A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source.

microorganisms.codes

Format

A data.frame with 5,171 observations and 2 variables:

certe

Commonly used code of a microorganism

mo

ID of the microorganism in the microorganisms data set

Catalogue of Life


This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (http://www.catalogueoflife.org). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.

Click here for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with catalogue_of_life_version().

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

See also