#' Example Analysis Output of a Simulated Dataset
#'
#' Simulated 30-taxon coalescent tree and simulated character data from a Brownian Motion
#' intrinsic model (\code{\link{brownianIntrinsic}}), with saved generating parameters.
#' Character data was generated under this model using \code{doSimulation}.
#' Also includes results from an example analysis.
#'
#'
#' @name simRunExample
#' @aliases
#' simRunExample
#' simPhyExample simCharExample
#' resultsBMExample resultsBoundExample
#' genRateExample ancStateExample
#simCharOut
#' @docType data
#' @format
#' Loading the \code{simRunExample} example dataset adds seven new
#' objects to the namespace:
#'
#' \describe{
#' \item{\code{simPhyExample}}{A simulated 30-tip coalescent
#' phylogeny in typical \code{phylo} format.}
#' \item{\code{ancStateExample}}{The starting ancestral value,
#' used for generating the simulated continuous trait data.}
#' \item{\code{genRateExample}}{The true rate of trait change under Brownian Motion,
#' used for generating the simulated continuous trait data.}
# \item{\code{simCharOutExample}}{The raw output
# of \code{\link{doSimulation}} on \code{simPhyExample},
# under the model \code{\link{brownianIntrinsic}}.}
#' \item{\code{simCharExample}}{The output of \code{\link{doSimulation}} on \code{simPhyExample},
#' under the model \code{\link{brownianIntrinsic}}. composed of just the simulated
#' trait values as a one-column matrix with row names indicating tip
#' labels, as desired by \code{doRun} functions.}
#' \item{\code{resultsBMExample}}{The results of \code{\link{doRun_prc}},
#' under the generating model of \code{\link{brownianIntrinsic}}}
#' \item{\code{resultsBoundExample}}{The results of
#' \code{\link{doRun_prc}}, under the incorrect model
#' of \code{\link{boundaryMinIntrinsic}}}
#' }
#'
#' The objects \code{resultsBMExample} and \code{resultsBoundExample}
#' are lists composed of a number of elements (see the documentation
#' for the \code{\link{doRun_prc}} function for more detail).
#' @examples
#'
#' data(simRunExample)
#'
#' # ...things to do with this data?
#'
#' ###################
#'
#' # This data was generated using this process:
#'
#' \dontrun{
#'
#' library(TreEvo)
#'
#' set.seed(1)
#' simPhyExample <- rcoal(20)
#' # get realistic edge lengths
#' simPhyExample$edge.length <- simPhyExample$edge.length*20
#'
#' # plot with time axis (root is about ~15 Ma)
#' plot(simPhyExample)
#' axisPhylo()
#'
#' genRateExample <- c(0.001)
#' ancStateExample <- c(10)
#'
#' #Simple Brownian motion
#' simCharExample <- doSimulation(
#' phy = simPhyExample,
#' intrinsicFn = brownianIntrinsic,
#' extrinsicFn = nullExtrinsic,
#' startingValues = ancStateExample, #root state
#' intrinsicValues = genRateExample,
#' extrinsicValues = c(0),
#' generation.time = 10000
#' )
#'
#' resultsBMExample <- doRun_prc(
#' phy = simPhyExample,
#' traits = simCharExample,
#' intrinsicFn = brownianIntrinsic,
#' extrinsicFn = nullExtrinsic,
#' startingPriorsFns = "normal",
#' startingPriorsValues = list(c(mean(simCharExample[, 1]), sd(simCharExample[, 1]))),
#' intrinsicPriorsFns = c("exponential"),
#' intrinsicPriorsValues = list(10),
#' extrinsicPriorsFns = c("fixed"),
#' extrinsicPriorsValues = list(0),
#' generation.time = 10000,
#' nRuns = 2,
#' nStepsPRC = 3,
#' numParticles = 20,
#' nInitialSimsPerParam = 10,
#' jobName = "examplerun_prc",
#' stopRule = FALSE,
#' multicore = FALSE,
#' verboseParticles = TRUE,
#' coreLimit = 1
#' )
#'
#' resultsBoundExample <- doRun_prc(
#' phy = simPhyExample,
#' traits = simCharExample,
#' intrinsicFn = boundaryMinIntrinsic,
#' extrinsicFn = nullExtrinsic,
#' startingPriorsFns = "normal",
#' startingPriorsValues = list(c(mean(simCharExample[, 1]), sd(simCharExample[, 1]))),
#' intrinsicPriorsFns = c("exponential", "normal"),
#' intrinsicPriorsValues = list(10,c(-10,1)),
#' extrinsicPriorsFns = c("fixed"),
#' extrinsicPriorsValues = list(0),
#' generation.time = 10000,
#' nRuns = 2,
#' nStepsPRC = 3,
#' numParticles = 20,
#' nInitialSimsPerParam = 10,
#' jobName = "examplerun_prc_bound",
#' stopRule = FALSE,
#' multicore = FALSE,
#' verboseParticles = TRUE,
#' coreLimit = 1
#' )
#'
#' rm(.Random.seed)
#' save.image(file = "simRunExample.rdata")
#' if(interactive()){savehistory("simRunExample.Rhistory")}
#'
#' }
#'
#'
# @keywords datasets
NULL
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