diff --git a/DESCRIPTION b/DESCRIPTION index 1095c44e..618e56c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.0.0.9001 +Version: 1.0.0.9002 Date: 2020-02-20 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index f6e4f198..45e97681 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.0.0.9001 - +# AMR 1.0.0.9002 +## Last updated: 20-Feb-2020 ### Changed * Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole diff --git a/R/rsi.R b/R/rsi.R index e875069a..33d0aa4f 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -338,7 +338,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL } i <- 0 - ab_cols <- colnames(x)[sapply(x, function(y) { + ab_cols <- colnames(x)[sapply(x, function(y) { i <<- i + 1 check <- is.mic(y) | is.disk(y) ab <- colnames(x)[i] diff --git a/codecov.yml b/codecov.yml index 258110cd..765dd5a9 100644 --- a/codecov.yml +++ b/codecov.yml @@ -20,8 +20,7 @@ # ==================================================================== # codecov: - notify: - require_ci_to_pass: no # allow fail + require_ci_to_pass: no # allow fail ci: - !appveyor # ignore CI builds by AppVeyor diff --git a/docs/404.html b/docs/404.html index 34c00121..87b19b90 100644 --- a/docs/404.html +++ b/docs/404.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index be4400d5..5e578863 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002 diff --git a/docs/articles/index.html b/docs/articles/index.html index 33d525f9..6cbfb963 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002 diff --git a/docs/authors.html b/docs/authors.html index 65c54bec..45518727 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002 diff --git a/docs/extra.css b/docs/extra.css index 8e7e6302..2a84d142 100644 --- a/docs/extra.css +++ b/docs/extra.css @@ -191,7 +191,7 @@ thead ~ tbody { /* only when it has a header */ border-bottom: 2px solid black; } -th { +thead th { text-align: inherit; } table a:not(.btn), .table a:not(.btn) { diff --git a/docs/index.html b/docs/index.html index 6f437a44..54443350 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002 diff --git a/docs/news/index.html b/docs/news/index.html index 9680a3be..e0ac389c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002 @@ -219,10 +219,14 @@ -
+

-AMR 1.0.0.9001 Unreleased +AMR 1.0.0.9002 Unreleased

+
+

+Last updated: 20-Feb-2020 +

Changed

@@ -240,6 +244,7 @@

  • Added uti (as abbreviation of urinary tract infections) as parameter to as.rsi(), so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs

    • +

    @@ -1468,7 +1473,7 @@

    Contents

      -
    • 1.0.0.9001
      • +
    • 1.0.0.9002
    • 1.0.0
    • 0.9.0
    • 0.8.0
      • diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index e724b727..42774997 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -79,7 +79,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002
    diff --git a/docs/reference/index.html b/docs/reference/index.html index c1c71427..19e10a72 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 1.0.0.9001 + 1.0.0.9002

    diff --git a/pkgdown/extra.css b/pkgdown/extra.css index 8e7e6302..2a84d142 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -191,7 +191,7 @@ thead ~ tbody { /* only when it has a header */ border-bottom: 2px solid black; } -th { +thead th { text-align: inherit; } table a:not(.btn), .table a:not(.btn) {