diff --git a/DESCRIPTION b/DESCRIPTION index 9f368b5f..6d1d13d9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9060 +Version: 1.7.1.9061 Date: 2021-12-05 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index d7758f4f..f8e2a2f8 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9060 +# `AMR` 1.7.1.9061 ## Last updated: 5 December 2021 ### Breaking changes diff --git a/R/ab_property.R b/R/ab_property.R index 5956a2e4..d104ed07 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -109,7 +109,7 @@ #' #' # set_ab_names() works with any AB property: #' example_isolates %>% -#' set_ab_names("atc") +#' set_ab_names(property = "atc") #' #' example_isolates %>% #' set_ab_names(where(is.rsi)) %>% diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index d49a30d2..4852569a 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 8713ed11..a3c48787 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9060 + 1.7.1.9061 diff --git a/docs/news/index.html b/docs/news/index.html index fb0cf8a1..8af5985a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.7.1.9060 + 1.7.1.9061 @@ -157,19 +157,19 @@
-

-AMR 1.7.1.9060

+

+AMR 1.7.1.9061

-

Last updated: 5 December 2021

+

Last updated: 5 December 2021

-

Breaking changes

+

Breaking changes

  • Removed p_symbol() and all filter_*() functions (except for filter_first_isolate()), which were all deprecated in a previous package version
  • Removed the key_antibiotics() and key_antibiotics_equal() functions, which were deprecated and superseded by key_antimicrobials() and antimicrobials_equal()
  • Removed all previously implemented 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.
-

New

+

New

  • Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021), effective in the eucast_rules() function. This is now the default guideline (all other guidelines are still available).

  • Function set_ab_names() to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:

    @@ -181,7 +181,7 @@

  • Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese

-

Changed

+

Changed

  • Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new staphylococcal species named since 1 January last year
  • The 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:
    • Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
      • @@ -247,7 +247,7 @@ get_episode() and is_new_episode() can now cope with NAs
-

Other

+

Other

  • This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index b2da4944..7f72a4f2 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -17,7 +17,7 @@ AMR (for R) - 1.7.1.9058 + 1.7.1.9061
@@ -322,7 +322,7 @@ The lifecycle of this function is stable# set_ab_names() works with any AB property: example_isolates %>% - set_ab_names("atc") + set_ab_names(property = "atc") example_isolates %>% set_ab_names(where(is.rsi)) %>% diff --git a/docs/reference/index.html b/docs/reference/index.html index 3489518b..ab168a89 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.7.1.9058 + 1.7.1.9061 diff --git a/inst/tinytest/test-ab_property.R b/inst/tinytest/test-ab_property.R index 68a6363e..bf7e5040 100644 --- a/inst/tinytest/test-ab_property.R +++ b/inst/tinytest/test-ab_property.R @@ -67,7 +67,7 @@ expect_identical(colnames(set_ab_names(example_isolates[, 20:25])), c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")) expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)), c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")) -expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")), +expect_identical(colnames(set_ab_names(example_isolates[, 20:25], property = "atc")), c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")) if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { expect_identical(example_isolates %>% set_ab_names(), diff --git a/man/ab_property.Rd b/man/ab_property.Rd index 08e358e1..4fba759b 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -176,7 +176,7 @@ if (require("dplyr")) { # set_ab_names() works with any AB property: example_isolates \%>\% - set_ab_names("atc") + set_ab_names(property = "atc") example_isolates \%>\% set_ab_names(where(is.rsi)) \%>\%