diff --git a/DESCRIPTION b/DESCRIPTION index 6306240..3547a77 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: abxaware Title: AWaRe classification of Antibiotic Usage Data -Version: 0.0.1 -Date: 2024-01-31 +Version: 0.0.0.9000 +Date: 2021-09-19 Authors@R: c(person(given = "Jacob", family = "Anhøj", @@ -12,11 +12,7 @@ Authors@R: family = "Boel", role = c("aut"), email = "", - comment = c(ORCID = "0000-0003-3085-0930")), - person(given = "Marc Trunjer Kusk", - family = "Nielsen", - role = c("aut"), - email = "marc.mtk@gmail.com")) + comment = c(ORCID = "0000-0003-3085-0930"))) Description: Aggregate and plot antibiotic usage data by access, watch, and reserve (AWaRe) groups. diff --git a/R/awr_funs.R b/R/awr_funs.R index c276c06..5eb6fca 100644 --- a/R/awr_funs.R +++ b/R/awr_funs.R @@ -157,10 +157,9 @@ awr_plot <- function(df, ...) cols <- c( - 'global reserve' = '#800080', # purple - 'reserve' = '#F07E6E', # red - 'watch' = '#FBB258', # amber - 'access' = '#90CD97' # green + 'reserve' = '#F07E6E', # red + 'watch' = '#FBB258', # amber + 'access' = '#90CD97' # green ) if('other' %in% levels(d$aware)) { diff --git a/data-raw/abx_aware.R b/data-raw/abx_aware.R index 8949e3d..58c7f92 100644 --- a/data-raw/abx_aware.R +++ b/data-raw/abx_aware.R @@ -11,8 +11,7 @@ library(tidyverse) library(docxtractr) -awr_levels <- c('global reserve', - 'reserve', +awr_levels <- c('reserve', 'watch', 'access') diff --git a/data-raw/data/atc.rds b/data-raw/data/atc.rds index ad2be1a..67c2743 100644 Binary files a/data-raw/data/atc.rds and b/data-raw/data/atc.rds differ diff --git a/data-raw/data/aware_dk.tsv b/data-raw/data/aware_dk.tsv index 8ff2e50..0193966 100644 --- a/data-raw/data/aware_dk.tsv +++ b/data-raw/data/aware_dk.tsv @@ -13,10 +13,10 @@ J01AA08 minocycline reserve J01AA09 rolitetracycline NA J01AA10 penimepicycline NA J01AA11 clomocycline NA -J01AA12 tigecycline global reserve -J01AA13 eravacycline global reserve +J01AA12 tigecycline reserve +J01AA13 eravacycline reserve J01AA14 sarecycline NA -J01AA15 omadacycline global reserve +J01AA15 omadacycline NA J01AA20 combinations of tetracyclines NA J01AA56 oxytetracycline, combinations NA J01B AMPHENICOLS NA @@ -125,7 +125,7 @@ J01DD16 cefditoren watch J01DD17 cefcapene watch J01DD18 cefteram watch J01DD51 cefotaxime and beta-lactamase inhibitor NA -J01DD52 ceftazidime and beta-lactamase inhibitor global reserve +J01DD52 ceftazidime and beta-lactamase inhibitor reserve J01DD54 ceftriaxone, combinations NA J01DD62 cefoperazone and beta-lactamase inhibitor NA J01DD63 ceftriaxone and beta-lactamase inhibitor NA @@ -134,25 +134,25 @@ J01DE Fourth-generation cephalosporins NA J01DE01 cefepime watch J01DE02 cefpirome watch J01DE03 cefozopran watch -J01DF Monobactams global reserve -J01DF01 aztreonam global reserve +J01DF Monobactams NA +J01DF01 aztreonam reserve J01DF02 carumonam NA -J01DH Carbapenems reserve +J01DH Carbapenems NA J01DH02 meropenem reserve -J01DH03 ertapenem reserve -J01DH04 doripenem reserve -J01DH05 biapenem reserve -J01DH06 tebipenem pivoxil reserve -J01DH51 imipenem and cilastatin reserve -J01DH52 meropenem and vaborbactam global reserve +J01DH03 ertapenem watch +J01DH04 doripenem watch +J01DH05 biapenem watch +J01DH06 tebipenem pivoxil watch +J01DH51 imipenem and cilastatin watch +J01DH52 meropenem and vaborbactam reserve J01DH55 panipenem and betamipron NA -J01DH56 imipenem, cilastatin and relebactam global reserve -J01DI Other cephalosporins and penems in ATC global reserve +J01DH56 imipenem, cilastatin and relebactam NA +J01DI Other cephalosporins and penems in ATC NA J01DI01 ceftobiprole medocaril reserve J01DI02 ceftaroline fosamil reserve J01DI03 faropenem reserve -J01DI04 cefiderocol global reserve -J01DI54 ceftolozane and beta-lactamase inhibitor global reserve +J01DI04 cefiderocol NA +J01DI54 ceftolozane and beta-lactamase inhibitor reserve J01E SULFONAMIDES AND TRIMETHOPRIM ANTIBACTERIALS FOR SYSTEMIC USE NA J01EA Trimethoprim and derivatives, systemic antibacterials NA J01EA01 trimethoprim access @@ -288,11 +288,11 @@ J01XA Glycopeptide antibacterials NA J01XA01 vancomycin watch J01XA02 teicoplanin watch J01XA03 telavancin reserve -J01XA04 dalbavancin global reserve +J01XA04 dalbavancin reserve J01XA05 oritavancin reserve J01XB Polymyxins NA -J01XB01 colistin global reserve -J01XB02 polymyxin B global reserve +J01XB01 colistin reserve +J01XB02 polymyxin B reserve J01XC Steroid antibacterials NA J01XC01 fusidic acid watch J01XD Imidazole derivatives, antibacterial for systemic use NA @@ -305,18 +305,15 @@ J01XE02 nifurtoinol NA J01XE03 furazidin NA J01XE51 nitrofurantoin, combinations NA J01XX Other antibacterials in ATC NA -J01XX01 fosfomycin global reserve +J01XX01 fosfomycin reserve J01XX02 xibornol NA J01XX03 clofoctol watch J01XX04 spectinomycin access J01XX05 methenamine NA J01XX06 mandelic acid NA J01XX07 nitroxoline NA -J01XX08 linezolid global reserve -J01XX09 daptomycin global reserve +J01XX08 linezolid reserve +J01XX09 daptomycin reserve J01XX10 bacitracin NA J01XX11 tedizolid reserve J01XX12 lefamulin NA -J04AB02 rifampicin watch -P01AB01 metronidazole access -A07AA09 vancomycin watch diff --git a/data/abx_aware.rda b/data/abx_aware.rda index 1567480..bc33e7f 100644 Binary files a/data/abx_aware.rda and b/data/abx_aware.rda differ diff --git a/man/abxaware-package.Rd b/man/abxaware-package.Rd index 5097502..bac552f 100644 --- a/man/abxaware-package.Rd +++ b/man/abxaware-package.Rd @@ -21,7 +21,6 @@ Useful links: Authors: \itemize{ \item Jonas Bredtoft Boel (\href{https://orcid.org/0000-0003-3085-0930}{ORCID}) - \item Marc Trunjer Kusk Nielsen \email{marc.mtk@gmail.com} } } diff --git a/man/figures/README-example-1.png b/man/figures/README-example-1.png index 5b490ff..868d8c1 100644 Binary files a/man/figures/README-example-1.png and b/man/figures/README-example-1.png differ