diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 5fdf647c..449fcdd9 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -127,6 +127,7 @@ jobs:
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION')"
+ Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[gsub(' +', '', readLines('AMR/DESCRIPTION')) != ''], 'AMR/DESCRIPTION')"
find AMR -name 'DESCRIPTION' -exec cat '{}' \; || true
shell: bash
diff --git a/DESCRIPTION b/DESCRIPTION
index fdb9ef3d..257c9916 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.6.0.9048
+Version: 1.6.0.9049
Date: 2021-05-19
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index 26b8fd5b..709c4861 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9048
+# `AMR` 1.6.0.9049
## Last updated: 19 May 2021
### Breaking change
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index d4728c45..a3543351 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -509,7 +509,7 @@ create_eucast_ab_documentation <- function() {
# separate drugs, such as `AMX`
val <- as.ab(val)
} else {
- stop_("antimicrobial agent (group) not found in EUCAST rules file: ", val.bak, call = FALSE)
+ val <- as.rsi(NA)
}
ab <- c(ab, val)
}
diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R
index 0381717b..d8414af3 100644
--- a/R/ab_class_selectors.R
+++ b/R/ab_class_selectors.R
@@ -299,6 +299,7 @@ all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
cols_ab <- c(...)
result <- cols_ab[toupper(cols_ab) %in% c("R", "S", "I")]
if (length(result) == 0) {
+ message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "R", "S" or "I"')
result <- c("R", "S", "I")
}
cols_ab <- cols_ab[!cols_ab %in% result]
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index 0a40c9e7..ae4a6546 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/docs/404.html b/docs/404.html
index 7cc6f01e..9d728adf 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
NEWS.md
-
AMR
1.6.0.9048AMR
1.6.0.9049Use these function for the analysis part. You can use susceptibility()
or resistance()
on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using first_isolate()
or is_new_episode()
. You can also filter your data on certain resistance in certain antibiotic classes (filter_ab_class()
), or determine multi-drug resistant microorganisms (MDRO, mdro()
).
Use these function for the analysis part. You can use susceptibility()
or resistance()
on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using first_isolate()
or is_new_episode()
. You can also filter your data on certain resistance in certain antibiotic classes (carbapenems()
, aminoglycosides()
), or determine multi-drug resistant microorganisms (MDRO, mdro()
).
Antibiotic Class Selectors
p_symbol()
filter_first_weighted_isolate()
key_antibiotics()
key_antibiotics_equal()
filter_ab_class()
filter_aminoglycosides()
filter_betalactams()
filter_carbapenems()
filter_cephalosporins()
filter_1st_cephalosporins()
filter_2nd_cephalosporins()
filter_3rd_cephalosporins()
filter_4th_cephalosporins()
filter_5th_cephalosporins()
filter_fluoroquinolones()
filter_glycopeptides()
filter_macrolides()
filter_oxazolidinones()
filter_penicillins()
filter_tetracyclines()
Deprecated Functions
resistance_predict()
rsi_predict()
plot(<resistance_predict>)
ggplot(<resistance_predict>)
ggplot_rsi_predict()