(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.
rsi
sir
as.sir()
breakpoint_type = "animal"
host
clinical_breakpoints
ab_url()
as.double()
NA
summary()
scale_*_mic()
scale_x_mic()
scale_y_mic()
scale_colour_mic()
scale_fill_mic()
rescale_mic()
mo_group_members()
mo_group_members("Strep group C")
ab
mo
uti
as.sir(..., ab = "column1", mo = "column2", uti = "column3")
nitrofurans()
rifamycins()
CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing, 2011-2024, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m100/.
CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals, 2019-2024, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/veterinary-medicine/documents/vet01//.
EUCAST Breakpoint tables for interpretation of MICs and zone diameters, 2011-2024, European Committee on Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.
WHONET as a source for machine-reading clinical breakpoints ((read more here)https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet), 1989-2024, WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. https://whonet.org/.
WHONET as a source for machine-reading the clinical breakpoints (read more here), 1989-2024, WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. https://whonet.org/.