R/paleobioDB-package.R

In ropensci/paleobioDB: Download and Process Data from the Paleobiology Database

#' We have developed paleobioDB, an R-package designed to make easy
#' and flexible queries of the Paleobiology Database, as well as to
#' visualize and download selected data. This package will make it
#' easy to access paleontological data in a way that should allow
#' those data to be further analyzed, including via packages and
#' libraries available in R.
#'
#' We programmed two different groups of functions. First, we
#' developed a set of general and flexible functions to wrap the
#' [PaleobioDB API](https://paleobiodb.org/data1.2/). These
#' functions connect R with each of the endpoints of the PaleobioDB
#' API. Second, based on these base functions, we programmed a second
#' set of functions intended to explore and visualize the fossil
#' occurrences in their geographic, temporal and taxonomic dimensions.
#'
#' @name paleobioDB
#' @aliases paleobioDB-package
#' @docType package
#' @title paleobioDB: An R-package for downloading, visualizing and
#'   processing data from the Paleobiology Database
#' @author Sara Varela \email{sara.varela@@uvigo.gal}
#' @author Javier Gonzalez \email{javigzz@@yahoo.es}
#' @author Luciano Fabris Sgarbi \email{luciano.f.sgarbi@@gmail.com}
#' @references Sara Varela, Javier González-Hernández, Luciano Fabris
#'   Sgarbi, Charles Marshall, Mark D. Uhen, Shanan Peters, Michael
#'   McClennen, 2015. paleobioDB: an R package for downloading,
#'   visualizing and processing data from the Paleobiology
#'   Database. Ecography, 38:
#'   419-425. \doi{10.1111/ecog.01154}
#'
#' @keywords internal
#'
#' @seealso {
#' <https://paleobiodb.org>
#' }
#'
#' @examples \dontrun{
#' canidae <- pbdb_occurrences(
#'   vocab = "pbdb",
#'   limit = "all",
#'   base_name = "canidae",
#'   interval = "Quaternary",
#'   show = c("coords", "classext", "ident")
#' )
#'
#' ## to explore the number of subtaxa
#' pbdb_subtaxa(canidae)
#'
#' ## to explore the temporal resolution of the fossil records
#' pbdb_temporal_resolution(canidae)
#'
#' ## returns a data frame and a plot with the temporal span
#' ## of the species, genera, etc.
#' pbdb_temp_range(canidae, rank = "genus", names = FALSE)
#'
#' ## returns a data frame and a plot showing the species, genera, etc.
#' ## richness across time
#' pbdb_richness(canidae, rank = "species", temporal_extent = c(0, 10), res = 1)
#'
#' ## returns a data frame and a plot showing the evolutionary
#' ## and extinction rates across time
#'
#' ## evolutionary rates: orig_ext = 1
#' pbdb_orig_ext(
#'   canidae,
#'   rank = "species", temporal_extent = c(0, 10), res = 1,
#'   orig_ext = 1
#' )
#'
#' ## extinction rates: orig_ext = 2
#' pbdb_orig_ext(
#'   canidae,
#'   rank = "species", temporal_extent = c(0, 10), res = 1,
#'   orig_ext = 2
#' )
#'
#' ## maps the fossil occurrences
#' pbdb_map(canidae, main = "Canidae", pch = 19, cex = 0.7)
#'
#' ## maps the sampling effort
#' pbdb_map_occur(canidae, res = 5)
#'
#' ## maps the species, genera, etc. richness
#' pbdb_map_richness(canidae, rank = "species", res = 5)
#'
#' }
#'
"_PACKAGE"

## usethis namespace: start
#' @importFrom graphics abline
#' @importFrom graphics axis
#' @importFrom graphics barplot
#' @importFrom graphics hist
#' @importFrom graphics legend
#' @importFrom graphics mtext
#' @importFrom graphics par
#' @importFrom graphics plot.new
#' @importFrom graphics plot.window
#' @importFrom graphics points
#' @importFrom graphics polygon
#' @importFrom graphics rect
#' @importFrom graphics segments
#' @importFrom graphics text
#' @importFrom graphics title
#' @importFrom terra ext
#' @importFrom terra rast
#' @importFrom terra rasterize
#' @importFrom terra res
#' @importFrom terra res<-
#' @importFrom terra values
#' @importFrom terra values<-
#' @importMethodsFrom terra plot
## usethis namespace: end
NULL