diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6a9f0c00..b7127048 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -62,6 +62,7 @@ R-release:
allow_failure: false
script:
- Rscript -e 'sessionInfo()'
+ - Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
@@ -77,6 +78,7 @@ R-devel:
allow_failure: false
script:
- Rscriptdevel -e 'sessionInfo()'
+ - Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
# install missing and outdated packages
- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
- Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
diff --git a/DESCRIPTION b/DESCRIPTION
index 8416b237..c41350f4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.1.0.9005
+Version: 1.1.0.9006
Date: 2020-05-16
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index fce08c36..ee4e81ae 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.1.0.9005
+# AMR 1.1.0.9006
## Last updated: 16-May-2020
### Breaking
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 1bff1aca..a0232f69 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -63,16 +63,14 @@ filter_join_worker <- function(x, y, by = NULL, type = c("anti", "semi")) {
# No export, no Rd
addin_insert_in <- function() {
- if (!require("rstudioapi")) {
- insertText(" %in% ")
- }
+ stopifnot_installed_package("rstudioapi")
+ get("insertText", envir = asNamespace("rstudioapi"))(" %in% ")
}
# No export, no Rd
addin_insert_like <- function() {
- if (!require("rstudioapi")) {
- insertText(" %like% ")
- }
+ stopifnot_installed_package("rstudioapi")
+ get("insertText", envir = asNamespace("rstudioapi"))(" %like% ")
}
check_dataset_integrity <- function() {
diff --git a/R/atc_online.R b/R/atc_online.R
index 9ef534c7..0b056755 100644
--- a/R/atc_online.R
+++ b/R/atc_online.R
@@ -59,7 +59,7 @@
#' @inheritSection AMR Read more on our website!
#' @source NEWS.md
-
p.symbol()
- it was replaced with p_symbol()
+vctrs
package for data transformation and data joining. In newer versions of e.g. the dplyr
package, a function like bind_rows()
would not preserve the right class for microorganisms (class mo
) and antibiotics (class ab
). This is fixed in this version.dplyr
package (such as bind_rows()
) would not preserve the right class for microorganisms (class mo
) and antibiotics (class ab
)eucast_rules()
+AMR
package to work properly: crayon
, data.table
, dplyr
, ggplot2
, R6
, rlang
and tidyr
. This is a major code change, but will probably not be noticeable by users. Making this package independent on especially the tidyverse (packages dplyr
, ggplot2
and tidyr
) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. The only dependencies that remained are for extending methods of other packages, like pillar
and vctrs
for printing and working with tibbles using our classes mo
and ab
.read.4d()
, that was only useful for reading from an old test database.as.rsi()
for years 2010-2019 (thanks to Anthony Underwood)dplyr
version 1.0.0rsi
and mic
@@ -378,9 +396,9 @@
CITATION
filemicroorganisms
data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like Morganellaceae and Yersiniaceae). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with mdro()
will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
clean
to cleaner
, as this package was renamed accordingly upon CRAN requestDetermination of first isolates now excludes all ‘unknown’ microorganisms at default, i.e. microbial code "UNKNOWN"
. They can be included with the new parameter include_unknown
:
also_single_tested
w
filter_ab_class()
to be more reliable and to support 5th generation cephalosporinsavailability()
now uses portion_R()
instead of portion_IR()
, to comply with EUCAST insightsage()
and age_groups()
now have a na.rm
parameter to remove empty valuesp.symbol()
to p_symbol()
(the former is now deprecated and will be removed in a future version)p.symbol()
to p_symbol()
(the former is now deprecated and will be removed in a future version)x
in age_groups()
will now introduce NA
s and not return an error anymorekey_antibiotics()
on foreign systemsalso_single_tested
w
as.mic()
)lintr
packagealso_single_tested
w
as.mo(..., allow_uncertain = 3)if using different lengths of pattern and x in %like%
, it will now return the call
as.mo(..., allow_uncertain = 3)Percentages will now will rounded more logically (e.g. in freq
function)
crayon
, to support formatted text in the consoletidyr
is now mandatory (went to Import
field) since portion_df
and count_df
rely on itas.mo(..., allow_uncertain = 3)
as.mo(..., allow_uncertain = 3)Other small fixes
as.mo(..., allow_uncertain = 3)Functions as.rsi
and as.mic
now add the package name and version as attributes
README.md
with more examples