diff --git a/DESCRIPTION b/DESCRIPTION index 3b74194e..7165b521 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.4.0.9048 +Version: 1.4.0.9049 Date: 2020-12-27 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 3f264538..24bcf467 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.4.0.9048 +# AMR 1.4.0.9049 ## Last updated: 27 December 2020 ### New diff --git a/R/globals.R b/R/globals.R index 8bf6f55f..bc7fc2e0 100755 --- a/R/globals.R +++ b/R/globals.R @@ -60,6 +60,7 @@ globalVariables(c(".rowid", "old_name", "pattern", "R", + "reference.rule", "reference.rule_group", "reference.version", "rsi_translation", diff --git a/docs/404.html b/docs/404.html index 4463130d..2fcd8e66 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5062e46c..0ebd4ab2 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049 diff --git a/docs/articles/index.html b/docs/articles/index.html index 476f5aa0..eb22e187 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049 diff --git a/docs/authors.html b/docs/authors.html index b20f4ceb..691261d5 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049 diff --git a/docs/index.html b/docs/index.html index 8f53a05a..849cadac 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049 diff --git a/docs/news/index.html b/docs/news/index.html index 49165a29..35b24adf 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.4.0.9048 Unreleased +
+

+AMR 1.4.0.9049 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index dd910b3e..709059a9 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: 2020-12-27T13:22Z +last_built: 2020-12-27T14:06Z 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 d84f7781..a338ac6b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049

diff --git a/docs/survey.html b/docs/survey.html index 7c11af22..56eb7252 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9048 + 1.4.0.9049
diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R index 575ace55..55d74f98 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/tests/testthat/test-eucast_rules.R @@ -122,19 +122,19 @@ test_that("EUCAST rules work", { expect_identical( eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.rsi(c("S", "S"))), - ampc_derepressed_cephalosporins = "R", + ampc_cephalosporin_resistance = "R", info = FALSE)$cefotax, as.rsi(c("S", "R"))) expect_identical( eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.rsi(c("S", "S"))), - ampc_derepressed_cephalosporins = NA, + ampc_cephalosporin_resistance = NA, info = FALSE)$cefotax, as.rsi(c("S", NA))) expect_identical( eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.rsi(c("S", "S"))), - ampc_derepressed_cephalosporins = NULL, + ampc_cephalosporin_resistance = NULL, info = FALSE)$cefotax, as.rsi(c("S", "S")))