diff --git a/DESCRIPTION b/DESCRIPTION
index 02a971ed..c0295067 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 1.1.0.9015
-Date: 2020-05-20
+Version: 1.1.0.9016
+Date: 2020-05-21
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index ef77ddd9..c86846d4 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# AMR 1.1.0.9015
-## Last updated: 20-May-2020
+# AMR 1.1.0.9016
+## Last updated: 21-May-2020
### Breaking
* Removed code dependency on all other R packages, making this package fully independent on the development process of others. This is a major code change, but will probably not be noticeable by most users.
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 70837e7f..2d976865 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -252,9 +252,9 @@ dataset_UTF8_to_ASCII <- function(df) {
}
-# replace crayon::has_color
+# replace crayon::has_color, but now also FALSE on non-interactive mode
has_colour <- function() {
- if (Sys.getenv("TERM") == "dumb") {
+ if (Sys.getenv("TERM") == "dumb" | !interactive()) {
return(FALSE)
}
if (tolower(Sys.info()["sysname"]) == "windows") {
diff --git a/R/ab.R b/R/ab.R
index adf56f69..cac11131 100755
--- a/R/ab.R
+++ b/R/ab.R
@@ -215,6 +215,8 @@ as.ab <- function(x, ...) {
x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
# replace multiple same characters to single one with '+', like "ll" -> "l+"
x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
+ # replace spaces and slashes with a possibility on both
+ x_spelling <- gsub("[ /]", "( |/)", x_spelling)
# try if name starts with it
found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab
diff --git a/R/atc_online.R b/R/atc_online.R
index 2ddbc599..dac70119 100644
--- a/R/atc_online.R
+++ b/R/atc_online.R
@@ -128,7 +128,7 @@ atc_online_property <- function(atc_code,
returnvalue <- rep(NA_character_, length(atc_code))
}
- progress <- progress_estimated(n = length(atc_code))
+ progress <- progress_estimated(n = length(atc_code), 3)
on.exit(close(progress))
for (i in seq_len(length(atc_code))) {
@@ -160,7 +160,7 @@ atc_online_property <- function(atc_code,
as.data.frame(stringsAsFactors = FALSE)
# case insensitive column names
- colnames(tbl) <- tolower(colnames(tbl)) %>% gsub("^atc.*", "atc", .)
+ colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
if (length(tbl) == 0) {
warning("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call. = FALSE)
diff --git a/R/eucast_rules.R b/R/eucast_rules.R
index cc5f68e5..d261f837 100755
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@@ -599,7 +599,7 @@ eucast_rules <- function(x,
}
}
- if (!any(c("other", "all") %in% rules, na.rm = TRUE)) {
+ if (info == TRUE & !any(c("other", "all") %in% rules, na.rm = TRUE)) {
cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n"))
}
diff --git a/R/sysdata.rda b/R/sysdata.rda
index be08c5f4..6fc9133a 100644
Binary files a/R/sysdata.rda and b/R/sysdata.rda differ
diff --git a/data-raw/eucast_rules.tsv b/data-raw/eucast_rules.tsv
index 21ed2e1a..9518c084 100644
--- a/data-raw/eucast_rules.tsv
+++ b/data-raw/eucast_rules.tsv
@@ -16,10 +16,13 @@ genus like .* AMX S AMP S Non-EUCAST: inherit amoxicillin results for unavailabl
genus like .* AMX I AMP I Non-EUCAST: inherit amoxicillin results for unavailable ampicillin Other rules
genus like .* AMX R AMP R Non-EUCAST: inherit amoxicillin results for unavailable ampicillin Other rules
genus like .* AMC R AMP, AMX R Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R Other rules
+genus like .* SAM R AMP, AMX R Non-EUCAST: set ampicillin = R where ampicillin/sulbactam = R Other rules
genus like .* TZP R PIP R Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R Other rules
genus like .* SXT R TMP R Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R Other rules
genus like .* AMP S AMC S Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S Other rules
genus like .* AMX S AMC S Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S Other rules
+genus like .* AMP S SAM S Non-EUCAST: set ampicillin/sulbactam = S where ampicillin = S Other rules
+genus like .* AMX S SAM S Non-EUCAST: set ampicillin/sulbactam = S where ampicillin = S Other rules
genus like .* PIP S TZP S Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S Other rules
genus like .* TMP S SXT S Non-EUCAST: set trimethoprim/sulfa = S where trimethoprim = S Other rules
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints
diff --git a/docs/404.html b/docs/404.html
index d911055f..c11fc012 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.1.0.9015
+ 1.1.0.9016
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index affda865..e29fb5b0 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.1.0.9015
+ 1.1.0.9016
diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html
index 9144cfc4..4f787ab1 100644
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@@ -39,7 +39,7 @@
AMR (for R)
- 1.1.0.9015
+ 1.1.0.9016
@@ -186,7 +186,7 @@
How to apply EUCAST rules
Matthijs S. Berends
- 20 May 2020
+ 21 May 2020
Source: vignettes/EUCAST.Rmd
EUCAST.Rmd
@@ -218,10 +218,6 @@
# 2 Escherichia S
eucast_rules(oops, info = FALSE)
-# [31m
-# Skipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.
-# Use eucast_rules(..., rules = "all") to also apply those rules.
-# [39m
# mo ampicillin
# 1 Klebsiella R
# 2 Escherichia S