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 4,731 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 from the authoritative and comprehensive Catalogue of Life (http://www.catalogueoflife.org). This data is updated annually - check the included version with catalogue_of_life_version.
Included are:
All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses
All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera Aspergillus, Candida, Pneumocystis, Saccharomyces and Trichophyton).
All ~15,000 previously accepted names of (sub)species that have been taxonomically renamed
The complete taxonomic tree of all included (sub)species: from kingdom to subspecies
The responsible author(s) and year of scientific publication
The Catalogue of Life (http://www.catalogueoflife.org) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The syntax used to transform the original data to a cleansed R format, can be found here: https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R.
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.