R/data.R

In UtrechtUniversity/SCCA: Spectral Clustering Correspondence Analysis in R

#' Geographical distributions of the mammalian order Carnivora
#'
#' This common-used dataset in Ecology, gives the geographical distributions of the mammalian order Carnivora.
#' The data set is comprised by an incidence matrix M
#' (i.e. presence-absence matrix), with 41,580 non-empty sites (rows) and 288 extant terrestrial and marine species (columns).
#' The sites represent grid-cells rasterised at a resolution of 0.78 latitudinal degrees.
#' The distributional data results from rasterizing range map distributions published as part of
#' the Phylacine v1.2 dataset \strong{Faurby 2019}, which includes
#' data on the geographic distributions of mammals both extant and extinct over the last 130,000 years.
#' The data was downloaded (last accessed on November 2019) and pruned
#' to only include carnivores.
#' Data was processed in R (R Core Development Team 2014) and mapped in QGIS v2.18.16 (QGIS Development Team 2015).
#'
#'
#' @format A matrix with 41,580 rows (sites) and and 288 columns (species)
#' \describe{
#'   \item{\strong{cell value}}{absence-presence (0/1) values}
#'   \item{\strong{row name}}{label which can be used to retrieve the site specs from the data frame \code{carnivora_sites}}
#'   \item{\strong{column name}}{label which can be used to retrieve the species name from the data frame \code{carnivora_species}}
#' }
#'
#' @references
#' Faurby, Søren et al. (2019), Data from: PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology, Dryad, Dataset, \url{https://doi.org/10.5061/dryad.bp26v20}
"carnivora"

#' Species of the Carnivora Incidence matrix
#'
#' This table has two columns: species_id and species_name. The first column contains labels (column names) of the Carnivora
#' incidence matrix. The second column contains the names of the species.
#'
#' @format A data frame with 288 rows (species)
#' \describe{
#'   \item{species_id}{Species labels used in matrix \code{carnivora} as column names}
#'   \item{species_name}{The actual names of the species}
#' }
#'
#' @source \url{https://datadryad.org/stash/dataset/doi:10.5061/dryad.bp26v20}
"carnivora_species"

#' Sites of the Carnivora Incidence matrix
#'
#' @format A data frame with 41,580 rows (sites) and 3 columns
#' \describe{
#'   \item{site}{Site labels used in matrix \code{carnivora} as row names}
#'   \item{lon}{Longitude of the site. See details.}
#'   \item{lat}{Lattitude of the site. See details.}
#' }
#'
#' @source \url{https://datadryad.org/stash/dataset/doi:10.5061/dryad.bp26v20}
#'
#' @details
#' The Behrman cylindrical equal area projection is used with
#' a resolution of 96.5 km by 96.5 km at 30° North and 30° South.
#' The full projection description following R-notation is
#' “+proj=cea +lon_0=0+lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs +ellps=WGS84+towgs84=0,0,0”.
#' Only the area between 90°N and 60°S is included.
"carnivora_sites"