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
ITIS
This package contains the complete microbial taxonomic data (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov).
All ~20,000 (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
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.