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 @@
NEWS.md
-
Pattern Matching
Calculate the matching score for microorganisms