vignettes/datasets.Rmd
datasets.Rmd
This data set is in R available as microorganisms, after you load the AMR package.
microorganisms
AMR
It was last updated on 16 July 2024 12:51:57 UTC. Find more info +
It was last updated on 17 July 2024 12:29:55 UTC. Find more info about the structure of this data set here.
Direct download links:
This data set contains the full microbial taxonomy of six kingdoms -from the List of Prokaryotic names with Standing in Nomenclature (LPSN) -and the Global Biodiversity Information Facility (GBIF):
This data set is in R available as antibiotics, after you load the AMR package.
antibiotics
It was last updated on 14 June 2024 20:39:01 UTC. Find more info +
It was last updated on 19 September 2024 09:44:56 UTC. Find more info about the structure of this data set here.
(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.)
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, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
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.
rsi
sir
as.sir()
breakpoint_type = "animal"
host
clinical_breakpoints
as.mo()
only_fungi
only_fungi = TRUE
AMR_only_fungi
options(AMR_only_fungi = TRUE)
mo_group_members()
mo_group_members("Strep group C")
ab
mo
uti
as.sir(..., ab = "column1", mo = "column2", uti = "column3")
antibiogram()
combine_IR
count_df()
proportion_df()
sir_df()
combine_SI
units
ab_ddd(..., units = "...")
ab_ddd_units()
data.frame
data.table::data.table
janitor::tabyl
tibble::tibble
tsibble::tsibble
bug_drug_combinations()
tibble