Translation table for microorganism codes
microorganisms.codes.RdA 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:
certeCommonly used code of a microorganism
moID of the microorganism in the
microorganismsdata 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.