R/model-bisse-t.R

In diversitree: Comparative 'Phylogenetic' Analyses of Diversification

make.bisse.t <- function(tree, states, functions, unresolved=NULL,
                         sampling.f=NULL, strict=TRUE, control=list(),
                         truncate=FALSE, spline.data=NULL) {
  cache <- make.cache.bisse.t(tree, states, functions,
                              unresolved, sampling.f, strict,
                              truncate, spline.data)
  all_branches <- make.all_branches.t.dtlik(cache, control,
                                            initial.conditions.bisse)
  rootfunc <- make.rootfunc.t(cache, rootfunc.musse)

  ll <- function(pars, condition.surv=TRUE, root=ROOT.OBS,
                 root.p=NULL, intermediates=FALSE) {
    ans <- all_branches(pars, intermediates)
    rootfunc(ans, pars, condition.surv, root, root.p, intermediates)
  }
  class(ll) <- c("bisse.t", "bisse", "dtlik.t", "dtlik", "function")
  ll
}

make.cache.bisse.t <- function(tree, states, functions,
                               unresolved, sampling.f, strict,
                               truncate, spline.data) {
  nt.extra <- 10 # fixed, as we're going to ignore unresolved.
  cache <- make.cache.bisse(tree, states, unresolved, sampling.f,
                            nt.extra, strict)
  if ( !is.null(cache$unresolved) )
    stop("Cannot do time-varying birth-death with unresolved clades")
  update.cache.t(cache, functions,
                 nonnegative=TRUE, truncate=truncate, with.q=FALSE,
                 spline.data=spline.data) 
}