diff --git a/DESCRIPTION b/DESCRIPTION index 4e139437..d26a3483 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9065 +Version: 1.7.1.9066 Date: 2021-12-11 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 04e69995..4bfe5c4d 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9065 +# `AMR` 1.7.1.9066 ## Last updated: 11 December 2021 ### Breaking changes diff --git a/R/mdro.R b/R/mdro.R index 38c7854d..b683258f 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -286,7 +286,7 @@ mdro <- function(x = NULL, } if (guideline == "eucast") { # turn into latest EUCAST guideline - guideline <- "eucast3.2" + guideline <- "eucast3.3" } if (guideline == "nl") { guideline <- "brmo" @@ -294,7 +294,7 @@ mdro <- function(x = NULL, if (guideline == "de") { guideline <- "mrgn" } - stop_ifnot(guideline %in% c("brmo", "mrgn", "eucast3.1", "eucast3.2", "tb", "cmi2012"), + stop_ifnot(guideline %in% c("brmo", "mrgn", "eucast3.1", "eucast3.2", "eucast3.3", "tb", "cmi2012"), "invalid guideline: ", guideline.bak) guideline <- list(code = guideline) diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index f889fe46..0deeacf5 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 85335aa3..283b1f57 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@
diff --git a/docs/news/index.html b/docs/news/index.html index 949b2327..e714e501 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ @@ -157,19 +157,19 @@AMR
1.7.1.9065AMR
1.7.1.9066p_symbol()
and all filter_*()
functions (except for filter_first_isolate()
), which were all deprecated in a previous package versionkey_antibiotics()
and key_antibiotics_equal()
functions, which were deprecated and superseded by key_antimicrobials()
and antimicrobials_equal()
ggplot2::ggplot()
generics for classes <mic>
, <disk>
, <rsi>
and <resistance_predict>
as they did not follow the ggplot2
logic. They were replaced with ggplot2::autoplot()
generics.Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for eucast_rules()
, mo_intrinsic_resistant()
and mdro()
. The intrinsic_resistant
data set was also updated accordingly.
Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
Function ab_ddd_units()
to get units of DDDs (daily defined doses), deprecating the use of ab_ddd(..., units = TRUE)
to be more consistent in data types of function output
antibiotics
data set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that:
get_episode()
and is_new_episode()
can now cope with NA
s