R/data_docs.R

In phylopath: Perform Phylogenetic Path Analysis

#' Rhinogrades traits.
#'
#' A simulated dataset, as used by Gonzalez-Voyer and Von Hardenberg as an
#' example, containing variables on body mass (BM), litter size (LS), nose
#' length (NL), dispersal distance (DD) and range size (RS).
#'
#' @source Gonzalez-Voyer A & von Hardenberg A. 2014. An Introduction to
#'   Phylogenetic Path Analysis. Chapter 8. In: Garamszegi LZ (ed.), Modern
#'   Phylogenetic Comparative Methods and Their Application in Evolutionary
#'   Biology. pp. 201-229. Springer-Verlag Berlin Heidelberg.
#'   doi:10.1111/j.1558-5646.2012.01790.x
"rhino"

#' Rhinogrades phylogeny.
#'
#' A phylogenetic tree for the 100 species of the \code{rhino} dataset.
#'
#' @source Gonzalez-Voyer A & von Hardenberg A. 2014. An Introduction to
#'   Phylogenetic Path Analysis. Chapter 8. In: Garamszegi LZ (ed.), Modern
#'   Phylogenetic Comparative Methods and Their Application in Evolutionary
#'   Biology. pp. 201-229. Springer-Verlag Berlin Heidelberg.
#'   doi:10.1111/j.1558-5646.2012.01790.x
"rhino_tree"

#' Cichlid traits and the evolution of cooperative breeding.
#'
#' A data set with binary traits, used in an analysis on the evolution of
#' cooperative breeding by Dey et al 2017. Variable names are shortened for
#' easy of use and consist of cooperative breeding (C), mating system (M),
#' parental care (P), social grouping (G) and diet (D). All traits are coded as
#' two level factors.
#'
#' @source Dey, C.J., O'Connor, C.M., Wilkinson, H., Shultz, S., Balshine, S. &
#'   Fitzpatrick, J.L. 2017. Direct benefits and evolutionary transitions to
#'   complex societies. Nat Ecol Evol 1: 137.
"cichlids"

#' Cichlid phylogeny.
#'
#' The phylogenetic tree of cichlid species that accompanies the `cichlids`
#' dataset. The phylogeny is based on five nuclear genes and three
#' mitochondrial genes.
#'
#' @source Dey, C.J., O'Connor, C.M., Wilkinson, H., Shultz, S., Balshine, S. &
#'   Fitzpatrick, J.L. 2017. Direct benefits and evolutionary transitions to
#'   complex societies. Nat Ecol Evol 1: 137.
"cichlids_tree"

#' Data on brain size, life history and vulnerability to extinction
#'
#' A dataset with continuous variables affecting the conservation `Status` of
#' mammalian species (the IUCN red list of threatened species).
#'
#' It includes the following variables: brain size (`Br`), body size (`B`),
#' gestation period (`G`), litter size (`L`), weening age (`W`), population
#' density (`P`) and vulnerability to extinction (`Status`).
#'
#' @source Gonzalez-Voyer A, Gonzalez-Suarez M, Vila C, Revilla E (2016) Larger
#'   brain size indirectly increases vulnerability to extinction in mammals.
#'   Evolution 70:1364-1375. doi: 10.1111/evo.12943
"red_list"

#' Mammalian phylogeny
#'
#' This is the accompanying phylogeny for the red_list data set. It is based
#' on the updated mammalian supertree by Bininda-Emonds et al. 2007 & Fritz
#' et al. 2009.
#'
#' @source Gonzalez-Voyer, A. Gonzalez-Suarez M. Vila C. and Revilla E. 2016.
#'   Larger brain size indirectly increases vulnerability to extinction in
#'   mammals. Evolution 70:1364-1375. doi: 10.1111/evo.12943.
#'
#' Bininda-Emonds, O. R. P., M. Cardillo, K. E. Jones, R. D. E. MacPhee, R. M. D.
#'   Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman, and A. Purvis.
#'   2007. The delayed rise of present-day mammals. Nature 446:507-512.
#'
#' Fritz, S. A., O. R. P. Bininda-Emonds, and A. Purvis. 2009. Geographical
#'   variation in predictors of mammalian extinction risk: big is bad, but
#'   only in the tropics. Ecol. Lett. 12:538-549.
#'
"red_list_tree"