diff --git a/404.html b/404.html index af8d75dc9..70b74424c 100644 --- a/404.html +++ b/404.html @@ -6,33 +6,33 @@ Page not found (404) • AMR (for R) - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - Skip to contents + Skip to contents
-

Page not found (404)

+

Page not found (404)

diff --git a/AMRforRGPT.svg b/AMRforRGPT.svg index 7202662aa..df6df486d 100644 --- a/AMRforRGPT.svg +++ b/AMRforRGPT.svg @@ -1,2307 +1,443 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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2.1.1.9234 + 2.1.1.9235

Preparation @@ -113,14 +113,14 @@ yet, I suggest you read about it on their website: 
 library(dplyr) # part of tidyverse
 library(ggplot2) # part of tidyverse
-library(AMR) # this package
+library(AMR) # this package
 library(cleaner) # to create frequency tables

We will have to transform some variables to simplify and automate the analysis:

Get started

-

To find out how to conduct AMR data analysis, please continue reading here to get started or click a link in the ‘How to’ menu.

+

To find out how to conduct AMR data analysis, please continue reading here to get started or click a link in the ‘How to’ menu.

Partners diff --git a/news/index.html b/news/index.html index f7534b39d..65537e799 100644 --- a/news/index.html +++ b/news/index.html @@ -1,5 +1,5 @@ -Changelog • AMR (for R) +Changelog • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

-

AMR 2.1.1.9234

-

(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using the instructions here.)

+

AMR 2.1.1.9235

+

(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using the instructions here.)

-
A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
+
A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)

This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island’s Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.

-

Breaking

+

Breaking

  • Dataset antibiotics has been renamed to antimicrobials as the data set contains more than just antibiotics. Using antibiotics will still work, but now returns a warning.
  • Removed all functions and references that used the deprecated rsi class, which were all replaced with their sir equivalents over two years ago.
    • -
  • Function resistance_predict() is now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.
    • +
  • Function resistance_predict() is now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.
-

New

+

New

  • One Health implementation
    • Function as.sir() now has extensive support for veterinary breakpoints from CLSI. Use breakpoint_type = "animal" and set the host argument to a variable that contains animal species names.
      • -
    • The clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page.
      • +
    • The clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page.
    • The (new) antimicrobials data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
    • ab_atc() now supports ATC codes of veterinary antibiotics (that all start with “Q”)
      • @@ -106,7 +106,7 @@
  • Support for tidymodels -
    • All antimicrobial selectors (such as aminoglycosides() and betalactams()) are now supported in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using these AMR functions for predictive modelling.
      • +
      • All antimicrobial selectors (such as aminoglycosides() and betalactams()) are now supported in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using these AMR functions for predictive modelling.
    • Other @@ -116,7 +116,7 @@
-

Changed

+

Changed

  • SIR interpretation
    • It is now possible to use column names for argument ab, mo, and uti: as.sir(..., ab = "column1", mo = "column2", uti = "column3"). This greatly improves the flexibility for users.
    • Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
      • @@ -195,7 +195,7 @@
    • Added console colours support of sir class for Positron
-

Other

+

Other

  • Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
  • Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
  • Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes
    • @@ -204,7 +204,7 @@
  • Stopped support for SAS (.xpt) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
-

Older Versions

+

Older Versions

This changelog only contains changes from AMR v3.0 (March 2025) and later.

  • For prior v2 versions, please see our v2 archive.
  • For prior v1 versions, please see our v1 archive.
    • diff --git a/pkgdown.yml b/pkgdown.yml index d9c3772db..4319e5fb3 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: PCA: PCA.html welcome_to_AMR: welcome_to_AMR.html WHONET: WHONET.html -last_built: 2025-04-07T16:45Z +last_built: 2025-04-08T15:07Z urls: - reference: https://msberends.github.io/AMR/reference - article: https://msberends.github.io/AMR/articles + reference: https://amr-for-r.org/reference + article: https://amr-for-r.org/articles diff --git a/reference/%like%.html b/reference/%like%.html index e456eb274..9b9358e21 100644 --- a/reference/%like%.html +++ b/reference/%like%.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/%like_case%.html b/reference/%like_case%.html index e456eb274..9b9358e21 100644 --- a/reference/%like_case%.html +++ b/reference/%like_case%.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/%unlike%.html b/reference/%unlike%.html index e456eb274..9b9358e21 100644 --- a/reference/%unlike%.html +++ b/reference/%unlike%.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/%unlike_case%.html b/reference/%unlike_case%.html index e456eb274..9b9358e21 100644 --- a/reference/%unlike_case%.html +++ b/reference/%unlike_case%.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/3MRGN.html b/reference/3MRGN.html index 9ccef1b51..99f17baa0 100644 --- a/reference/3MRGN.html +++ b/reference/3MRGN.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/4MRGN.html b/reference/4MRGN.html index 9ccef1b51..99f17baa0 100644 --- a/reference/4MRGN.html +++ b/reference/4MRGN.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index efee52d72..9eb9f8ffe 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -1,5 +1,5 @@ -Deprecated Functions — AMR-deprecated • AMR (for R) +Deprecated Functions — AMR-deprecated • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

-

Useful links:

  • https://msberends.github.io/AMR/

    • +

    Useful links:

    diff --git a/reference/ATC.html b/reference/ATC.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ATC.html +++ b/reference/ATC.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/BRMO.html b/reference/BRMO.html index 9ccef1b51..99f17baa0 100644 --- a/reference/BRMO.html +++ b/reference/BRMO.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/EUCAST.html b/reference/EUCAST.html index 211fd0c07..15cfe037f 100644 --- a/reference/EUCAST.html +++ b/reference/EUCAST.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/MDR.html b/reference/MDR.html index 9ccef1b51..99f17baa0 100644 --- a/reference/MDR.html +++ b/reference/MDR.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/NA_disk_.html b/reference/NA_disk_.html index ed1f99ab0..dd209fb91 100644 --- a/reference/NA_disk_.html +++ b/reference/NA_disk_.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/NA_mic_.html b/reference/NA_mic_.html index 977eb978a..54ba17d92 100644 --- a/reference/NA_mic_.html +++ b/reference/NA_mic_.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/NA_sir_.html b/reference/NA_sir_.html index c99d19d99..622a624a5 100644 --- a/reference/NA_sir_.html +++ b/reference/NA_sir_.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/PDR.html b/reference/PDR.html index 9ccef1b51..99f17baa0 100644 --- a/reference/PDR.html +++ b/reference/PDR.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 47053d77d..b17c98851 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -1,5 +1,5 @@ -WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R) +WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235
diff --git a/reference/XDR.html b/reference/XDR.html index 9ccef1b51..99f17baa0 100644 --- a/reference/XDR.html +++ b/reference/XDR.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab.html b/reference/ab.html index 3d47cb198..cef95015e 100644 --- a/reference/ab.html +++ b/reference/ab.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_atc.html b/reference/ab_atc.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_atc.html +++ b/reference/ab_atc.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_atc_group1.html b/reference/ab_atc_group1.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_atc_group1.html +++ b/reference/ab_atc_group1.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_atc_group2.html b/reference/ab_atc_group2.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_atc_group2.html +++ b/reference/ab_atc_group2.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_cid.html b/reference/ab_cid.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_cid.html +++ b/reference/ab_cid.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_class.html b/reference/ab_class.html index 82c1a131d..20234010d 100644 --- a/reference/ab_class.html +++ b/reference/ab_class.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_ddd.html b/reference/ab_ddd.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_ddd.html +++ b/reference/ab_ddd.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_ddd_units.html b/reference/ab_ddd_units.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_ddd_units.html +++ b/reference/ab_ddd_units.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 1200f52ed..ea9eaab15 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -1,5 +1,5 @@ -Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R) +Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/ab_reset_session.html b/reference/ab_reset_session.html index 3d47cb198..cef95015e 100644 --- a/reference/ab_reset_session.html +++ b/reference/ab_reset_session.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_selector.html b/reference/ab_selector.html index 82c1a131d..20234010d 100644 --- a/reference/ab_selector.html +++ b/reference/ab_selector.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_synonyms.html b/reference/ab_synonyms.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_synonyms.html +++ b/reference/ab_synonyms.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_tradenames.html b/reference/ab_tradenames.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_tradenames.html +++ b/reference/ab_tradenames.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/ab_url.html b/reference/ab_url.html index 07fd0ee02..0fcf022fb 100644 --- a/reference/ab_url.html +++ b/reference/ab_url.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 48b905816..01c5c89e9 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -1,5 +1,5 @@ -Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R) +Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

WHOCC

diff --git a/reference/antimicrobials_equal.html b/reference/antimicrobials_equal.html index f43b48c00..a573e4da3 100644 --- a/reference/antimicrobials_equal.html +++ b/reference/antimicrobials_equal.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/antimycobacterials.html b/reference/antimycobacterials.html index 8bd8e9fd0..168688bb7 100644 --- a/reference/antimycobacterials.html +++ b/reference/antimycobacterials.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/antivirals.html b/reference/antivirals.html index c2d604900..02bc621f5 100644 --- a/reference/antivirals.html +++ b/reference/antivirals.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/as.ab.html b/reference/as.ab.html index c0730e5f0..39b678ebc 100644 --- a/reference/as.ab.html +++ b/reference/as.ab.html @@ -1,5 +1,5 @@ -Transform Input to an Antibiotic ID — as.ab • AMR (for R) +Transform Input to an Antibiotic ID — as.ab • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/as.av.html b/reference/as.av.html index 3a5aa70c3..91a515cb4 100644 --- a/reference/as.av.html +++ b/reference/as.av.html @@ -1,5 +1,5 @@ -Transform Input to an Antiviral Drug ID — as.av • AMR (for R) +Transform Input to an Antiviral Drug ID — as.av • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/as.disk.html b/reference/as.disk.html index fb441ea57..895d91cf6 100644 --- a/reference/as.disk.html +++ b/reference/as.disk.html @@ -1,5 +1,5 @@ -Transform Input to Disk Diffusion Diameters — as.disk • AMR (for R) +Transform Input to Disk Diffusion Diameters — as.disk • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/as.sir.data.frame.html b/reference/as.sir.data.frame.html index c99d19d99..622a624a5 100644 --- a/reference/as.sir.data.frame.html +++ b/reference/as.sir.data.frame.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/as.sir.default.html b/reference/as.sir.default.html index c99d19d99..622a624a5 100644 --- a/reference/as.sir.default.html +++ b/reference/as.sir.default.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/as.sir.disk.html b/reference/as.sir.disk.html index c99d19d99..622a624a5 100644 --- a/reference/as.sir.disk.html +++ b/reference/as.sir.disk.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/as.sir.html b/reference/as.sir.html index 24e9f81e3..99cad33d3 100644 --- a/reference/as.sir.html +++ b/reference/as.sir.html @@ -1,5 +1,5 @@ -Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • AMR (for R)Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir • AMR (for R) +All breakpoints used for interpretation are available in our clinical_breakpoints data set."> Skip to contents @@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/av_synonyms.html b/reference/av_synonyms.html index ce5470f8a..0ecb1da7f 100644 --- a/reference/av_synonyms.html +++ b/reference/av_synonyms.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/av_tradenames.html b/reference/av_tradenames.html index ce5470f8a..0ecb1da7f 100644 --- a/reference/av_tradenames.html +++ b/reference/av_tradenames.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/av_url.html b/reference/av_url.html index ce5470f8a..0ecb1da7f 100644 --- a/reference/av_url.html +++ b/reference/av_url.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/availability.html b/reference/availability.html index 70fe95b5b..86ccbbe0c 100644 --- a/reference/availability.html +++ b/reference/availability.html @@ -1,5 +1,5 @@ -Check Availability of Columns — availability • AMR (for R) +Check Availability of Columns — availability • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/count.html b/reference/count.html index 6a7741883..311941ef0 100644 --- a/reference/count.html +++ b/reference/count.html @@ -1,7 +1,7 @@ Count Available Isolates — count • AMR (for R) +count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates."> Skip to contents @@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 2.1.1.9234 + 2.1.1.9235
diff --git a/reference/droplevels.mic.html b/reference/droplevels.mic.html index 977eb978a..54ba17d92 100644 --- a/reference/droplevels.mic.html +++ b/reference/droplevels.mic.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/eucast_dosage.html b/reference/eucast_dosage.html index 211fd0c07..15cfe037f 100644 --- a/reference/eucast_dosage.html +++ b/reference/eucast_dosage.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/eucast_exceptional_phenotypes.html b/reference/eucast_exceptional_phenotypes.html index 9ccef1b51..99f17baa0 100644 --- a/reference/eucast_exceptional_phenotypes.html +++ b/reference/eucast_exceptional_phenotypes.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/eucast_rules.html b/reference/eucast_rules.html index 3a6007c71..d1787468c 100644 --- a/reference/eucast_rules.html +++ b/reference/eucast_rules.html @@ -1,7 +1,7 @@ Apply EUCAST Rules — eucast_rules • AMR (for R) +To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details."> Skip to contents @@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 2.1.1.9234 + 2.1.1.9235
diff --git a/reference/example_isolates.html b/reference/example_isolates.html index e164e0783..ff93f1b76 100644 --- a/reference/example_isolates.html +++ b/reference/example_isolates.html @@ -1,5 +1,5 @@ -Data Set with 2 000 Example Isolates — example_isolates • AMR (for R) +Data Set with 2 000 Example Isolates — example_isolates • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235
-

A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website.

+

A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website.

@@ -74,7 +74,7 @@

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

-

Visit our website for direct download links, or explore the actual files in our GitHub repository.

+

Visit our website for direct download links, or explore the actual files in our GitHub repository.

diff --git a/reference/example_isolates_unclean.html b/reference/example_isolates_unclean.html index c910a4394..2819ca4a6 100644 --- a/reference/example_isolates_unclean.html +++ b/reference/example_isolates_unclean.html @@ -1,5 +1,5 @@ -Data Set with Unclean Data — example_isolates_unclean • AMR (for R) +Data Set with Unclean Data — example_isolates_unclean • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235
diff --git a/reference/export_ncbi_biosample.html b/reference/export_ncbi_biosample.html index d8cbb2229..bf6863607 100644 --- a/reference/export_ncbi_biosample.html +++ b/reference/export_ncbi_biosample.html @@ -1,5 +1,5 @@ -Export Data Set as NCBI BioSample Antibiogram — export_ncbi_biosample • AMR (for R) +Export Data Set as NCBI BioSample Antibiogram — export_ncbi_biosample • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235
diff --git a/reference/is.ab.html b/reference/is.ab.html index 3d47cb198..cef95015e 100644 --- a/reference/is.ab.html +++ b/reference/is.ab.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is.av.html b/reference/is.av.html index 49816e58a..45740ce74 100644 --- a/reference/is.av.html +++ b/reference/is.av.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is.disk.html b/reference/is.disk.html index ed1f99ab0..dd209fb91 100644 --- a/reference/is.disk.html +++ b/reference/is.disk.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is.mic.html b/reference/is.mic.html index 977eb978a..54ba17d92 100644 --- a/reference/is.mic.html +++ b/reference/is.mic.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is.mo.html b/reference/is.mo.html index e68bf46d9..626779946 100644 --- a/reference/is.mo.html +++ b/reference/is.mo.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is.sir.html b/reference/is.sir.html index c99d19d99..622a624a5 100644 --- a/reference/is.sir.html +++ b/reference/is.sir.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is_new_episode.html b/reference/is_new_episode.html index 8a0a58ba2..673c82f1c 100644 --- a/reference/is_new_episode.html +++ b/reference/is_new_episode.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/is_sir_eligible.html b/reference/is_sir_eligible.html index c99d19d99..622a624a5 100644 --- a/reference/is_sir_eligible.html +++ b/reference/is_sir_eligible.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/isoxazolylpenicillins.html b/reference/isoxazolylpenicillins.html index 8bd8e9fd0..168688bb7 100644 --- a/reference/isoxazolylpenicillins.html +++ b/reference/isoxazolylpenicillins.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/italicise_taxonomy.html b/reference/italicise_taxonomy.html index af8274706..e87cd640f 100644 --- a/reference/italicise_taxonomy.html +++ b/reference/italicise_taxonomy.html @@ -1,5 +1,5 @@ -Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy • AMR (for R) +Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/microorganisms.groups.html b/reference/microorganisms.groups.html index d4a278d08..68b4b04f8 100644 --- a/reference/microorganisms.groups.html +++ b/reference/microorganisms.groups.html @@ -1,5 +1,5 @@ -Data Set with 534 Microorganisms In Species Groups — microorganisms.groups • AMR (for R) +Data Set with 534 Microorganisms In Species Groups — microorganisms.groups • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/microorganisms.html b/reference/microorganisms.html index 9e1469c79..9af83fccf 100644 --- a/reference/microorganisms.html +++ b/reference/microorganisms.html @@ -1,7 +1,7 @@ Data Set with 78 679 Taxonomic Records of Microorganisms — microorganisms • AMR (for R) +This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF) for all others taxons."> Skip to contents @@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/mo.html b/reference/mo.html index e68bf46d9..626779946 100644 --- a/reference/mo.html +++ b/reference/mo.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_authors.html b/reference/mo_authors.html index 32a922060..f275b5782 100644 --- a/reference/mo_authors.html +++ b/reference/mo_authors.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_class.html b/reference/mo_class.html index 32a922060..f275b5782 100644 --- a/reference/mo_class.html +++ b/reference/mo_class.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_cleaning_regex.html b/reference/mo_cleaning_regex.html index e68bf46d9..626779946 100644 --- a/reference/mo_cleaning_regex.html +++ b/reference/mo_cleaning_regex.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_current.html b/reference/mo_current.html index 32a922060..f275b5782 100644 --- a/reference/mo_current.html +++ b/reference/mo_current.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_domain.html b/reference/mo_domain.html index 32a922060..f275b5782 100644 --- a/reference/mo_domain.html +++ b/reference/mo_domain.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_failures.html b/reference/mo_failures.html index e68bf46d9..626779946 100644 --- a/reference/mo_failures.html +++ b/reference/mo_failures.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_family.html b/reference/mo_family.html index 32a922060..f275b5782 100644 --- a/reference/mo_family.html +++ b/reference/mo_family.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_fullname.html b/reference/mo_fullname.html index 32a922060..f275b5782 100644 --- a/reference/mo_fullname.html +++ b/reference/mo_fullname.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_gbif.html b/reference/mo_gbif.html index 32a922060..f275b5782 100644 --- a/reference/mo_gbif.html +++ b/reference/mo_gbif.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_genus.html b/reference/mo_genus.html index 32a922060..f275b5782 100644 --- a/reference/mo_genus.html +++ b/reference/mo_genus.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_gramstain.html b/reference/mo_gramstain.html index 32a922060..f275b5782 100644 --- a/reference/mo_gramstain.html +++ b/reference/mo_gramstain.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_group_members.html b/reference/mo_group_members.html index 32a922060..f275b5782 100644 --- a/reference/mo_group_members.html +++ b/reference/mo_group_members.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_info.html b/reference/mo_info.html index 32a922060..f275b5782 100644 --- a/reference/mo_info.html +++ b/reference/mo_info.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_is_anaerobic.html b/reference/mo_is_anaerobic.html index 32a922060..f275b5782 100644 --- a/reference/mo_is_anaerobic.html +++ b/reference/mo_is_anaerobic.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_is_gram_negative.html b/reference/mo_is_gram_negative.html index 32a922060..f275b5782 100644 --- a/reference/mo_is_gram_negative.html +++ b/reference/mo_is_gram_negative.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_is_gram_positive.html b/reference/mo_is_gram_positive.html index 32a922060..f275b5782 100644 --- a/reference/mo_is_gram_positive.html +++ b/reference/mo_is_gram_positive.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_is_intrinsic_resistant.html b/reference/mo_is_intrinsic_resistant.html index 32a922060..f275b5782 100644 --- a/reference/mo_is_intrinsic_resistant.html +++ b/reference/mo_is_intrinsic_resistant.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_is_yeast.html b/reference/mo_is_yeast.html index 32a922060..f275b5782 100644 --- a/reference/mo_is_yeast.html +++ b/reference/mo_is_yeast.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_kingdom.html b/reference/mo_kingdom.html index 32a922060..f275b5782 100644 --- a/reference/mo_kingdom.html +++ b/reference/mo_kingdom.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_lpsn.html b/reference/mo_lpsn.html index 32a922060..f275b5782 100644 --- a/reference/mo_lpsn.html +++ b/reference/mo_lpsn.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_matching_score.html b/reference/mo_matching_score.html index d58629c33..fb9f31992 100644 --- a/reference/mo_matching_score.html +++ b/reference/mo_matching_score.html @@ -1,5 +1,5 @@ -Calculate the Matching Score for Microorganisms — mo_matching_score • AMR (for R) +Calculate the Matching Score for Microorganisms — mo_matching_score • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235
diff --git a/reference/mo_mycobank.html b/reference/mo_mycobank.html index 32a922060..f275b5782 100644 --- a/reference/mo_mycobank.html +++ b/reference/mo_mycobank.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_name.html b/reference/mo_name.html index 32a922060..f275b5782 100644 --- a/reference/mo_name.html +++ b/reference/mo_name.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_order.html b/reference/mo_order.html index 32a922060..f275b5782 100644 --- a/reference/mo_order.html +++ b/reference/mo_order.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_oxygen_tolerance.html b/reference/mo_oxygen_tolerance.html index 32a922060..f275b5782 100644 --- a/reference/mo_oxygen_tolerance.html +++ b/reference/mo_oxygen_tolerance.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_pathogenicity.html b/reference/mo_pathogenicity.html index 32a922060..f275b5782 100644 --- a/reference/mo_pathogenicity.html +++ b/reference/mo_pathogenicity.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_phylum.html b/reference/mo_phylum.html index 32a922060..f275b5782 100644 --- a/reference/mo_phylum.html +++ b/reference/mo_phylum.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_property.html b/reference/mo_property.html index 0332cb10c..a90deea08 100644 --- a/reference/mo_property.html +++ b/reference/mo_property.html @@ -1,5 +1,5 @@ -Get Properties of a Microorganism — mo_property • AMR (for R) +Get Properties of a Microorganism — mo_property • AMR (for R) Skip to contents @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9234 + 2.1.1.9235

See also

diff --git a/reference/mo_rank.html b/reference/mo_rank.html index 32a922060..f275b5782 100644 --- a/reference/mo_rank.html +++ b/reference/mo_rank.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_ref.html b/reference/mo_ref.html index 32a922060..f275b5782 100644 --- a/reference/mo_ref.html +++ b/reference/mo_ref.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_renamed.html b/reference/mo_renamed.html index e68bf46d9..626779946 100644 --- a/reference/mo_renamed.html +++ b/reference/mo_renamed.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_reset_session.html b/reference/mo_reset_session.html index e68bf46d9..626779946 100644 --- a/reference/mo_reset_session.html +++ b/reference/mo_reset_session.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_shortname.html b/reference/mo_shortname.html index 32a922060..f275b5782 100644 --- a/reference/mo_shortname.html +++ b/reference/mo_shortname.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_snomed.html b/reference/mo_snomed.html index 32a922060..f275b5782 100644 --- a/reference/mo_snomed.html +++ b/reference/mo_snomed.html @@ -1,8 +1,8 @@ - + - + diff --git a/reference/mo_source.html b/reference/mo_source.html index a14d1b39c..058385a26 100644 --- a/reference/mo_source.html +++ b/reference/mo_source.html @@ -1,7 +1,7 @@ User-Defined Reference Data Set for Microorganisms — mo_source • AMR (for R) +This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once."> Skip to contents @@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 2.1.1.9234 + 2.1.1.9235