diff --git a/DESCRIPTION b/DESCRIPTION index e5921f77..6d0273a5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9002 +Version: 1.7.1.9003 Date: 2021-06-14 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index ae25ba85..dbf01028 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9002 +# `AMR` 1.7.1.9003 ## Last updated: 14 June 2021 ### Changed diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 2eaa3bdc..20929691 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -713,9 +713,9 @@ meet_criteria <- function(object, return(invisible()) } -get_current_data <- function(arg_name, call, reuse_equal_call = TRUE) { +get_current_data <- function(arg_name, call, reuse_from_1st_call = TRUE) { # check if retrieved before, then get it from package environment to improve speed - if (reuse_equal_call == TRUE && + if (reuse_from_1st_call == TRUE && identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) { return(pkg_env$get_current_data.out) } diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index d9586309..09022039 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index b7b9f89e..1c20f110 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 6bfda843..ee2efb42 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 62ef922e..766be8e5 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 diff --git a/docs/articles/index.html b/docs/articles/index.html index 076b7206..0cde0e7d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 diff --git a/docs/authors.html b/docs/authors.html index de4a968c..3046f59d 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 diff --git a/docs/index.html b/docs/index.html index cd303566..cd49a985 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 @@ -223,9 +223,9 @@ #> ℹ Using column 'mo' as input for `mo_is_gram_negative()` #> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()` #> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic -#> Resistance and Unusual Phenotypes' v3.2 (2020) +#> Resistance and Unusual Phenotypes' v3.2 (2020) #> ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN' -#> (kanamycin) and 'TOB' (tobramycin) +#> (kanamycin) and 'TOB' (tobramycin) #> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)

With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (mo_is_gram_negative() and mo_is_intrinsic_resistant()) and a column selection on two antibiotic groups (aminoglycosides() and carbapenems()), the reference data about all microorganisms and all antibiotics in the AMR package make sure you get what you meant:

diff --git a/docs/news/index.html b/docs/news/index.html index 794a5a4a..da14c8df 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9002

+
+

+ Unreleased AMR 1.7.1.9003

Last updated: 14 June 2021 @@ -307,7 +307,7 @@
  • Function betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
    • -
  • A ggplot() method for resistance_predict() +
  • A ggplot() method for resistance_predict()

    • @@ -408,7 +408,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info

    • -

  • ggplot() generics for classes <mic> and <disk>

    • +

  • ggplot() generics for classes <mic> and <disk>

  • Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:

    @@ -465,7 +465,7 @@
 
  • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
    • 
 
  • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
    • 
 
  • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
    • 
-
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    • 
+
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    •
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 18f2ebe2..c0dcb1fb 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-06-14T20:03Z +last_built: 2021-06-14T20:36Z 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 39309e8a..431c240c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003
    diff --git a/docs/survey.html b/docs/survey.html index a4b75df7..9616b05c 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9002 + 1.7.1.9003 diff --git a/index.md b/index.md index 3f4ee79a..5b39b463 100644 --- a/index.md +++ b/index.md @@ -31,9 +31,9 @@ example_isolates %>% #> ℹ Using column 'mo' as input for `mo_is_gram_negative()` #> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()` #> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic -#> Resistance and Unusual Phenotypes' v3.2 (2020) +#> Resistance and Unusual Phenotypes' v3.2 (2020) #> ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN' -#> (kanamycin) and 'TOB' (tobramycin) +#> (kanamycin) and 'TOB' (tobramycin) #> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem) ```