diff --git a/DESCRIPTION b/DESCRIPTION index b8a09a25..b62ab3c7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9023 +Version: 1.3.0.9024 Date: 2020-09-19 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 3205a48c..601bdac2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.3.0.9023 +# AMR 1.3.0.9024 ## Last updated: 19 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! diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index c7297c21..60cd993b 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -68,5 +68,5 @@ mo_matching_score <- function(x, fullname, uncertainty = 1) { var_U <- uncertainty # matching score: - (var_F - 0.5 * L) / (var_F * var_P * var_K * var_U) + (var_F - 0.5 * var_L) / (var_F * var_P * var_K * var_U) } diff --git a/R/rsi_calc.R b/R/rsi_calc.R index 237f46a6..4f813c49 100755 --- a/R/rsi_calc.R +++ b/R/rsi_calc.R @@ -263,7 +263,6 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both" # based on pm_apply_grouped_function apply_group <- function(.data, fn, groups, drop = FALSE, ...) { - #groups <- get_groups(.data) grouped <- pm_split_into_groups(.data, groups, drop) res <- do.call(rbind, unname(lapply(grouped, fn, ...))) if (any(groups %in% colnames(res))) { diff --git a/R/sysdata.rda b/R/sysdata.rda index b1429c5c..f648c9f7 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/_pkgdown.yml b/_pkgdown.yml index 6f616594..a306d0d8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -172,7 +172,7 @@ reference: - "`ggplot_pca`" - "`join`" - "`like`" - - "`mo_matching_score" + - "`mo_matching_score`" - "`pca`" - title: "Other: statistical tests" diff --git a/data-raw/eucast_rules.tsv b/data-raw/eucast_rules.tsv index cada2dbe..4dfbad5f 100644 --- a/data-raw/eucast_rules.tsv +++ b/data-raw/eucast_rules.tsv @@ -1,5 +1,5 @@ # ------------------------------------------------------------------------------------------------------------------------------- -# For editing this EUCAST reference file, these values can all be used for target antibiotics: +# For editing this EUCAST reference file, these values can all be used for targeting antibiotics: # 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_except_CAZ', # 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins' # and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'. @@ -8,7 +8,7 @@ # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx). # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<< # ------------------------------------------------------------------------------------------------------------------------------- -if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group +if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints diff --git a/docs/404.html b/docs/404.html index 09119032..f4cc0b85 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index dc284ceb..b1314264 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024 diff --git a/docs/articles/index.html b/docs/articles/index.html index 0aaa5b9a..9b2bb8d3 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024 diff --git a/docs/authors.html b/docs/authors.html index bacef9da..5716e1ca 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024 diff --git a/docs/index.html b/docs/index.html index 070bf979..c79a7877 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024 diff --git a/docs/news/index.html b/docs/news/index.html index ba7f4760..f887c09e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.3.0.9023 Unreleased +
+

+AMR 1.3.0.9024 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 860aaa8a..c2bcfec3 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: 2020-09-19T09:53Z +last_built: 2020-09-19T10:17Z 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 79a1c00d..8f2273b6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024

@@ -586,6 +586,12 @@

Pattern Matching

+ +

mo_matching_score()

+ +

Calculate the matching score for microorganisms

+ +

pca()

diff --git a/docs/survey.html b/docs/survey.html index 49171f41..8b1de042 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9023 + 1.3.0.9024
diff --git a/tests/testthat/test-_all_examples.R b/tests/testthat/test-_all_examples.R index d0c3c0bd..4b7b04a0 100755 --- a/tests/testthat/test-_all_examples.R +++ b/tests/testthat/test-_all_examples.R @@ -18,4 +18,3 @@ # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # Visit our website for more info: https://msberends.github.io/AMR. # # ==================================================================== # -