diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 7e6b468b..d46756d5 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -64,8 +64,8 @@ jobs:
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ # - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ # - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@@ -75,8 +75,8 @@ jobs:
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+ # - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+ # - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env:
diff --git a/DESCRIPTION b/DESCRIPTION
index 56a98629..140c7b25 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.5.0.9006
+Version: 1.5.0.9007
Date: 2021-01-18
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index fc73dceb..73246277 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.5.0.9006
+# AMR 1.5.0.9007
## Last updated: 18 January 2021
### New
diff --git a/R/mdro.R b/R/mdro.R
index 8959fcca..28770e7e 100755
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -805,6 +805,7 @@ mdro <- function(x,
x[which(x$genus == "Escherichia" & x$species == "hermannii"), ab_NA(c(TCC, TZP))] <- NA
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
+ | (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Morganella" & x$species == "morganii")
@@ -824,6 +825,7 @@ mdro <- function(x,
x[which((x$genus == "Citrobacter" & x$species == "koseri")
| (x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
+ | (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Escherichia" & x$species == "hermannii")
| (x$genus == "Hafnia" & x$species == "alvei")
@@ -836,6 +838,7 @@ mdro <- function(x,
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMP)] <- NA
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
+ | (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Morganella" & x$species == "morganii")
@@ -845,6 +848,7 @@ mdro <- function(x,
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Citrobacter" & x$species == "koseri")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
+ | (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Providencia" & x$species == "rettgeri")
diff --git a/data-raw/AMR_1.5.0.9006.tar.gz b/data-raw/AMR_1.5.0.9007.tar.gz
similarity index 79%
rename from data-raw/AMR_1.5.0.9006.tar.gz
rename to data-raw/AMR_1.5.0.9007.tar.gz
index 071885c9..af5e782e 100644
Binary files a/data-raw/AMR_1.5.0.9006.tar.gz and b/data-raw/AMR_1.5.0.9007.tar.gz differ
diff --git a/docs/404.html b/docs/404.html
index 2c54c76f..e4192c1a 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
NEWS.md
-