From c7a93af3d09cb5506c1ed167021b95991ea08f70 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 14 Feb 2020 20:03:43 +0100 Subject: [PATCH] (v0.9.0.9024) global vars fix --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/data.R | 2 +- R/globals.R | 3 +++ docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 4 ++-- docs/news/index.html | 8 ++++---- docs/reference/index.html | 2 +- docs/reference/rsi_translation.html | 6 +++--- index.md | 2 +- man/rsi_translation.Rd | 2 +- tests/testthat/test-ggplot_rsi.R | 2 ++ 15 files changed, 24 insertions(+), 19 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8ee636f4..86f86803 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.9.0.9023 +Version: 0.9.0.9024 Date: 2020-02-14 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 088feacd..3bb51ede 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.9.0.9023 +# AMR 0.9.0.9024 ## Last updated: 14-Feb-2020 ### New diff --git a/R/data.R b/R/data.R index 99b6b7d8..fae09317 100755 --- a/R/data.R +++ b/R/data.R @@ -196,7 +196,7 @@ catalogue_of_life <- list( #' Data set for R/SI interpretation #' -#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use [as.rsi()] to transform MICs or disks measurements to R/SI values. +#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use [as.rsi()] to transform MICs or disks measurements to R/SI values. #' @format A [`data.frame`] with 13,975 observations and 9 variables: #' - `guideline`\cr Name of the guideline #' - `method`\cr Either "MIC" or "DISK" diff --git a/R/globals.R b/R/globals.R index b5060c7a..3121afed 100755 --- a/R/globals.R +++ b/R/globals.R @@ -25,6 +25,7 @@ globalVariables(c(".", "ab_txt", "abbreviations", "antibiotic", + "antibiotics", "CNS_CPS", "col_id", "count", @@ -57,6 +58,7 @@ globalVariables(c(".", "median", "microorganisms", "microorganisms.codes", + "microorganisms.old", "missing_names", "mo", "mono_count", @@ -82,6 +84,7 @@ globalVariables(c(".", "R", "real_first_isolate", "ref", + "rsi_translation", "rule_group", "rule_name", "S", diff --git a/docs/404.html b/docs/404.html index 8ce2e1f8..9729dc6f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9023 + 0.9.0.9024 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 361ad66b..1b8f67ed 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9023 + 0.9.0.9024 diff --git a/docs/articles/index.html b/docs/articles/index.html index fb6845a4..6676e67c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9023 + 0.9.0.9024 diff --git a/docs/authors.html b/docs/authors.html index d84c2e98..ddc32b81 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9023 + 0.9.0.9024 diff --git a/docs/index.html b/docs/index.html index a5e387f9..e0d92dc3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.9.0.9023 + 0.9.0.9024 @@ -240,7 +240,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
  • Applying EUCAST expert rules (manual)
  • Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code (manual)
  • Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code (manual)
    • -
  • Machine reading the EUCAST and CLSI guidelines from 2011-2019 to translate MIC values and disk diffusion diameters to R/SI (link)
    • +
  • Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (link)

    • This package is ready-to-use for specialists in many fields: