diff --git a/docs/authors.html b/docs/authors.html index fdf28b76..c26fc9cb 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ diff --git a/docs/index.html b/docs/index.html index 098cf2fb..c42af85e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ @@ -201,7 +201,7 @@
What is AMR (for R)?
AMR is a free, open-source and independent R package (see Copyright) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
The AMR package is available in 
Danish, 
Dutch, 
English, 
French, 
German, 
Italian, 
Portuguese, 
Russian, 
Spanish and 
Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package formed the basis of two PhD theses (DOI 10.33612/diss.177417131 and DOI 10.33612/diss.192486375) but is actively and durably maintained by two public healthcare organisations in the Netherlands.
-AMR 1.7.1.9070
+
+AMR 1.7.1.9071
Last updated: 13 December 2021
+Last updated: 13 December 2021
All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
Breaking changes
+Breaking changes
- Removed
p_symbol()and allfilter_*()functions (except forfilter_first_isolate()), which were all deprecated in a previous package version - Removed the
key_antibiotics()andkey_antibiotics_equal()functions, which were deprecated and superseded bykey_antimicrobials()andantimicrobials_equal()
@@ -171,8 +171,8 @@
- Renamed function
get_locale()toget_AMR_locale()to prevent conflicts with other packages
New
-Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the
rsi_translationdata set
+Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the
rsi_translationdata set. This data set now more strictly follows the WHONET software as well.Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for
eucast_rules(),mo_is_intrinsic_resistant()andmdro(). Theintrinsic_resistantdata set was also updated accordingly.Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish
- @@ -186,7 +186,7 @@
Function
ab_ddd_units()to get units of DDDs (daily defined doses), deprecating the use ofab_ddd(..., units = TRUE)to be more consistent in data types of function output
New
+Changed
+Changed
- Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new staphylococcal species named since 1 January last year
- The
antibioticsdata set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that:- Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5) @@ -256,7 +256,7 @@
get_episode()andis_new_episode()can now cope withNAs
Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
diff --git a/inst/tinytest/test-data.R b/inst/tinytest/test-data.R
index 2ee78e7c..e3cbcb22 100644
--- a/inst/tinytest/test-data.R
+++ b/inst/tinytest/test-data.R
@@ -44,6 +44,11 @@ expect_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
expect_true(all(dosage$ab %in% antibiotics$ab))
expect_true(all(dosage$name %in% antibiotics$name))
+# check valid disks/MICs
+expect_false(any(is.na(as.mic(rsi_translation[which(rsi_translation$method == "MIC"), "breakpoint_S"]))))
+expect_false(any(is.na(as.mic(rsi_translation[which(rsi_translation$method == "MIC"), "breakpoint_R"]))))
+expect_false(any(is.na(as.disk(rsi_translation[which(rsi_translation$method == "DISK"), "breakpoint_S"]))))
+expect_false(any(is.na(as.disk(rsi_translation[which(rsi_translation$method == "DISK"), "breakpoint_R"]))))
# antibiotic names must always be coercible to their original AB code
expect_identical(as.ab(antibiotics$name), antibiotics$ab)
diff --git a/inst/tinytest/test-mic.R b/inst/tinytest/test-mic.R
index 1d73a8b8..a52a15d7 100755
--- a/inst/tinytest/test-mic.R
+++ b/inst/tinytest/test-mic.R
@@ -27,6 +27,9 @@ expect_true(as.mic(8) == as.mic("8"))
expect_true(as.mic("1") > as.mic("<=0.0625"))
expect_true(as.mic("1") < as.mic(">=32"))
expect_true(is.mic(as.mic(8)))
+# expect_true(as.mic(1024) < as.mic(">1024"))
+# expect_true(as.mic("<1024") > as.mic("1024"))
+
expect_equal(as.double(as.mic(">=32")), 32)
expect_equal(as.numeric(as.mic(">=32")), 32)