diff --git a/DESCRIPTION b/DESCRIPTION index ef335c31..89e7b702 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.8.0.9005 -Date: 2019-10-26 +Version: 0.8.0.9006 +Date: 2019-10-27 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 9627f8cd..b7d95eab 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 0.8.0.9005 -Last updated: 26-Oct-2019 +# AMR 0.8.0.9006 +Last updated: 27-Oct-2019 ### New * Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012). **This is now the new default guideline for the `mdro()` function.** @@ -11,7 +11,7 @@ * Fix for interpreting MIC values with `as.rsi()` where the input is `NA` * Added "imi" as allowed abbreviation for Imipenem * Fix for automatically determining columns with antibiotic results in `mdro()` and `eucast_rules()` -* Added ATC codes for ceftaroline, ceftobiprole and faropenem +* Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the `antibiotics` data set # AMR 0.8.0 diff --git a/R/eucast_rules.R b/R/eucast_rules.R index d94ddf49..e1daabc6 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -99,7 +99,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" #' \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}), #' \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}), #' \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}), -#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}), +#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}), #' \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}), #' \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}), #' \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}), @@ -109,7 +109,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" #' \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}), #' \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}), #' \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}), -#' \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), +#' \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), #' \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}), #' \strong{STH}: streptomycin-high (no ATC code), #' \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}), diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index a3ae34ac..c7812506 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -318,6 +318,12 @@ antibiotics[which(antibiotics$ab == "FAR"), "atc"] <- "J01DI03" # ceftobiprole antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01" +# typo +antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin" + +antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01" + + antibiotics <- antibiotics %>% arrange(name) # set cephalosporins groups for the ones that could not be determined automatically: diff --git a/data/antibiotics.rda b/data/antibiotics.rda index 898a512a..d2fc0e81 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/docs/404.html b/docs/404.html index 6c2205c5..9dd49105 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 896e346a..7120f5ba 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 diff --git a/docs/articles/index.html b/docs/articles/index.html index aa9e1380..59df090e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 diff --git a/docs/authors.html b/docs/authors.html index 859e03c2..6d9f5b0c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 diff --git a/docs/index.html b/docs/index.html index 1749dd9b..c699cf16 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 diff --git a/docs/news/index.html b/docs/news/index.html index 14ef92d4..b648810d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 @@ -231,11 +231,11 @@ -
+

-AMR 0.8.0.9005 Unreleased +AMR 0.8.0.9006 Unreleased

-

Last updated: 26-Oct-2019

+

Last updated: 27-Oct-2019

New

@@ -257,7 +257,7 @@
  • Added “imi” as allowed abbreviation for Imipenem
  • Fix for automatically determining columns with antibiotic results in mdro() and eucast_rules()
    • -
  • Added ATC codes for ceftaroline, ceftobiprole and faropenem
    • +
  • Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the antibiotics data set
    • @@ -1321,7 +1321,7 @@ Using as.mo(..., allow_uncertain = 3)

    Contents

    @@ -352,7 +352,7 @@ NOV: novobiocin (QJ01XX95), OFX: ofloxacin (J01MA01), OXA: oxacillin (J01CF04), - PEN: penicillin G (J01RA01), + PEN: penicillin G (J01CE01), PIP: piperacillin (J01CA12), TZP: piperacillin/tazobactam (J01CR05), PLB: polymyxin B (J01XB02), @@ -362,7 +362,7 @@ RIB: rifabutin (J04AB04), RIF: rifampicin (J04AB02), RFP: rifapentine (J04AB05), - RXT: roxithromicin (J01FA06), + RXT: roxithromycin (J01FA06), SIS: sisomicin (J01GB08), STH: streptomycin-high (no ATC code), TEC: teicoplanin (J01XA02), diff --git a/docs/reference/index.html b/docs/reference/index.html index 0c99ec26..ceeff6a7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9005 + 0.8.0.9006 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index fae93673..74095cb8 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9004 + 0.8.0.9006 @@ -365,7 +365,7 @@ NOV: novobiocin (QJ01XX95), OFX: ofloxacin (J01MA01), OXA: oxacillin (J01CF04), - PEN: penicillin G (J01RA01), + PEN: penicillin G (J01CE01), PIP: piperacillin (J01CA12), TZP: piperacillin/tazobactam (J01CR05), PLB: polymyxin B (J01XB02), @@ -375,7 +375,7 @@ RIB: rifabutin (J04AB04), RIF: rifampicin (J04AB02), RFP: rifapentine (J04AB05), - RXT: roxithromicin (J01FA06), + RXT: roxithromycin (J01FA06), SIS: sisomicin (J01GB08), STH: streptomycin-high (no ATC code), TEC: teicoplanin (J01XA02), diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 8870158a..f2085a29 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -111,7 +111,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}} \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}), \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}), \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}), - \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}), + \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}), \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}), \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}), \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}), @@ -121,7 +121,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}} \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}), \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}), \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}), - \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), + \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}), \strong{STH}: streptomycin-high (no ATC code), \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}), diff --git a/man/mdro.Rd b/man/mdro.Rd index 54c33c64..7c839bb8 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -123,7 +123,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}} \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}), \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}), \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}), - \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}), + \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}), \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}), \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}), \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}), @@ -133,7 +133,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}} \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}), \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}), \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}), - \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), + \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}), \strong{STH}: streptomycin-high (no ATC code), \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),