From 3136bc54aa52ec3449e5838ebb554d93d97b638b Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 30 Sep 2020 10:54:23 +0200 Subject: [PATCH] (v1.3.0.9037) pre-release --- DESCRIPTION | 2 +- NEWS.md | 8 +++----- R/mdro.R | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 31 +++++++++++++------------------ docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- docs/survey.html | 2 +- 12 files changed, 26 insertions(+), 33 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 65c73de1..8d178f70 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9036 +Version: 1.3.0.9037 Date: 2020-09-30 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 39c83ff4..bb126962 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,7 @@ -# AMR 1.3.0.9036 +# AMR 1.3.0.9037 ## Last updated: 30 September 2020 -Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly! - -### Breaking -* Removed functions `portion_R()`, `portion_S()` and `portion_I()` that were deprecated since version 0.9.0 (November 2019) and were replaced with `proportion_R()`, `proportion_S()` and `proportion_I()`. +Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt about this package to. We are those reviewers very grateful for going through our code so thoroughly! ### New * Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the parameters `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`. @@ -70,6 +67,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th * Added support for using `unique()` on classes ``, ``, ``, `` and `` ### Other +* Removed functions `portion_R()`, `portion_S()` and `portion_I()` that were deprecated since version 0.9.0 (November 2019) and were replaced with `proportion_R()`, `proportion_S()` and `proportion_I()` * Removed unnecessary references to the `base` package * Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file diff --git a/R/mdro.R b/R/mdro.R index d342c2fe..a4e5d684 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -954,7 +954,7 @@ mdro <- function(x, "any") trans_tbl(3, which(x$mo %in% MO_CONS), # coagulase-negative Staphylococcus - c( VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC), + c(VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC), "any") trans_tbl(3, which(x$genus == "Corynebacterium"), diff --git a/docs/404.html b/docs/404.html index 3dae917e..b78b3d38 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 8e2935e8..0b98d63f 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037 diff --git a/docs/articles/index.html b/docs/articles/index.html index d86f8b20..a14ad9c7 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037 diff --git a/docs/authors.html b/docs/authors.html index 885b7c06..716cea40 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037 diff --git a/docs/index.html b/docs/index.html index 3b6a5e94..430fc0ec 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037 diff --git a/docs/news/index.html b/docs/news/index.html index 68c6ced5..998a32df 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037 @@ -236,22 +236,15 @@ Source: NEWS.md -
-

-AMR 1.3.0.9036 Unreleased +
+

+AMR 1.3.0.9037 Unreleased

Last updated: 30 September 2020

-

Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!

-
-

-Breaking

- -
+

Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt about this package to. We are those reviewers very grateful for going through our code so thoroughly!

New

@@ -344,6 +337,8 @@

Other

    +
  • Removed functions portion_R(), portion_S() and portion_I() that were deprecated since version 0.9.0 (November 2019) and were replaced with proportion_R(), proportion_S() and proportion_I() +
  • Removed unnecessary references to the base package
  • Added packages that could be useful for some functions to the Suggests field of the DESCRIPTION file
@@ -437,9 +432,9 @@

AMR 1.2.0 2020-05-28

-
+

-Breaking

+Breaking

  • Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.

    @@ -647,9 +642,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    AMR 0.9.0 2019-11-29

    -
    +

    -Breaking

    +Breaking
    • Adopted Adeolu et al. (2016), PMID 27620848 for the microorganisms data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like Morganellaceae and Yersiniaceae). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with mdro() will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
        @@ -755,9 +750,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

        AMR 0.8.0 2019-10-15

        -
        +

        -Breaking

        +Breaking

        • Determination of first isolates now excludes all ‘unknown’ microorganisms at default, i.e. microbial code "UNKNOWN". They can be included with the new parameter include_unknown:

          diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b55cbd43..2a3d850f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.7.3 pkgdown: 1.5.1.9000 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f articles: [] -last_built: 2020-09-30T08:23Z +last_built: 2020-09-30T08:54Z 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 9f8038dd..88e1b7ff 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037
        diff --git a/docs/survey.html b/docs/survey.html index 57d00987..15797756 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9036 + 1.3.0.9037