Nothing
make.bd.t <- function(tree, functions, sampling.f=NULL,
unresolved=NULL, control=list(),
truncate=FALSE, spline.data=NULL) {
cache <- make.cache.bd.t(tree, functions, unresolved, sampling.f,
truncate, spline.data)
all_branches <- make.all_branches.t.dtlik(cache, control,
initial.conditions.bd.ode)
rootfunc <- make.rootfunc.t(cache, rootfunc.bd.ode)
const <- cache$const
ll <- function(pars, condition.surv=TRUE, intermediates=FALSE) {
ans <- all_branches(pars, intermediates)
rootfunc(ans, pars, condition.surv, intermediates, const)
}
class(ll) <- c("bd.t", "bd", "dtlik.t", "dtlik", "function")
ll
}
make.cache.bd.t <- function(tree, functions, unresolved, sampling.f,
truncate, spline.data) {
cache <- make.cache.bd.ode(tree, sampling.f, unresolved)
if ( !is.null(cache$unresolved) )
stop("Cannot do time-varying birth-death with unresolved clades")
cache$info$ml.default <- "subplex"
update.cache.t(cache, functions,
nonnegative=TRUE, truncate=truncate, with.q=FALSE,
spline.data=spline.data)
}
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