Emanil\", \"Heratil\", \"Herpesil\", \"Herpid\", \"Herpidu\", \"Herplex\", \"HERPLEX\", \"Herplex liquifilm\", \"Idexur\", \"Idossuridina\", \"Idoxene\", \"Idoxuridin\", \"Idoxuridina\", \"Idoxuridine\", \"Idoxuridinum\", \"Idu Oculos\", \"Iducher\", \"Idulea\", \"Iduoculos\", \"Iduridin\", \"Iduviran\", \"Iododeoxyridine\", \"Iododeoxyuridine\", \"Iodoxuridine\", \"Joddeoxiuridin\", \"Kerecid\", \"Kerecide\", \"Ophthalmadine\", \"Spectanefran\", \"Stoxil\", \"Synmiol\", \"Virudox\")"
"J05AE02" 5362440 "indinavir" "Protease inhibitors" "c(\"Compound J\", \"Crixivan\", \"Indinavir\", \"Indinavir anhydrous\", \"Propolis+Indinavir\")" 2.4 "g"
"J05AX05" 135449284 "inosine pranobex" "Other antivirals" "c(\"Aviral\", \"Delimmun\", \"Immunovir\", \"Imunovir\", \"Inosine pranobex\", \"Inosiplex\", \"Isoprinosin\", \"Isoprinosina\", \"Isoprinosine\", \"Isoviral\", \"Methisoprinol\", \"Methysoprinol\", \"Metisoprinol\", \"Viruxan\")" 3 "g"
"J05AF05" 60825 "lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epivir\", \"Hepitec\", \"Heptivir\", \"Heptodin\", \"Heptovir\", \"Lamivir\", \"Lamivudin\", \"Lamivudina\", \"Lamivudine\", \"Lamivudinum\", \"Zeffix\")" 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" "c(\"Letermovir\", \"Prevymis\")" 0.48 "g" 0.48 "g"
"J05AR10" 11979606 "lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "c(\"Aluvia\", \"Kaletra\")" 0.8 "g"
"J05AX02" 24839946 "lysozyme" "Other antivirals" "c(\"Lysozyme chloride\", \"Lysozyme Chloride\", \"Lysozyme G\")"
"J05AX09" 3002977 "maraviroc" "Other antivirals" "c(\"Celsentri\", \"Maraviroc\", \"Selzentry\")" 0.6 "g"
"J05AX10" 471161 "maribavir" "Other antivirals" "c(\"Benzimidavir\", \"Camvia\", \"Maribavir\")"
"J05AA01" 667492 "metisazone" "Thiosemicarbazones" "c(\"Kemoviran\", \"Marboran\", \"Marborane\", \"Methisazon\", \"Methisazone\", \"Methsazone\", \"Metisazon\", \"Metisazona\", \"Metisazone\", \"Metisazonum\", \"Viruzona\")"
"J05AX01" 71655 "moroxydine" "Other antivirals" "c(\"Bimolin\", \"Flumidine\", \"Influmine\", \"Moroxidina\", \"Moroxydine\", \"Moroxydinum\", \"Vironil\", \"Virugon\", \"Virumin\", \"Wirumin\")" 0.3 "g"
"J05AE04" 64143 "nelfinavir" "Protease inhibitors" "c(\"Nelfinavir\", \"Viracept\")" 2.25 "g"
"J05AG01" 4463 "nevirapine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Nevirapine\", \"Nevirapine anhydrous\", \"Viramune\", \"Viramune IR\", \"Viramune XR\")" 0.4 "g"
"J05AP53" "ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
"J05AH02" 65028 "oseltamivir" "Neuraminidase inhibitors" "c(\"Agucort\", \"Oseltamivir\", \"Tamiflu\", \"Tamvir\")" 0.15 "g"
"J05AB13" 135398748 "penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenovir\", \"Denavir\", \"Penciceovir\", \"Penciclovir\", \"Penciclovirum\", \"Pencyclovir\", \"Vectavir\")"
"J05AX21" 9942657 "pentanedioic acid imidazolyl ethanamide" "Other antivirals" "Ingamine" 90 "mg"
"J05AH03" 154234 "peramivir" "Neuraminidase inhibitors" "c(\"PeramiFlu\", \"Peramivir\", \"Rapiacta\", \"RAPIVAB\")"
"J05AX06" 1684 "pleconaril" "Other antivirals" "c(\"Picovir\", \"Pleconaril\", \"Pleconarilis\")"
"J05AX08" 54671008 "raltegravir" "Other antivirals" "c(\"Isentress\", \"Raltegravir\")" 0.8 "g"
"J05AP01" 37542 "ribavirin" "Antivirals for treatment of HCV infections" "c(\"Copegus\", \"Cotronak\", \"Drug: Ribavirin\", \"Ravanex\", \"Rebetol\", \"Rebetron\", \"Rebretron\", \"Ribacine\", \"Ribamide\", \"Ribamidil\", \"Ribamidyl\", \"Ribasphere\", \"Ribavirin\", \"Ribavirin Capsules\", \"Ribavirina\", \"Ribavirine\", \"Ribavirinum\", \"Ribovirin\", \"Tribavirin\", \"Varazid\", \"Vilona\", \"Viramid\", \"Viramide\", \"Virazid\", \"Virazide\", \"Virazole\")" 1 "g"
"J05AG05" 6451164 "rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Edurant\", \"Rilpivirine\")" 25 "mg"
"J05AC02" 5071 "rimantadine" "Cyclic amines" "c(\"Remantadine\", \"Riamantadine\", \"Rimant\", \"RIMANTADIN\", \"Rimantadin A\", \"Rimantadina\", \"Rimantadine\", \"Rimantadinum\")" 0.2 "g"
"J05AE03" 392622 "ritonavir" "Protease inhibitors" "c(\"Norvir\", \"Norvir Sec\", \"Norvir Softgel\", \"Ritonavir\", \"Ritonavire\", \"Ritonavirum\")" 1.2 "g"
"J05AE01" 441243 "saquinavir" "Protease inhibitors" "c(\"Fortovase\", \"Invirase\", \"Saquinavir\")" 1.8 "g"
"J05AP05" 24873435 "simeprevir" "Antivirals for treatment of HCV infections" "c(\"Olysio\", \"Simeprevir sodium\")" 0.15 "g"
"J05AP08" 45375808 "sofosbuvir" "Antivirals for treatment of HCV infections" "c(\"Hepcinat\", \"Hepcvir\", \"Sofosbuvir\", \"Sovaldi\", \"SOVALDI\", \"SoviHep\")" 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" "Epclusa Tablet"
"J05AP56" "sofosbuvir, velpatasvir and voxilaprevir" "Antivirals for treatment of HCV infections" ""
"J05AF04" 18283 "stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Estavudina\", \"Sanilvudine\", \"Stavudin\", \"Stavudine\", \"Stavudinum\", \"Zerit Xr\", \"Zerut XR\")" 80 "mg"
"J05AR07" 15979285 "stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" "STAVUDIINE"
"J05AP02" 3010818 "telaprevir" "Antivirals for treatment of HCV infections" "c(\"Incivek\", \"Incivo\", \"Telaprevir\", \"Telavic\")" 2.25 "g"
"J05AF11" 159269 "telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epavudine\", \"Sebivo\", \"Telbivudin\", \"Telbivudine\", \"Tyzeka\")" 0.6 "g"
"J05AF13" 9574768 "tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Vemlidy" 25 "mg"
"J05AF07" 5481350 "tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"BisPMPA\", \"PMPA prodrug\", \"Tenofovir\", \"Viread\")" 0.245 "g"
"J05AR03" "tenofovir disoproxil and emtricitabine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AX19" 5475 "tilorone" "Other antivirals" "c(\"Amiksin\", \"Amixin\", \"Amixin IC\", \"Amyxin\", \"Tiloron\", \"Tilorona\", \"Tilorone\", \"Tiloronum\")" 0.125 "g"
"J05AE09" 54682461 "tipranavir" "Protease inhibitors" "c(\"Aptivus\", \"Tipranavir\")" 1 "g"
"J05AC03" 64377 "tromantadine" "Cyclic amines" "c(\"Tromantadina\", \"Tromantadine\", \"Tromantadinum\", \"Viruserol\")"
"J05AX13" 131411 "umifenovir" "Other antivirals" "c(\"Arbidol\", \"Arbidol base\", \"Umifenovir\")" 0.8 "g"
"J05AB11" 135398742 "valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Talavir\", \"Valaciclovir\", \"Valaciclovirum\", \"ValACV\", \"Valcivir\", \"Valcyclovir\", \"Valtrex\", \"Virval\", \"Zelitrex\")" 3 "g"
"J05AB14" 135413535 "valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cymeval\", \"Valganciclovir\")" 0.9 "g"
"J05AB03" 21704 "vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenine arabinoside\", \"Araadenosine\", \"Arabinoside adenine\", \"Arabinosyl adenine\", \"Arabinosyladenine\", \"Spongoadenosine\", \"Vidarabin\", \"Vidarabina\", \"Vidarabine\", \"Vidarabine anhydrous\", \"Vidarabinum\", \"Vira A\", \"Vira ATM\")"
"J05AF03" 24066 "zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Dideoxycytidine\", \"Interferon AD + ddC\", \"Zalcitabine\", \"Zalcitibine\")" 2.25 "mg"
"J05AH01" 60855 "zanamivir" "Neuraminidase inhibitors" "c(\"MODIFIED SIALIC ACID\", \"Relenza\", \"Zanamavir\", \"Zanamir\", \"Zanamivi\", \"Zanamivir\", \"Zanamivir hydrate\")"
"J05AF01" 35370 "zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Azidothymidine\", \"AZT Antiviral\", \"Beta interferon\", \"Compound S\", \"Propolis+AZT\", \"Retrovir\", \"Zidovudina\", \"Zidovudine\", \"ZIDOVUDINE\", \"Zidovudine EP III\", \"Zidovudinum\")" 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" ""
"J05AF06" 441300 "Abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Abacavir\", \"Abacavir sulfate\", \"Ziagen\")" 0.6 "g"
"J05AB01" 135398513 "Aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Acicloftal\", \"Aciclovier\", \"Aciclovir\", \"Aciclovirum\", \"Activir\", \"AcycloFoam\", \"Acycloguanosine\", \"Acyclovir\", \"Acyclovir Lauriad\", \"ACYCLOVIR SODIUM\", \"Avirax\", \"Cargosil\", \"Cyclovir\", \"Genvir\", \"Gerpevir\", \"Hascovir\", \"Herpevir\", \"Maynar\", \"Poviral\", \"Sitavig\", \"Sitavir\", \"Vipral\", \"Virolex\", \"Viropump\", \"Virorax\", \"Zovirax\", \"Zovirax topical\", \"Zyclir\")" 4 "g" 4 "g"
"J05AF08" 60871 "Adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Adefovir di ester\", \"Adefovir dipivoxil\", \"Adefovir Dipivoxil\", \"Adefovir dipivoxyl\", \"Adefovir pivoxil\", \"Adefovirdipivoxl\", \"Bisadenine\", \"BISADENINE\", \"BisPMEA\", \"Hepsera\", \"Preveon\", \"YouHeDing\")" 10 "mg"
"J05AE05" 65016 "Amprenavir" "Protease inhibitors" "c(\"Agenerase\", \"Amprenavir\", \"Amprenavirum\", \"Prozei\", \"Vertex\")" 1.2 "g"
"J05AP06" 16076883 "Asunaprevir" "Antivirals for treatment of HCV infections" "c(\"Asunaprevir\", \"Sunvepra\")"
"J05AE08" 148192 "Atazanavir" "Protease inhibitors" "c(\"Atazanavir\", \"Atazanavir Base\", \"Latazanavir\", \"Reyataz\", \"Zrivada\")" 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" "c(\"Bocepravir\", \"Boceprevir\", \"Victrelis\")" 2.4 "g"
"J05AB15" 446727 "Brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Bridic\", \"Brivox\", \"Brivudin\", \"Brivudina\", \"Brivudine\", \"Brivudinum\", \"BrVdUrd\", \"Helpin\", \"Zerpex\", \"Zostex\")" 0.125 "g"
"J05AB12" 60613 "Cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cidofovir\", \"Cidofovir anhydrous\", \"Cidofovir gel\", \"Cidofovirum\", \"Forvade\", \"Vistide\")" 25 "mg"
"J05AF12" 73115 "Clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Clevudine\", \"Levovir\", \"Revovir\")" 30 "mg"
"J05AP07" 25154714 "Daclatasvir" "Antivirals for treatment of HCV infections" "c(\"Daclatasvir\", \"Daklinza\")" 60 "mg"
"J05AE10" 213039 "Darunavir" "Protease inhibitors" "c(\"Darunavir\", \"Darunavirum\", \"Prezista\", \"Prezista Naive\")" 1.2 "g"
"J05AR14" "Darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
"J05AP09" 56640146 "Dasabuvir" "Antivirals for treatment of HCV infections" "Dasabuvir" 0.5 "g"
"J05AP52" "Dasabuvir, ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
"J05AG02" 5625 "Delavirdine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"BHAP der\", \"Delavirdin\", \"Delavirdina\", \"Delavirdine\", \"Delavirdinum\", \"PIPERAZINE\", \"Rescriptor\")" 1.2 "g"
"J05AF02" 135398739 "Didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Didanosina\", \"Didanosine\", \"Didanosinum\", \"Dideoxyinosine\", \"DIDEOXYINOSINE\", \"Hypoxanthine ddN\", \"Videx\", \"Videx EC\")" 0.4 "g"
"J05AX12" 54726191 "Dolutegravir" "Other antivirals" "c(\"Dolutegravir\", \"Dolutegravir Sodium\", \"Soltegravir\", \"Tivicay\")" 50 "mg"
"J05AR21" 131801472 "Dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AG06" 58460047 "Doravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Doravirine\", \"Pifeltro\")"
"J05AG03" 64139 "Efavirenz" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Efavirenz\", \"Efavirenzum\", \"Eravirenz\", \"Stocrin\", \"Strocin\", \"Sustiva\")" 0.6 "g"
"J05AP54" 91669168 "Elbasvir and grazoprevir" "Antivirals for treatment of HCV infections" ""
"J05AX11" 5277135 "Elvitegravir" "Other antivirals" "c(\"Elvitegravir\", \"Vitekta\")"
"J05AF09" 60877 "Emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Coviracil\", \"Emtricitabin\", \"Emtricitabina\", \"Emtricitabine\", \"Emtricitabinum\", \"Emtritabine\", \"Emtriva\", \"Racivir\")" 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" "c(\"Enfurvitide\", \"Enfuvirtide\", \"Fuzeon\", \"Pentafuside\")" 0.18 "g"
"J05AX17" 10089466 "Enisamium iodide" "Other antivirals" "Enisamium iodide" 1.5 "g"
"J05AF10" 135398508 "Entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Baraclude\", \"Entecavir\", \"Entecavir anhydrous\", \"Entecavirum\")" 0.5 "mg"
"J05AG04" 193962 "Etravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"DAPY deriv\", \"Etravine\", \"Etravirine\", \"Intelence\")" 0.4 "g"
"J05AP04" 42601552 "Faldaprevir" "Antivirals for treatment of HCV infections" "Faldaprevir"
"J05AB09" 3324 "Famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Famciclovir\", \"Famciclovirum\", \"Famvir\", \"Oravir\")" 0.75 "g"
"J05AE07" 131536 "Fosamprenavir" "Protease inhibitors" "c(\"Amprenavir phosphate\", \"Fosamprenavir\", \"Lexiva\", \"Telzir\")" 1.4 "g"
"J05AD01" 3415 "Foscarnet" "Phosphonic acid derivatives" "c(\"Forscarnet\", \"Forscarnet sodium\", \"Foscarmet\", \"Foscarnet\", \"Phosphonoformate\", \"Phosphonoformic acid\")" 6.5 "g"
"J05AD02" 546 "Fosfonet" "Phosphonic acid derivatives" "c(\"Fosfonet\", \"Fosfonet sodium\", \"Fosfonet Sodium\", \"Fosfonoacetate\", \"Fosfonoacetic acid\", \"Phosphonacetate\", \"Phosphonacetic acid\")"
"J05AB06" 135398740 "Ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Citovirax\", \"Cymevan\", \"Cymeven\", \"Cymevene\", \"Cytovene\", \"Cytovene IV\", \"Ganciclovir\", \"Ganciclovirum\", \"Gancyclovir\", \"Hydroxyacyclovir\", \"Virgan\", \"Vitrasert\", \"Zirgan\")" 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" "c(\"Antizona\", \"Dendrid\", \"Emanil\", \"Heratil\", \"Herpesil\", \"Herpid\", \"Herpidu\", \"Herplex\", \"HERPLEX\", \"Herplex liquifilm\", \"Idexur\", \"Idossuridina\", \"Idoxene\", \"Idoxuridin\", \"Idoxuridina\", \"Idoxuridine\", \"Idoxuridinum\", \"Idu Oculos\", \"Iducher\", \"Idulea\", \"Iduoculos\", \"Iduridin\", \"Iduviran\", \"Iododeoxyridine\", \"Iododeoxyuridine\", \"Iodoxuridine\", \"Joddeoxiuridin\", \"Kerecid\", \"Kerecide\", \"Ophthalmadine\", \"Spectanefran\", \"Stoxil\", \"Synmiol\", \"Virudox\")"
"J05AE02" 5362440 "Indinavir" "Protease inhibitors" "c(\"Compound J\", \"Crixivan\", \"Indinavir\", \"Indinavir anhydrous\", \"Propolis+Indinavir\")" 2.4 "g"
"J05AX05" 135449284 "Inosine pranobex" "Other antivirals" "c(\"Aviral\", \"Delimmun\", \"Immunovir\", \"Imunovir\", \"Inosine pranobex\", \"Inosiplex\", \"Isoprinosin\", \"Isoprinosina\", \"Isoprinosine\", \"Isoviral\", \"Methisoprinol\", \"Methysoprinol\", \"Metisoprinol\", \"Viruxan\")" 3 "g"
"J05AF05" 60825 "Lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epivir\", \"Hepitec\", \"Heptivir\", \"Heptodin\", \"Heptovir\", \"Lamivir\", \"Lamivudin\", \"Lamivudina\", \"Lamivudine\", \"Lamivudinum\", \"Zeffix\")" 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" "c(\"Letermovir\", \"Prevymis\")" 0.48 "g" 0.48 "g"
"J05AR10" 11979606 "Lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "c(\"Aluvia\", \"Kaletra\")" 0.8 "g"
"J05AX02" 24839946 "Lysozyme" "Other antivirals" "c(\"Lysozyme chloride\", \"Lysozyme Chloride\", \"Lysozyme G\")"
"J05AX09" 3002977 "Maraviroc" "Other antivirals" "c(\"Celsentri\", \"Maraviroc\", \"Selzentry\")" 0.6 "g"
"J05AX10" 471161 "Maribavir" "Other antivirals" "c(\"Benzimidavir\", \"Camvia\", \"Maribavir\")"
"J05AA01" 667492 "Metisazone" "Thiosemicarbazones" "c(\"Kemoviran\", \"Marboran\", \"Marborane\", \"Methisazon\", \"Methisazone\", \"Methsazone\", \"Metisazon\", \"Metisazona\", \"Metisazone\", \"Metisazonum\", \"Viruzona\")"
"J05AX01" 71655 "Moroxydine" "Other antivirals" "c(\"Bimolin\", \"Flumidine\", \"Influmine\", \"Moroxidina\", \"Moroxydine\", \"Moroxydinum\", \"Vironil\", \"Virugon\", \"Virumin\", \"Wirumin\")" 0.3 "g"
"J05AE04" 64143 "Nelfinavir" "Protease inhibitors" "c(\"Nelfinavir\", \"Viracept\")" 2.25 "g"
"J05AG01" 4463 "Nevirapine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Nevirapine\", \"Nevirapine anhydrous\", \"Viramune\", \"Viramune IR\", \"Viramune XR\")" 0.4 "g"
"J05AP53" "Ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
"J05AH02" 65028 "Oseltamivir" "Neuraminidase inhibitors" "c(\"Agucort\", \"Oseltamivir\", \"Tamiflu\", \"Tamvir\")" 0.15 "g"
"J05AB13" 135398748 "Penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenovir\", \"Denavir\", \"Penciceovir\", \"Penciclovir\", \"Penciclovirum\", \"Pencyclovir\", \"Vectavir\")"
"J05AX21" 9942657 "Pentanedioic acid imidazolyl ethanamide" "Other antivirals" "Ingamine" 90 "mg"
"J05AH03" 154234 "Peramivir" "Neuraminidase inhibitors" "c(\"PeramiFlu\", \"Peramivir\", \"Rapiacta\", \"RAPIVAB\")"
"J05AX06" 1684 "Pleconaril" "Other antivirals" "c(\"Picovir\", \"Pleconaril\", \"Pleconarilis\")"
"J05AX08" 54671008 "Raltegravir" "Other antivirals" "c(\"Isentress\", \"Raltegravir\")" 0.8 "g"
"J05AP01" 37542 "Ribavirin" "Antivirals for treatment of HCV infections" "c(\"Copegus\", \"Cotronak\", \"Drug: Ribavirin\", \"Ravanex\", \"Rebetol\", \"Rebetron\", \"Rebretron\", \"Ribacine\", \"Ribamide\", \"Ribamidil\", \"Ribamidyl\", \"Ribasphere\", \"Ribavirin\", \"Ribavirin Capsules\", \"Ribavirina\", \"Ribavirine\", \"Ribavirinum\", \"Ribovirin\", \"Tribavirin\", \"Varazid\", \"Vilona\", \"Viramid\", \"Viramide\", \"Virazid\", \"Virazide\", \"Virazole\")" 1 "g"
"J05AG05" 6451164 "Rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Edurant\", \"Rilpivirine\")" 25 "mg"
"J05AC02" 5071 "Rimantadine" "Cyclic amines" "c(\"Remantadine\", \"Riamantadine\", \"Rimant\", \"RIMANTADIN\", \"Rimantadin A\", \"Rimantadina\", \"Rimantadine\", \"Rimantadinum\")" 0.2 "g"
"J05AE03" 392622 "Ritonavir" "Protease inhibitors" "c(\"Norvir\", \"Norvir Sec\", \"Norvir Softgel\", \"Ritonavir\", \"Ritonavire\", \"Ritonavirum\")" 1.2 "g"
"J05AE01" 441243 "Saquinavir" "Protease inhibitors" "c(\"Fortovase\", \"Invirase\", \"Saquinavir\")" 1.8 "g"
"J05AP05" 24873435 "Simeprevir" "Antivirals for treatment of HCV infections" "c(\"Olysio\", \"Simeprevir sodium\")" 0.15 "g"
"J05AP08" 45375808 "Sofosbuvir" "Antivirals for treatment of HCV infections" "c(\"Hepcinat\", \"Hepcvir\", \"Sofosbuvir\", \"Sovaldi\", \"SOVALDI\", \"SoviHep\")" 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" "Epclusa Tablet"
"J05AP56" "Sofosbuvir, velpatasvir and voxilaprevir" "Antivirals for treatment of HCV infections" ""
"J05AF04" 18283 "Stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Estavudina\", \"Sanilvudine\", \"Stavudin\", \"Stavudine\", \"Stavudinum\", \"Zerit Xr\", \"Zerut XR\")" 80 "mg"
"J05AR07" 15979285 "Stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" "STAVUDIINE"
"J05AP02" 3010818 "Telaprevir" "Antivirals for treatment of HCV infections" "c(\"Incivek\", \"Incivo\", \"Telaprevir\", \"Telavic\")" 2.25 "g"
"J05AF11" 159269 "Telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epavudine\", \"Sebivo\", \"Telbivudin\", \"Telbivudine\", \"Tyzeka\")" 0.6 "g"
"J05AF13" 9574768 "Tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Vemlidy" 25 "mg"
"J05AF07" 5481350 "Tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"BisPMPA\", \"PMPA prodrug\", \"Tenofovir\", \"Viread\")" 0.245 "g"
"J05AR03" "Tenofovir disoproxil and emtricitabine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AX19" 5475 "Tilorone" "Other antivirals" "c(\"Amiksin\", \"Amixin\", \"Amixin IC\", \"Amyxin\", \"Tiloron\", \"Tilorona\", \"Tilorone\", \"Tiloronum\")" 0.125 "g"
"J05AE09" 54682461 "Tipranavir" "Protease inhibitors" "c(\"Aptivus\", \"Tipranavir\")" 1 "g"
"J05AC03" 64377 "Tromantadine" "Cyclic amines" "c(\"Tromantadina\", \"Tromantadine\", \"Tromantadinum\", \"Viruserol\")"
"J05AX13" 131411 "Umifenovir" "Other antivirals" "c(\"Arbidol\", \"Arbidol base\", \"Umifenovir\")" 0.8 "g"
"J05AB11" 135398742 "Valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Talavir\", \"Valaciclovir\", \"Valaciclovirum\", \"ValACV\", \"Valcivir\", \"Valcyclovir\", \"Valtrex\", \"Virval\", \"Zelitrex\")" 3 "g"
"J05AB14" 135413535 "Valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cymeval\", \"Valganciclovir\")" 0.9 "g"
"J05AB03" 21704 "Vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenine arabinoside\", \"Araadenosine\", \"Arabinoside adenine\", \"Arabinosyl adenine\", \"Arabinosyladenine\", \"Spongoadenosine\", \"Vidarabin\", \"Vidarabina\", \"Vidarabine\", \"Vidarabine anhydrous\", \"Vidarabinum\", \"Vira A\", \"Vira ATM\")"
"J05AF03" 24066 "Zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Dideoxycytidine\", \"Interferon AD + ddC\", \"Zalcitabine\", \"Zalcitibine\")" 2.25 "mg"
"J05AH01" 60855 "Zanamivir" "Neuraminidase inhibitors" "c(\"MODIFIED SIALIC ACID\", \"Relenza\", \"Zanamavir\", \"Zanamir\", \"Zanamivi\", \"Zanamivir\", \"Zanamivir hydrate\")"
"J05AF01" 35370 "Zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Azidothymidine\", \"AZT Antiviral\", \"Beta interferon\", \"Compound S\", \"Propolis+AZT\", \"Retrovir\", \"Zidovudina\", \"Zidovudine\", \"ZIDOVUDINE\", \"Zidovudine EP III\", \"Zidovudinum\")" 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" ""

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<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure of the data sets look like. If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.</p>
<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
<p class="dataset-within-r">
If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
</p>
<div id="microorganisms-currently-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘snomed’</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 July 2020 20:52:40 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file (.rds)</a>, 2.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel workbook (.xlsx)</a>, 6.1 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file (.sav)</a>, 28.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">Stata file (.dta)</a>, 25.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas">SAS file (.sas)</a>, 26.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">tab separated file (.txt)</a>, 13.3 MB.</p>
<p>It was last updated on 28 July 2020 20:52:40 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds" target="_blank"><img src="download_rds.png" height="70px" title="2.7 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx" target="_blank"><img src="download_xlsx.png" height="70px" title="6.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt" target="_blank"><img src="download_txt.png" height="70px" title="13.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas" target="_blank"><img src="download_sas.png" height="70px" title="26.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav" target="_blank"><img src="download_sav.png" height="70px" title="28.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta" target="_blank"><img src="download_dta.png" height="70px" title="25.2 MB"></a></p>
<div id="source" class="section level3">
<h3 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h3>
@ -219,10 +223,9 @@
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
</ul>
</div>
<div id="structure" class="section level3">
<div id="example-content" class="section level3">
<h3 class="hasAnchor">
<a href="#structure" class="anchor"></a>Structure</h3>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
<a href="#example-content" class="anchor"></a>Example content</h3>
<p>Included (sub)species per taxonomic kingdom:</p>
<table class="table">
<thead><tr class="header">
@ -410,9 +413,11 @@
<div id="microorganisms-previously-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
<p>A data set with 12,708 rows and 4 columns, containing the following column names:<br><em>‘fullname’, ‘fullname_new’, ‘ref’, ‘prevalence’</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 May 2020 11:17:56 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file (.rds)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel workbook (.xlsx)</a>, 0.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file (.sav)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">Stata file (.dta)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas">SAS file (.sas)</a>, 1.9 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">tab separated file (.txt)</a>, 0.8 MB.</p>
<p>It was last updated on 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds" target="_blank"><img src="download_rds.png" height="70px" title="0.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx" target="_blank"><img src="download_xlsx.png" height="70px" title="0.4 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt" target="_blank"><img src="download_txt.png" height="70px" title="0.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas" target="_blank"><img src="download_sas.png" height="70px" title="1.9 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav" target="_blank"><img src="download_sav.png" height="70px" title="1.9 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta" target="_blank"><img src="download_dta.png" height="70px" title="1.8 MB"></a></p>
<div id="source-1" class="section level3">
<h3 class="hasAnchor">
<a href="#source-1" class="anchor"></a>Source</h3>
@ -424,11 +429,9 @@
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
</ul>
</div>
<div id="structure-1" class="section level3">
<div id="example-content-1" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-1" class="anchor"></a>Structure</h3>
<p>A data set with 12,708 rows and 4 columns, containing the following column names:<br><em>fullname, fullname_new, ref, prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>fullname</em>. For the scientific reference of the new names, i.e. of column <em>fullname_new</em>, see the <code>microorganisms</code> data set.</p>
<a href="#example-content-1" class="anchor"></a>Example content</h3>
<p>Example rows when filtering on <em>Escherichia</em>:</p>
<table class="table">
<thead><tr class="header">
@ -463,9 +466,10 @@
<div id="antibiotic-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 31 July 2020 12:12:13 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file (.rds)</a>, 37 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel workbook (.xlsx)</a>, 65 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file (.sav)</a>, 1.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">Stata file (.dta)</a>, 0.3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas">SAS file (.sas)</a>, 1.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">tab separated file (.txt)</a>, 0.1 MB.</p>
<p>It was last updated on 31 July 2020 12:12:13 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" target="_blank"><img src="download_rds.png" height="70px" title="37 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx" target="_blank"><img src="download_xlsx.png" height="70px" title="65 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt" target="_blank"><img src="download_txt.png" height="70px" title="0.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas" target="_blank"><img src="download_sas.png" height="70px" title="1.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav" target="_blank"><img src="download_sav.png" height="70px" title="1.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta" target="_blank"><img src="download_dta.png" height="70px" title="0.3 MB"></a></p>
<div id="source-2" class="section level3">
<h3 class="hasAnchor">
<a href="#source-2" class="anchor"></a>Source</h3>
@ -477,11 +481,9 @@
<li><a href="https://whonet.org">WHONET software 2019</a></li>
</ul>
</div>
<div id="structure-2" class="section level3">
<div id="example-content-2" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-2" class="anchor"></a>Structure</h3>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc</em>.</p>
<p>Example rows:</p>
<a href="#example-content-2" class="anchor"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="1%">
@ -619,9 +621,10 @@
<div id="antiviral-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>‘atc’, ‘cid’, ‘name’, ‘atc_group’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 23 November 2019 19:03:43 CET.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file (.rds)</a>, 5 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel workbook (.xlsx)</a>, 14 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file (.sav)</a>, 68 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">Stata file (.dta)</a>, 67 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas">SAS file (.sas)</a>, 80 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">tab separated file (.txt)</a>, 16 kB.</p>
<p>It was last updated on 29 August 2020 21:36:44 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antivirals.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds" target="_blank"><img src="download_rds.png" height="70px" title="5 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx" target="_blank"><img src="download_xlsx.png" height="70px" title="14 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt" target="_blank"><img src="download_txt.png" height="70px" title="16 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas" target="_blank"><img src="download_sas.png" height="70px" title="80 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav" target="_blank"><img src="download_sav.png" height="70px" title="68 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta" target="_blank"><img src="download_dta.png" height="70px" title="67 kB"></a></p>
<div id="source-3" class="section level3">
<h3 class="hasAnchor">
<a href="#source-3" class="anchor"></a>Source</h3>
@ -632,11 +635,9 @@
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
</ul>
</div>
<div id="structure-3" class="section level3">
<div id="example-content-3" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-3" class="anchor"></a>Structure</h3>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units</em>.</p>
<p>Example rows:</p>
<a href="#example-content-3" class="anchor"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="4%">
@ -664,7 +665,7 @@
<tr class="odd">
<td align="center">J05AF06</td>
<td align="center">441300</td>
<td align="center">abacavir</td>
<td align="center">Abacavir</td>
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
<td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
<td align="center">0.6</td>
@ -675,7 +676,7 @@
<tr class="even">
<td align="center">J05AB01</td>
<td align="center">135398513</td>
<td align="center">aciclovir</td>
<td align="center">Aciclovir</td>
<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
<td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
<td align="center">4.0</td>
@ -686,7 +687,7 @@
<tr class="odd">
<td align="center">J05AF08</td>
<td align="center">60871</td>
<td align="center">adefovir dipivoxil</td>
<td align="center">Adefovir dipivoxil</td>
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
<td align="center">10.0</td>
@ -697,7 +698,7 @@
<tr class="even">
<td align="center">J05AE05</td>
<td align="center">65016</td>
<td align="center">amprenavir</td>
<td align="center">Amprenavir</td>
<td align="center">Protease inhibitors</td>
<td align="center">Agenerase, Amprenavir, Amprenavirum, …</td>
<td align="center">1.2</td>
@ -708,7 +709,7 @@
<tr class="odd">
<td align="center">J05AP06</td>
<td align="center">16076883</td>
<td align="center">asunaprevir</td>
<td align="center">Asunaprevir</td>
<td align="center">Antivirals for treatment of HCV infections</td>
<td align="center">Asunaprevir, Sunvepra</td>
<td align="center"></td>
@ -719,7 +720,7 @@
<tr class="even">
<td align="center">J05AE08</td>
<td align="center">148192</td>
<td align="center">atazanavir</td>
<td align="center">Atazanavir</td>
<td align="center">Protease inhibitors</td>
<td align="center">Atazanavir, Atazanavir Base, Latazanavir, …</td>
<td align="center">0.3</td>
@ -734,20 +735,19 @@
<div id="intrinsic-bacterial-resistance" class="section level2">
<h2 class="hasAnchor">
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<p>A data set with 49,462 rows and 2 columns, containing the following column names:<br><em>‘microorganism’, ‘antibiotic’</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 August 2020 14:18:20 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file (.rds)</a>, 97 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel workbook (.xlsx)</a>, 0.5 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file (.sav)</a>, 4.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">Stata file (.dta)</a>, 3.7 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas">SAS file (.sas)</a>, 3.8 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">tab separated file (.txt)</a>, 1.8 MB.</p>
<p>It was last updated on 14 August 2020 14:18:20 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds" target="_blank"><img src="download_rds.png" height="70px" title="97 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx" target="_blank"><img src="download_xlsx.png" height="70px" title="0.5 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt" target="_blank"><img src="download_txt.png" height="70px" title="1.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas" target="_blank"><img src="download_sas.png" height="70px" title="3.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav" target="_blank"><img src="download_sav.png" height="70px" title="4.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta" target="_blank"><img src="download_dta.png" height="70px" title="3.7 MB"></a></p>
<div id="source-4" class="section level3">
<h3 class="hasAnchor">
<a href="#source-4" class="anchor"></a>Source</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
<p>The data set is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
</div>
<div id="structure-4" class="section level3">
<div id="example-content-4" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-4" class="anchor"></a>Structure</h3>
<p>A data set with 49,462 rows and 2 columns, containing the following column names:<br><em>microorganism, antibiotic</em>.</p>
<p>Example rows when filtering on <em>Klebsiella</em>:</p>
<a href="#example-content-4" class="anchor"></a>Example content</h3>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
<table class="table">
<thead><tr class="header">
<th align="center">microorganism</th>
@ -755,29 +755,81 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Klebsiella</td>
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">Ampicillin</td>
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin/clavulanic acid</td>
</tr>
<tr class="odd">
<td align="center">Klebsiella</td>
<td align="center">Enterobacter cloacae</td>
<td align="center">Ampicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Azithromycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefazolin</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">Clarithromycin</td>
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefoxitin</td>
</tr>
<tr class="odd">
<td align="center">Klebsiella</td>
<td align="center">Daptomycin</td>
<td align="center">Enterobacter cloacae</td>
<td align="center">Clarithromycin</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">Enterobacter cloacae</td>
<td align="center">Daptomycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Erythromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Fusidic acid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Lincomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Linezolid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Penicillin G</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pristinamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Quinupristin/dalfopristin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Rifampicin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Roxithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Teicoplanin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Vancomycin</td>
</tr>
</tbody>
</table>
</div>
@ -785,19 +837,18 @@
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
<h2 class="hasAnchor">
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘uti’</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 July 2020 13:12:34 CEST.</p>
<p>Direct download links:<br><a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file (.rds)</a>, 55 kB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel workbook (.xlsx)</a>, 0.6 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file (.sav)</a>, 3.4 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file (.dta)</a>, 3 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file (.sas)</a>, 3.2 MB – <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">tab separated file (.txt)</a>, 1.5 MB.</p>
<p>It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds" target="_blank"><img src="download_rds.png" height="70px" title="55 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx" target="_blank"><img src="download_xlsx.png" height="70px" title="0.6 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt" target="_blank"><img src="download_txt.png" height="70px" title="1.5 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas" target="_blank"><img src="download_sas.png" height="70px" title="3.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav" target="_blank"><img src="download_sav.png" height="70px" title="3.4 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta" target="_blank"><img src="download_dta.png" height="70px" title="3 MB"></a></p>
<div id="source-5" class="section level3">
<h3 class="hasAnchor">
<a href="#source-5" class="anchor"></a>Source</h3>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020).</p>
</div>
<div id="structure-5" class="section level3">
<div id="example-content-5" class="section level3">
<h3 class="hasAnchor">
<a href="#structure-5" class="anchor"></a>Structure</h3>
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti</em>.</p>
<p>Example rows:</p>
<a href="#example-content-5" class="anchor"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="8%">

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</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">1.3.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>

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@ -81,7 +81,7 @@
</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">1.3.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>

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@ -272,3 +272,6 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
.home-buttons .fa {
font-size: 3.5em;
}
.dataset-within-r {
display: none;
}

2
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@ -43,7 +43,7 @@
</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">1.3.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>

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@ -81,7 +81,7 @@
</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">1.3.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309011" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9011">
<a href="#amr-1309011" class="anchor"></a>AMR 1.3.0.9011<small> Unreleased </small>
<div id="amr-1309012" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9012">
<a href="#amr-1309012" class="anchor"></a>AMR 1.3.0.9012<small> Unreleased </small>
</h1>
<div id="last-updated-29-august-2020" class="section level2">
<h2 class="hasAnchor">
@ -299,6 +299,7 @@
<li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
<li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
<li><p>Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: <code>tibble</code> printing support for classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and <code>&lt;mo&gt;</code>. When using <code>tibble</code>s containing antimicrobial columns (class <code>&lt;rsi&gt;</code>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class <code>&lt;mo&gt;</code>) will emphasise on the genus and species, not on the kingdom.</p></li>
<li><p>Names of antiviral agents in data set <code>antivirals</code> now have a starting capital letter, like it is the case in the <code>antibiotics</code> data set</p></li>
</ul>
</div>
</div>

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pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-08-29T10:02Z
last_built: 2020-08-29T19:41Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -81,7 +81,7 @@
</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">1.3.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>

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@ -81,7 +81,7 @@
</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">1.3.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9012</span>
</span>
</div>

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.home-buttons .fa {
font-size: 3.5em;
}
.dataset-within-r {
display: none;
}

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@ -35,13 +35,13 @@ structure_txt <- function(dataset) {
paste0("A data set with ",
format(nrow(dataset), big.mark = ","), " rows and ",
ncol(dataset), " columns, containing the following column names: \n*",
paste0(colnames(dataset), collapse = ", "), "*.")
paste0("'", colnames(dataset), "'", collapse = ", "), "*.")
}
download_txt <- function(filename) {
msg <- paste0("It was last updated on ",
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z")),
".\n\nDirect download links: \n")
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", filename, ".html).\n")
github_base <- "https://github.com/msberends/AMR/raw/master/data-raw/"
filename <- paste0("../data-raw/", filename)
txt <- paste0(filename, ".txt")
@ -51,15 +51,25 @@ download_txt <- function(filename) {
sas <- paste0(filename, ".sas")
excel <- paste0(filename, ".xlsx")
create_txt <- function(filename, type) {
paste0("[", type, "](", github_base, filename, "), ", file_size(filename), " -- ")
paste0('<a class="dataset-download-button" href="', github_base, filename, '" target="_blank">',
'<img src="download_', type, '.png" height="70px" title="', file_size(filename), '">',
'</a>')
}
if (file.exists(rds)) msg <- c(msg, create_txt(rds, "R file (.rds)"))
if (file.exists(excel)) msg <- c(msg, create_txt(excel, "Excel workbook (.xlsx)"))
if (file.exists(spss)) msg <- c(msg, create_txt(spss, "SPSS file (.sav)"))
if (file.exists(stata)) msg <- c(msg, create_txt(stata, "Stata file (.dta)"))
if (file.exists(sas)) msg <- c(msg, create_txt(sas, "SAS file (.sas)"))
if (file.exists(txt)) msg <- c(msg, create_txt(txt, "tab separated file (.txt)"))
if (any(file.exists(rds),
file.exists(excel),
file.exists(txt),
file.exists(sas),
file.exists(spss),
file.exists(stata))) {
msg <- c(msg, "\n**Direct download links:** \n")
}
if (file.exists(rds)) msg <- c(msg, create_txt(rds, "rds"))
if (file.exists(excel)) msg <- c(msg, create_txt(excel, "xlsx"))
if (file.exists(txt)) msg <- c(msg, create_txt(txt, "txt"))
if (file.exists(sas)) msg <- c(msg, create_txt(sas, "sas"))
if (file.exists(spss)) msg <- c(msg, create_txt(spss, "sav"))
if (file.exists(stata)) msg <- c(msg, create_txt(stata, "dta"))
msg[length(msg)] <- gsub(" --", ".", msg[length(msg)], fixed = TRUE)
paste0(msg, collapse = "")
}
@ -67,9 +77,9 @@ download_txt <- function(filename) {
library(AMR)
library(dplyr)
print_df <- function(x) {
print_df <- function(x, rows = 6) {
x %>%
head() %>%
head(n = rows) %>%
mutate_all(function(x) {
if (is.list(x)) {
sapply(x, function(y) {
@ -92,10 +102,14 @@ print_df <- function(x) {
All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.
On this page, we explain how to download them and how the structure of the data sets look like. If you are reading this page from within R, please [visit our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
On this page, we explain how to download them and how the structure of the data sets look like.
<p class="dataset-within-r">If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.</p>
## Microorganisms (currently accepted names)
`r structure_txt(microorganisms)`
This data set is in R available as `microorganisms`, after you load the `AMR` package.
`r download_txt("microorganisms")`
@ -107,9 +121,7 @@ Our full taxonomy of microorganisms is based on the authoritative and comprehens
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, included version: `r AMR:::catalogue_of_life$yearmonth_DSMZ`)
### Structure
`r structure_txt(microorganisms)`
### Example content
Included (sub)species per taxonomic kingdom:
@ -133,6 +145,10 @@ microorganisms %>%
## Microorganisms (previously accepted names)
`r structure_txt(microorganisms.old)`
**Note:** remember that the 'ref' columns contains the scientific reference to the old taxonomic entries, i.e. of column *'fullname'*. For the scientific reference of the new names, i.e. of column *'fullname_new'*, see the `microorganisms` data set.
This data set is in R available as `microorganisms.old`, after you load the `AMR` package.
`r download_txt("microorganisms.old")`
@ -144,11 +160,7 @@ This data set contains old, previously accepted taxonomic names. The data source
* [Catalogue of Life](http://www.catalogueoflife.org) (included version: `r AMR:::catalogue_of_life$year`)
* [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) (LPSN, included version: `r AMR:::catalogue_of_life$yearmonth_DSMZ`)
### Structure
`r structure_txt(microorganisms.old)`
**Note:** remember that the 'ref' columns contains the scientific reference to the old taxonomic entries, i.e. of column *fullname*. For the scientific reference of the new names, i.e. of column *fullname_new*, see the `microorganisms` data set.
### Example content
Example rows when filtering on *Escherichia*:
@ -161,6 +173,8 @@ microorganisms.old %>%
## Antibiotic agents
`r structure_txt(antibiotics)`
This data set is in R available as `antibiotics`, after you load the `AMR` package.
`r download_txt("antibiotics")`
@ -173,11 +187,7 @@ This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET,
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
* [WHONET software 2019](https://whonet.org)
### Structure
`r structure_txt(antibiotics)`
Example rows:
### Example content
```{r, echo = FALSE}
antibiotics %>%
@ -188,6 +198,8 @@ antibiotics %>%
## Antiviral agents
`r structure_txt(antivirals)`
This data set is in R available as `antivirals`, after you load the `AMR` package.
`r download_txt("antivirals")`
@ -199,11 +211,7 @@ This data set contains all ATC codes gathered from WHO and all compound IDs from
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
### Structure
`r structure_txt(antivirals)`
Example rows:
### Example content
```{r, echo = FALSE}
antivirals %>%
@ -213,31 +221,31 @@ antivirals %>%
## Intrinsic bacterial resistance
`r structure_txt(intrinsic_resistant)`
This data set is in R available as `intrinsic_resistant`, after you load the `AMR` package.
`r download_txt("intrinsic_resistant")`
### Source
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations.
The data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r AMR:::EUCAST_VERSION_EXPERT_RULES`.
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r AMR:::EUCAST_VERSION_EXPERT_RULES`.
### Structure
### Example content
`r structure_txt(intrinsic_resistant)`
Example rows when filtering on *Klebsiella*:
Example rows when filtering on *Enterobacter cloacae*:
```{r, echo = FALSE}
intrinsic_resistant %>%
filter(microorganism %like% "^Klebsiella") %>%
print_df()
filter(microorganism == "Enterobacter cloacae") %>%
print_df(rows = Inf)
```
## Interpretation from MIC values / disk diameters to R/SI
`r structure_txt(rsi_translation)`
This data set is in R available as `rsi_translation`, after you load the `AMR` package.
`r download_txt("rsi_translation")`
@ -246,11 +254,7 @@ This data set is in R available as `rsi_translation`, after you load the `AMR` p
This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`).
### Structure
`r structure_txt(rsi_translation)`
Example rows:
### Example content
```{r, echo = FALSE}
rsi_translation %>%

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