-
Used in 155 countries
Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.
+ Used in 162 countries
Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.
- Unreleased AMR 1.6.0.9015
+
+
+ Unreleased
Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see
-Plotting is now possible with base R using
+Plotting is now possible with base R using
Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index a321ac6da..0da9d4cc1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-03T08:19Z
+last_built: 2021-05-03T11:04Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a4800456b..b909715a2 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
@@ -592,6 +592,12 @@
+
+
+
+
+
diff --git a/docs/survey.html b/docs/survey.html
index e1493254f..bf346fa24 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
diff --git a/index.md b/index.md
index 0f85e3163..c16924691 100644
--- a/index.md
+++ b/index.md
@@ -15,8 +15,8 @@ This package is [fully independent of any other R package](https://en.wikipedia.
+ Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.
##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
diff --git a/pkgdown/logos/countries.png b/pkgdown/logos/countries.png
index ba6bf274d..37b140610 100644
Binary files a/pkgdown/logos/countries.png and b/pkgdown/logos/countries.png differ
diff --git a/pkgdown/logos/countries_large.png b/pkgdown/logos/countries_large.png
index aa1018665..5c81f9dc6 100644
Binary files a/pkgdown/logos/countries_large.png and b/pkgdown/logos/countries_large.png differ
diff --git a/tests/testthat/test-italicise_taxonomy.R b/tests/testthat/test-italicise_taxonomy.R
new file mode 100644
index 000000000..859e84faf
--- /dev/null
+++ b/tests/testthat/test-italicise_taxonomy.R
@@ -0,0 +1,39 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 Berends MS, Luz CF et al. #
+# Developed at the University of Groningen, the Netherlands, in #
+# collaboration with non-profit organisations Certe Medical #
+# Diagnostics & Advice, and University Medical Center Groningen. #
+# #
+# This R package is free software; you can freely use and distribute #
+# it for both personal and commercial purposes under the terms of the #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by #
+# the Free Software Foundation. #
+# We created this package for both routine data analysis and academic #
+# research and it was publicly released in the hope that it will be #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
+# #
+# Visit our website for the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+context("italicise_taxonomy.R")
+
+test_that("italic taxonomy works", {
+ skip_on_cran()
+
+ expect_identical(italicise_taxonomy("test for E. coli"),
+ "test for *E. coli*")
+ expect_identical(italicise_taxonomy("test for E. coli"),
+ italicize_taxonomy("test for E. coli"))
+ if (has_colour()) {
+ expect_identical(italicise_taxonomy("test for E. coli", type = "ansi"),
+ "test for \033[3mE. coli\033[23m")
+ }
+})
+ Unreleased AMR 1.6.0.9016
Last updated: 3 May 2021 @@ -340,7 +340,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"
Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info
ggplot() generics for classes <mic> and <disk>
ggplot() generics for classes <mic> and <disk>
Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
@@ -397,7 +397,7 @@
translate)plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion valuesplot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion valuesmicroorganisms data setPCA Biplot with ggplot2
Italicise Taxonomic Families, Genera, Species, Subspecies
inner_join_microorganisms() left_join_microorganisms() right_join_microorganisms() full_join_microorganisms() semi_join_microorganisms() anti_join_microorganisms()
- Used in 155 countries
- Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.
+ Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.