as.rsi() on an MIC value (created with as.mic()), a disk diffusion value (created with the new as.disk()) or on a complete date set containing columns with MIC or disk diffusion values.mo_name() as alias of mo_fullname()
@@ -253,9 +270,9 @@
mdr_tb()) and added a new vignette about MDR. Read this tutorial here on our website.first_isolate() where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.eucast_rules() where antibiotics from WHONET software would not be recognisedeucast_rules() with verbose = TRUE
as.mo() to identify an MO code.as.atc()
New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the G-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR.
eucast_rules():
as.mo(..., allow_uncertain = 3)if using different lengths of pattern and x in %like%, it will now return the callas.mo(..., allow_uncertain = 3)
AMR 0.5.0 2018-11-30
-
+
-New
+New
- Repository moved to GitLab: https://gitlab.com/msberends/AMR
@@ -601,9 +618,9 @@ Using as.mo(..., allow_uncertain = 3)Functions mo_authors and mo_year to get specific values about the scientific reference of a taxonomic entry
-
+
-Changed
+Changed
- Functions
MDRO, BRMO, MRGN and EUCAST_exceptional_phenotypes were renamed to mdro, brmo, mrgn and eucast_exceptional_phenotypes
@@ -700,9 +717,9 @@ Using as.mo(..., allow_uncertain = 3)Percentages will now will rounded more logically (e.g. in freq function)
-
+
-Other
+Other
- New dependency on package
crayon, to support formatted text in the console
- Dependency
tidyr is now mandatory (went to Import field) since portion_df and count_df rely on it
@@ -714,9 +731,9 @@ Using as.mo(..., allow_uncertain = 3)
AMR 0.4.0 2018-10-01
-
+
-New
+New
- The data set
microorganisms now contains all microbial taxonomic data from ITIS (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set microorganisms.old contains all previously known taxonomic names from those kingdoms.
- New functions based on the existing function
mo_property:
@@ -785,9 +802,9 @@ Using as.mo(..., allow_uncertain = 3)Renamed septic_patients$sex to septic_patients$gender
-
+
-Changed
+Changed
- Added three antimicrobial agents to the
antibiotics data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
-
@@ -837,9 +854,9 @@ Using
as.mo(..., allow_uncertain = 3)
-
+
-Other
+Other
- More unit tests to ensure better integrity of functions
@@ -849,9 +866,9 @@ Using as.mo(..., allow_uncertain = 3)
AMR 0.3.0 2018-08-14
-
+
-New
+New
-
BREAKING:
rsi_df was removed in favour of new functions portion_R, portion_IR, portion_I, portion_SI and portion_S to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old rsi function. The old function still works, but is deprecated.
@@ -922,9 +939,9 @@ Using as.mo(..., allow_uncertain = 3)
-
+
-Changed
+Changed
- Improvements for forecasting with
resistance_predict and added more examples
- More antibiotics added as parameters for EUCAST rules
@@ -966,9 +983,9 @@ Using as.mo(..., allow_uncertain = 3)Other small fixes
-
+
-Other
+Other
- Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
@@ -986,9 +1003,9 @@ Using as.mo(..., allow_uncertain = 3)
AMR 0.2.0 2018-05-03
-
+
-New
+New
- Full support for Windows, Linux and macOS
- Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
@@ -1008,9 +1025,9 @@ Using as.mo(..., allow_uncertain = 3)New print format for tibbles and data.tables
-
+
-Changed
+Changed
- Fixed
rsi class for vectors that contain only invalid antimicrobial interpretations
- Renamed dataset
ablist to antibiotics
@@ -1028,9 +1045,9 @@ Using as.mo(..., allow_uncertain = 3)Functions as.rsi and as.mic now add the package name and version as attributes
-
+
-Other
+Other
- Expanded
README.md with more examples
- Added ORCID of authors to DESCRIPTION file
@@ -1067,6 +1084,7 @@ Using as.mo(..., allow_uncertain = 3)
Contents
diff --git a/docs/reference/age.html b/docs/reference/age.html
index 8201d5c7..d54be194 100644
--- a/docs/reference/age.html
+++ b/docs/reference/age.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index ef4208e7..7b6c4c50 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -80,7 +80,7 @@
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 061bfe15..7de4f598 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -78,7 +78,7 @@
diff --git a/git_premaster.sh b/git_premaster.sh
index ac9dd5d4..f763cb6b 100755
--- a/git_premaster.sh
+++ b/git_premaster.sh
@@ -26,6 +26,13 @@ current_tag=`git describe --tags --abbrev=0 | sed 's/v//'`
current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
# combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
+if [ -z "$new_version" ]; then
+ new_version="$current_tag.9000"
+ echo
+ echo "** COULD NOT CREATE NEW VERSION NUMBER! **"
+ echo "Are there some unpushed changes in a new tag?? Then mind NEWS.md. Assuming sequence number 9000."
+ echo
+fi
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
# update 1st line of NEWS.md
sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
@@ -35,6 +42,12 @@ echo
echo "First line of NEWS.md:"
head -1 NEWS.md
echo
+read -p "Continue (Y/n)? " choice
+case "$choice" in
+ n|N ) exit 1;;
+ * ) ;;
+esac
+echo
echo "•••••••••••••••••••••••••••••••••"
echo "• Reloading/documenting package •"
echo "•••••••••••••••••••••••••••••••••"