#' This package contains the complete taxonomic tree of almost all microorganisms (~60,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#' \link[=catalogue_of_life]{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 \code{\link{catalogue_of_life_version}()}.
#' \item{All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
#' \item{All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like \emph{Strongyloides} and \emph{Taenia})}
#' \item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
#' \item{The responsible author(s) and year of scientific publication}
#' }
#'
#' The Catalogue of Life (\url{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: \url{https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R}.
#' @inheritSection AMR Read more on our website!
#' @name catalogue_of_life
#' @rdname catalogue_of_life
#' @examples
#' # Get version info of included data set
#' catalogue_of_life_version()
#'
#'
#' # Get a note when a species was renamed
#' mo_shortname("Chlamydia psittaci")
#' # Note: 'Chlamydia psittaci' (Page, 1968) was renamed
#' # 'Chlamydophila psittaci' (Everett et al., 1999)
#' # [1] "C. psittaci"
#'
#' # Get any property from the entire taxonomic tree for all included species
#' mo_class("E. coli")
#' # [1] "Gammaproteobacteria"
#'
#' mo_family("E. coli")
#' # [1] "Enterobacteriaceae"
#'
#' mo_gramstain("E. coli") # based on kingdom and phylum, see ?mo_gramstain
#' # [1] "Gram negative"
#'
#' mo_ref("E. coli")
#' # [1] "Castellani et al., 1919"
#'
#' # Do not get mistaken - the package only includes microorganisms
#' mo_phylum("C. elegans")
#' # [1] "Cyanobacteria" # Bacteria?!
#' mo_fullname("C. elegans")
#' # [1] "Chroococcus limneticus elegans" # Because a microorganism was found
#' This function returns a list with info about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
