R/amph_trem.R

In Rtapas: Random Tanglegram Partitions

#' @docType data
#'
#' @title amph_trem dataset
#' @name amph_trem
#' @aliases am_matrix amphipod trematode amphipod_1000tr trematode_1000tr
#' @usage data(amph_trem)
#'
#' @description Data set of mitochondrial haplotypes of the trematode
#'              \emph{Coitocaecum parvum} (Crowcroft, 1945) and those of its
#'              amphipod host, \emph{Paracalliope fluviatilis} (Thomson, 1879)
#'              from several locations in South Island, New Zeland
#'              (Largue et al. 2016).
#'
#' @format This data set compresses five objects:
#'
#' \describe{
#'    \item{\code{am_matrix}}{Associations between 17 haplotypes of
#'    \emph{Coitocaecum parvum} and 59 haplotypes of
#'    \emph{Paracalliope fluviatilis}.
#'    A binary matrix with 59 rows (amphipod) and 17 variables (trematode).}
#'
#'    \item{\code{amphipod}}{\emph{Paracalliope fluviatilis} consensus tree.
#'    An object of class \code{"phylo"} containing a list with the details of
#'    the consensus phylogenetic tree (i.e. edges, edges length, nodes, and
#'    tips names).}
#'
#'    \item{\code{trematode}}{\emph{Coitocaecum parvum} consensus tree.
#'    An object of class \code{"phylo"} containing a list with the details of
#'    the phylogenetic tree (i.e. edges, edges length, nodes and tips names).}
#'
#'    \item{\code{amphipod_1000tr}}{1000 Bayesian posterior probability trees
#'    of \emph{Paracalliope fluviatilis}.
#'    List of class \code{"multiphylo"} containing a 1000 phylogenetic trees
#'    with their respective details (i.e. edges, edges length, nodes, and
#'    tips names).}
#'
#'    \item{\code{trematode_1000tr}}{1000 Bayesian posterior probability trees
#'    of \emph{Coitocaecum parvum}.
#'    List of class \code{"multiphylo"} containing a 1000 phylogenetic trees
#'    with their respective details (i.e. edges, edges length, nodes, and
#'    tips names).}
#'  }
#'
#'
#' @references
#' Lagrue C., Joannes A., Poulin R., Blasco-Costa I. (2016). Genetic structure
#' and host–parasite co‐divergence: evidence for trait‐specific local adaptation.
#' Biological Journal of the Linnean Society. 118:344–358.
#'
#' Balbuena J.A., Perez-Escobar O.A., Llopis-Belenguer C., Blasco-Costa I.
#' (2022). User’s Guide Random Tanglegram Partitions V.1.0.0. Zenodo.
#' \doi{10.5281/zenodo.6327235}
#'
#' @source
#' Balbuena J.A., Perez-Escobar O.A., Llopis-Belenguer C., Blasco-Costa I.
#' (2022). User’s Guide Random Tanglegram Partitions V.1.0.0. Zenodo.
#' \doi{10.5281/zenodo.6327235}
#'
#' @keywords datasets
#'
#'
#'
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