A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo().
microorganisms.oldFormat
A data.frame with 14,100 observations and 4 variables:
fullname
Old full taxonomic name of the microorganismfullname_new
New full taxonomic name of the microorganismref
Author(s) and year of concerning scientific publicationprevalence
Prevalence of the microorganism, seeas.mo()
Source
Catalogue of Life: Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org (check included annual version with catalogue_of_life_version()).
Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
Catalogue of Life
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.
Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with catalogue_of_life_version().
Reference Data Publicly Available
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
Read more on Our Website!
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.