diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index a1435dedd..46857eef8 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -27,6 +27,10 @@ on: 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 diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 4875f2d1e..51a7e5086 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -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} diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index c6b857465..82bb69ee5 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -26,7 +26,6 @@ on: - master pull_request: branches: - - premaster - master name: lintr diff --git a/DESCRIPTION b/DESCRIPTION index 3ccbb4c20..e4484222a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9011 +Version: 1.3.0.9012 Date: 2020-08-29 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 1a2e43022..66f3391d9 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.3.0.9011 +# AMR 1.3.0.9012 ## Last updated: 29 August 2020 ### New @@ -40,6 +40,7 @@ * 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 ``, ``, ``, `` and ``. When using `tibble`s containing antimicrobial columns (class ``), "S" will print in green, "I" will print in yellow and "R" will print in red. Microbial IDs (class ``) 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 diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index a72619ceb..f48541120 100644 Binary files a/data-raw/antibiotics.dta and b/data-raw/antibiotics.dta differ diff --git a/data-raw/antibiotics.sas b/data-raw/antibiotics.sas index 71ea9e2d7..109862d54 100644 Binary files a/data-raw/antibiotics.sas and b/data-raw/antibiotics.sas differ diff --git a/data-raw/antibiotics.sav b/data-raw/antibiotics.sav index 8c4426388..84b7eaa8d 100644 Binary files a/data-raw/antibiotics.sav and b/data-raw/antibiotics.sav differ diff --git a/data-raw/antibiotics.xlsx b/data-raw/antibiotics.xlsx index 7e13b05f9..3f8061018 100644 Binary files a/data-raw/antibiotics.xlsx and b/data-raw/antibiotics.xlsx differ diff --git a/data-raw/antivirals.dta b/data-raw/antivirals.dta index 265244961..d2d249625 100644 Binary files a/data-raw/antivirals.dta and b/data-raw/antivirals.dta differ diff --git a/data-raw/antivirals.rds b/data-raw/antivirals.rds index be76339af..2997918f5 100644 Binary files a/data-raw/antivirals.rds and b/data-raw/antivirals.rds differ diff --git a/data-raw/antivirals.sas b/data-raw/antivirals.sas index 73e1a9187..c3efb300e 100644 Binary files a/data-raw/antivirals.sas and b/data-raw/antivirals.sas differ diff --git a/data-raw/antivirals.sav b/data-raw/antivirals.sav index dfc49b5f3..b90b2c65f 100644 Binary files a/data-raw/antivirals.sav and b/data-raw/antivirals.sav differ diff --git a/data-raw/antivirals.txt b/data-raw/antivirals.txt index aa38c5c46..3fc31a11a 100644 --- a/data-raw/antivirals.txt +++ b/data-raw/antivirals.txt @@ -1,103 +1,103 @@ "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" "" diff --git a/data-raw/antivirals.xlsx b/data-raw/antivirals.xlsx index 4b75d649b..3100b23ac 100644 Binary files a/data-raw/antivirals.xlsx and b/data-raw/antivirals.xlsx differ diff --git a/data-raw/download_buttons.psd b/data-raw/download_buttons.psd new file mode 100644 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b/data-raw/rsi_translation.sas differ diff --git a/data-raw/rsi_translation.sav b/data-raw/rsi_translation.sav index 4c462eb16..f7214cdc2 100644 Binary files a/data-raw/rsi_translation.sav and b/data-raw/rsi_translation.sav differ diff --git a/data-raw/rsi_translation.xlsx b/data-raw/rsi_translation.xlsx index fa4cf525e..d3d26b367 100644 Binary files a/data-raw/rsi_translation.xlsx and b/data-raw/rsi_translation.xlsx differ diff --git a/data/antivirals.rda b/data/antivirals.rda index 8cda48486..a041649c7 100644 Binary files a/data/antivirals.rda and b/data/antivirals.rda differ diff --git a/docs/404.html b/docs/404.html index 17a9b6cf3..4c1e76382 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 832879a13..b422529e4 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 547c91f3c..acf508e75 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.3.0.9007 + 1.3.0.9012 @@ -201,13 +201,17 @@

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, 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.

+

+If you are reading this page from within R, please visit our website, which is automatically updated with every code change. +

Microorganisms (currently accepted names)

+

A data set with 67,151 rows and 16 columns, containing the following column names:
‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘snomed’.

This data set is in R available as microorganisms, after you load the AMR package.

-

It was last updated on 28 July 2020 20:52:40 CEST.

-

Direct download links:
R file (.rds), 2.7 MB – Excel workbook (.xlsx), 6.1 MB – SPSS file (.sav), 28.2 MB – Stata file (.dta), 25.2 MB – SAS file (.sas), 26.2 MB – tab separated file (.txt), 13.3 MB.

+

It was last updated on 28 July 2020 20:52:40 CEST. Find more info about the structure of this data set here.

+

Direct download links:

Source

@@ -219,10 +223,9 @@ List of Prokaryotic names with Standing in Nomenclature (LPSN, included version: May 2020)
-
+

-Structure

-

A data set with 67,151 rows and 16 columns, containing the following column names:
mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed.

+Example content

Included (sub)species per taxonomic kingdom:

@@ -410,9 +413,11 @@

Microorganisms (previously accepted names)

+

A data set with 12,708 rows and 4 columns, containing the following column names:
‘fullname’, ‘fullname_new’, ‘ref’, ‘prevalence’.

+

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.

-

It was last updated on 28 May 2020 11:17:56 CEST.

-

Direct download links:
R file (.rds), 0.3 MB – Excel workbook (.xlsx), 0.4 MB – SPSS file (.sav), 1.9 MB – Stata file (.dta), 1.8 MB – SAS file (.sas), 1.9 MB – tab separated file (.txt), 0.8 MB.

+

It was last updated on 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set here.

+

Direct download links:

Source

@@ -424,11 +429,9 @@ List of Prokaryotic names with Standing in Nomenclature (LPSN, included version: May 2020)
-
+

-Structure

-

A data set with 12,708 rows and 4 columns, containing the following column names:
fullname, fullname_new, ref, prevalence.

-

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:

@@ -463,9 +466,10 @@

Antibiotic agents

+

A data set with 456 rows and 14 columns, containing the following column names:
‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’.

This data set is in R available as antibiotics, after you load the AMR package.

-

It was last updated on 31 July 2020 12:12:13 CEST.

-

Direct download links:
R file (.rds), 37 kB – Excel workbook (.xlsx), 65 kB – SPSS file (.sav), 1.3 MB – Stata file (.dta), 0.3 MB – SAS file (.sas), 1.8 MB – tab separated file (.txt), 0.1 MB.

+

It was last updated on 31 July 2020 12:12:13 CEST. Find more info about the structure of this data set here.

+

Direct download links:

Source

@@ -477,11 +481,9 @@
  • WHONET software 2019
    • -
    +

    -Structure

    -

    A data set with 456 rows and 14 columns, containing the following column names:
    ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc.

    -

    Example rows:

    +Example content
    @@ -619,9 +621,10 @@

    Antiviral agents

    +

    A data set with 102 rows and 9 columns, containing the following column names:
    ‘atc’, ‘cid’, ‘name’, ‘atc_group’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’.

    This data set is in R available as antivirals, after you load the AMR package.

    -

    It was last updated on 23 November 2019 19:03:43 CET.

    -

    Direct download links:
    R file (.rds), 5 kB – Excel workbook (.xlsx), 14 kB – SPSS file (.sav), 68 kB – Stata file (.dta), 67 kB – SAS file (.sas), 80 kB – tab separated file (.txt), 16 kB.

    +

    It was last updated on 29 August 2020 21:36:44 CEST. Find more info about the structure of this data set here.

    +

    Direct download links:

    -
    +

    -Structure

    -

    A data set with 102 rows and 9 columns, containing the following column names:
    atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units.

    -

    Example rows:

    +Example content
    @@ -664,7 +665,7 @@ - + @@ -675,7 +676,7 @@ - + @@ -686,7 +687,7 @@ - + @@ -697,7 +698,7 @@ - + @@ -708,7 +709,7 @@ - + @@ -719,7 +720,7 @@ - + @@ -734,20 +735,19 @@

    Intrinsic bacterial resistance

    +

    A data set with 49,462 rows and 2 columns, containing the following column names:
    ‘microorganism’, ‘antibiotic’.

    This data set is in R available as intrinsic_resistant, after you load the AMR package.

    -

    It was last updated on 14 August 2020 14:18:20 CEST.

    -

    Direct download links:
    R file (.rds), 97 kB – Excel workbook (.xlsx), 0.5 MB – SPSS file (.sav), 4.2 MB – Stata file (.dta), 3.7 MB – SAS file (.sas), 3.8 MB – tab separated file (.txt), 1.8 MB.

    +

    It was last updated on 14 August 2020 14:18:20 CEST. Find more info about the structure of this data set here.

    +

    Direct download links:

    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 3.1, 2016.

    +

    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.

    -
    +

    -Structure

    -

    A data set with 49,462 rows and 2 columns, containing the following column names:
    microorganism, antibiotic.

    -

    Example rows when filtering on Klebsiella:

    +Example content +

    Example rows when filtering on Enterobacter cloacae:

    J05AF06 441300abacavirAbacavir Nucleoside and nucleotide reverse transcriptase inhibitors Abacavir, Abacavir sulfate, Ziagen 0.6
    J05AB01 135398513aciclovirAciclovir Nucleosides and nucleotides excl. reverse transcriptase inhibitors Acicloftal, Aciclovier, Aciclovir, … 4.0
    J05AF08 60871adefovir dipivoxilAdefovir dipivoxil Nucleoside and nucleotide reverse transcriptase inhibitors Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, … 10.0
    J05AE05 65016amprenavirAmprenavir Protease inhibitors Agenerase, Amprenavir, Amprenavirum, … 1.2
    J05AP06 16076883asunaprevirAsunaprevir Antivirals for treatment of HCV infections Asunaprevir, Sunvepra
    J05AE08 148192atazanavirAtazanavir Protease inhibitors Atazanavir, Atazanavir Base, Latazanavir, … 0.3
    @@ -755,29 +755,81 @@ - + - + + + + + - - + + + + + + - - + + - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    microorganism
    KlebsiellaEnterobacter cloacae Amoxicillin
    KlebsiellaEnterobacter cloacaeAmoxicillin/clavulanic acid
    Enterobacter cloacae Ampicillin
    Klebsiella
    Enterobacter cloacae Azithromycin
    Enterobacter cloacaeCefazolin
    KlebsiellaClarithromycinEnterobacter cloacaeCefoxitin
    KlebsiellaDaptomycinEnterobacter cloacaeClarithromycin
    KlebsiellaEnterobacter cloacaeDaptomycin
    Enterobacter cloacae Erythromycin
    Enterobacter cloacaeFusidic acid
    Enterobacter cloacaeLincomycin
    Enterobacter cloacaeLinezolid
    Enterobacter cloacaePenicillin G
    Enterobacter cloacaePristinamycin
    Enterobacter cloacaeQuinupristin/dalfopristin
    Enterobacter cloacaeRifampicin
    Enterobacter cloacaeRoxithromycin
    Enterobacter cloacaeTeicoplanin
    Enterobacter cloacaeVancomycin
    @@ -785,19 +837,18 @@

    Interpretation from MIC values / disk diameters to R/SI

    +

    A data set with 18,650 rows and 10 columns, containing the following column names:
    ‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘uti’.

    This data set is in R available as rsi_translation, after you load the AMR package.

    -

    It was last updated on 29 July 2020 13:12:34 CEST.

    -

    Direct download links:
    R file (.rds), 55 kB – Excel workbook (.xlsx), 0.6 MB – SPSS file (.sav), 3.4 MB – Stata file (.dta), 3 MB – SAS file (.sas), 3.2 MB – tab separated file (.txt), 1.5 MB.

    +

    It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set here.

    +

    Direct download links:

    Source

    This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020).

    -
    +

    -Structure

    -

    A data set with 18,650 rows and 10 columns, containing the following column names:
    guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti.

    -

    Example rows:

    +Example content diff --git a/docs/articles/index.html b/docs/articles/index.html index f88b0de6d..b2dbcdb69 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 diff --git a/docs/authors.html b/docs/authors.html index 51a5173c7..e6de22cda 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 diff --git a/docs/extra.css b/docs/extra.css index efc2e9996..b8b250c8d 100644 --- a/docs/extra.css +++ b/docs/extra.css @@ -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; +} diff --git a/docs/index.html b/docs/index.html index d4d2067c0..ece62a03c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 diff --git a/docs/news/index.html b/docs/news/index.html index 5110806c5..cd38e2212 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 @@ -236,9 +236,9 @@ Source: NEWS.md -
    -

    -AMR 1.3.0.9011 Unreleased +
    +

    +AMR 1.3.0.9012 Unreleased

    @@ -299,6 +299,7 @@

  • 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 tibbles 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

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5de820662..eaacadc39 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.7.3 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 diff --git a/docs/reference/index.html b/docs/reference/index.html index 24a26c33d..b16c72c91 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012

    diff --git a/docs/survey.html b/docs/survey.html index 0fd2d31e1..ce34de666 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9011 + 1.3.0.9012 diff --git a/pkgdown/extra.css b/pkgdown/extra.css index efc2e9996..b8b250c8d 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -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; +} diff --git a/vignettes/datasets.Rmd b/vignettes/datasets.Rmd index ae69b0548..63af4eba6 100644 --- a/vignettes/datasets.Rmd +++ b/vignettes/datasets.Rmd @@ -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('', + '', + '') } - 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. + +

    If you are reading this page from within R, please visit our website, which is automatically updated with every code change.

    ## 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. +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`. -The data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r AMR:::EUCAST_VERSION_EXPERT_RULES`. +### Example content -### Structure - -`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 %>% diff --git a/vignettes/download_dta.png b/vignettes/download_dta.png new file mode 100644 index 000000000..23a2d5d8a Binary files /dev/null and b/vignettes/download_dta.png differ diff --git a/vignettes/download_rds.png b/vignettes/download_rds.png new file mode 100644 index 000000000..a97dab3a2 Binary files /dev/null and b/vignettes/download_rds.png differ diff --git a/vignettes/download_sas.png b/vignettes/download_sas.png new file mode 100644 index 000000000..b4882c8aa Binary files /dev/null and b/vignettes/download_sas.png differ diff --git a/vignettes/download_sav.png b/vignettes/download_sav.png new file mode 100644 index 000000000..8ef2dffb3 Binary files /dev/null and b/vignettes/download_sav.png differ diff --git a/vignettes/download_txt.png b/vignettes/download_txt.png new file mode 100644 index 000000000..d5a7bbb37 Binary files /dev/null and b/vignettes/download_txt.png differ diff --git a/vignettes/download_xlsx.png b/vignettes/download_xlsx.png new file mode 100644 index 000000000..05f78fd23 Binary files /dev/null and b/vignettes/download_xlsx.png differ