Data set with old taxonomic data from ITIS
microorganisms.old.RdA data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by as.mo.
microorganisms.old
Format
A data.frame with 2,383 observations and 4 variables:
tsnOld Taxonomic Serial Number (TSN), as defined by ITIS
nameOld taxonomic name of the microorganism as found in ITIS, see Source
tsn_newNew Taxonomic Serial Number (TSN), as defined by ITIS
refAuthor(s) and year of concerning publication as found in ITIS, see Source
Source
[3] Integrated Taxonomic Information System (ITIS) on-line database, https://www.itis.gov.
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 ~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 all bacteria are classified into subkingdom Negibacteria or 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 omprehensive tutorial about how to conduct AMR analysis and find the complete documentation of all functions, which reads a lot easier than in R.