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dr. M.S. (Matthijs) BerendsandClaude Opus 5.5
83a4853936
- taxonomy build: released taxa (since v2.0.0) that are missing are restored from their last release with their old code and last known status, and are exempt from later removals (decision by Matthijs S. Berends) - exceptions are retired on purpose in data-raw/microorganisms_files/mo_code_retirements.csv with a reason: other organisms with the same genus name (e.g. the Graphium butterflies, wrongly in the Fungi until v3.0.1) and taxa whose genus is now only known in another domain; as.mo() translates these codes to NA with that reason - synonyms without a current name are linked to an accepted name in the same genus that only differs by a Latin gender ending (e.g. Candida glabratus -> Nakaseomyces glabratus) - placeholders such as "(unknown class)" never become records; codes of manually added records are matched by domain and name - integrity rule released_taxon_missing; known defects of the data on main updated Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
77 lines
4.6 KiB
Plaintext
77 lines
4.6 KiB
Plaintext
Package: AMR
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Version: 3.0.1.9097
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Date: 2026-10-03
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
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Authors@R: c(
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person(given = c("Matthijs", "S."), family = "Berends", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
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person(given = c("Dennis"), family = "Souverein", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
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person(given = c("Erwin", "E.", "A."), family = "Hassing", role = c("aut", "ctb")),
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person(given = c("Aislinn"), family = "Cook", role = "ctb", comment = c(ORCID = "0000-0002-9189-7815")),
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person(given = c("Andrew", "P."), family = "Norgan", role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
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person(given = c("Anita"), family = "Williams", role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")),
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person(given = c("Annick"), family = "Lenglet", role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
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person(given = c("Anthony"), family = "Underwood", role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")),
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person(given = c("Anton"), family = "Mymrikov", role = "ctb"),
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person(given = c("Bart", "C."), family = "Meijer", role = "ctb"),
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person(given = c("Christian", "F."), family = "Luz", role = "ctb", comment = c(ORCID = "0000-0001-5809-5995")),
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person(given = c("Dmytro"), family = "Mykhailenko", role = "ctb"),
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person(given = c("Eric", "H.", "L.", "C.", "M."), family = "Hazenberg", role = "ctb"),
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person(given = c("Gwen"), family = "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
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person(given = c("Jane"), family = "Hawkey", role = "ctb", comment = c(ORCID = "0000-0001-9661-5293")),
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person(given = c("Jason"), family = "Stull", role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
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person(given = c("Javier"), family = "Sanchez", role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
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person(given = c("Jonas"), family = "Salm", role = "ctb"),
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person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
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person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
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person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
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person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
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person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
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person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
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person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
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person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
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person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
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person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
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person(given = c("Casper", "J."), family = "Albers", role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
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person(given = c("Corinna"), family = "Glasner", role = "ths", comment = c(ORCID = "0000-0003-1241-1328")))
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Depends: R (>= 3.0.0)
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Suggests:
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cleaner,
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cli,
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crayon,
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curl,
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data.table,
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dplyr,
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future,
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future.apply,
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ggplot2,
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knitr,
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openxlsx,
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pillar,
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progress,
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readxl,
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recipes,
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rlang,
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rmarkdown,
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rstudioapi,
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rvest,
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skimr,
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testthat,
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tibble,
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tidymodels,
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tidyselect,
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tinytest,
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vctrs,
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xml2,
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usethis
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VignetteBuilder: knitr,rmarkdown
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URL: https://amr-for-r.org, https://github.com/msberends/AMR
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BugReports: https://github.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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Roxygen: list(markdown = TRUE)
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Config/roxygen2/version: 8.1.0
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