mirror of
https://github.com/msberends/AMR.git
synced 2026-11-16 00:10:57 +01:00
dr. M.S. (Matthijs) Berends
eb9a9c2fa5
WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
77 lines
4.6 KiB
Plaintext
77 lines
4.6 KiB
Plaintext
Package: AMR
|
|
Version: 3.0.1.9149
|
|
Date: 2026-10-15
|
|
Title: Antimicrobial Resistance Data Analysis
|
|
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
|
data analysis and to work with microbial and antimicrobial properties by
|
|
using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
|
|
Authors@R: c(
|
|
person(given = c("Matthijs", "S."), family = "Berends", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
|
|
person(given = c("Dennis"), family = "Souverein", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
|
|
person(given = c("Erwin", "E.", "A."), family = "Hassing", role = c("aut", "ctb")),
|
|
person(given = c("Aislinn"), family = "Cook", role = "ctb", comment = c(ORCID = "0000-0002-9189-7815")),
|
|
person(given = c("Andrew", "P."), family = "Norgan", role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
|
|
person(given = c("Anita"), family = "Williams", role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")),
|
|
person(given = c("Annick"), family = "Lenglet", role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
|
|
person(given = c("Anthony"), family = "Underwood", role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")),
|
|
person(given = c("Anton"), family = "Mymrikov", role = "ctb"),
|
|
person(given = c("Bart", "C."), family = "Meijer", role = "ctb"),
|
|
person(given = c("Christian", "F."), family = "Luz", role = "ctb", comment = c(ORCID = "0000-0001-5809-5995")),
|
|
person(given = c("Dmytro"), family = "Mykhailenko", role = "ctb"),
|
|
person(given = c("Eric", "H.", "L.", "C.", "M."), family = "Hazenberg", role = "ctb"),
|
|
person(given = c("Gwen"), family = "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
|
|
person(given = c("Jane"), family = "Hawkey", role = "ctb", comment = c(ORCID = "0000-0001-9661-5293")),
|
|
person(given = c("Jason"), family = "Stull", role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
|
|
person(given = c("Javier"), family = "Sanchez", role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
|
|
person(given = c("Jonas"), family = "Salm", role = "ctb"),
|
|
person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
|
|
person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
|
|
person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
|
|
person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
|
|
person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
|
|
person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
|
|
person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
|
|
person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
|
|
person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
|
|
person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
|
|
person(given = c("Casper", "J."), family = "Albers", role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
|
|
person(given = c("Corinna"), family = "Glasner", role = "ths", comment = c(ORCID = "0000-0003-1241-1328")))
|
|
Depends: R (>= 3.0.0)
|
|
Suggests:
|
|
cleaner,
|
|
cli,
|
|
crayon,
|
|
curl,
|
|
data.table,
|
|
dplyr,
|
|
future,
|
|
future.apply,
|
|
ggplot2,
|
|
knitr,
|
|
openxlsx,
|
|
pillar,
|
|
progress,
|
|
readxl,
|
|
recipes,
|
|
rlang,
|
|
rmarkdown,
|
|
rstudioapi,
|
|
rvest,
|
|
skimr,
|
|
testthat,
|
|
tibble,
|
|
tidymodels,
|
|
tidyselect,
|
|
tinytest,
|
|
vctrs,
|
|
xml2,
|
|
usethis
|
|
VignetteBuilder: knitr,rmarkdown
|
|
URL: https://amr-for-r.org, https://github.com/msberends/AMR
|
|
BugReports: https://github.com/msberends/AMR/issues
|
|
License: GPL-2 | file LICENSE
|
|
Encoding: UTF-8
|
|
LazyData: true
|
|
Roxygen: list(markdown = TRUE)
|
|
Config/roxygen2/version: 8.1.0
|