R/FossilSim.R

#' FossilSim: A package for simulating and plotting fossil and taxonomy data
#'
#' This package provides functions for simulating both taxonomy and fossil data from an existing phylogeny.
#'
#' @section Simulating taxonomy:
#' Taxonomy can be simulated in FossilSim under a mixed model of speciation that can incorporate three modes of speciation --
#' budding (or asymmetric), bifurcating (or symmetric) and anagenetic -- in addition to cryptic speciation.
#' A description of the resulting taxonomy objects and simulation functions can be found in the "Simulating taxonomy" vignette.
#'
#' @section Simulating fossil data:
#' Fossils can be simulated from a phylogeny or a taxonomy under a model of constant fossil recovery or
#' time-dependent, environment-dependent or species-dependent fossil recovery.
#' A description of the resulting fossil objects and simulation functions can be found in the "Simulating fossils" vignette.
#'
#' @section Plotting functions:
#' Both taxonomy and fossil objects are provided with custom plotting functions that highlight important features of the simulated objects
#' along the original phylogeny. More details about these functions can be found in the vignettes or by calling
#' \code{?plot.taxonomy} and \code{?plot.fossils}.
#'
#' @section Compatibility with other packages:
#' FossilSim is designed to use phylogenies in the ape format. It provides functions to convert to and from the fossilRecordSimulation
#' format used by the package paleotree (see the vignette "Converting from and to paleotree format"), as well as functions to convert to the
#' zero-edge format used by BEAST2 and RevBayes (see the vignette "Exporting sampled ancestor trees").
#'
#' @examples
#' # simulate a tree using TreeSim conditioned on tip number
#' t = TreeSim::sim.bd.taxa(n = 10, numbsim = 1, lambda = 1, mu = 0.2)[[1]]
#'
#' # simulate taxonomy under mixed speciation
#' s = sim.taxonomy(tree = t, beta = 0.5, lambda.a = 1, kappa = 0.1)
#' # plot the result
#' plot(s, tree = t, legend.position = "topleft")
#'
#' # simulate fossils using the phylogeny and a constant fossil recovery rate
#' f = sim.fossils.poisson(rate = 3, tree = t)
#' # plot the result
#' plot(f, tree = t)
#'
#' # simulate fossils using the taxonomy and a constant fossil recovery rate
#' f = sim.fossils.poisson(rate = 3, taxonomy = s)
#' # plot the result
#' plot(f, tree = t, taxonomy = s, show.taxonomy = TRUE)
#'
#' # simulate fossils using time-dependent fossil recovery rates
#' f = sim.fossils.intervals(tree = t, rates = c(1, 0.1, 1, 0.1), max.age = tree.max(t), strata = 4)
#' # plot the result, with the time intervals
#' plot(f, tree = t, show.strata = TRUE, max.age = tree.max(t), strata = 4)
#'
#' @docType package
#' @name FossilSim
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rachelwarnock/fossilsim documentation built on Oct. 27, 2019, 9:26 a.m.