is.in.ranges: Check whether parameters are in ranges.

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Check whether parameters are in ranges.

Description

is.in.ranges.params checks whether calculated parameters in the EM are in the defined ranges.

Usage

is.in.ranges(p, min, max)

Arguments

min	list of minimum values for the parameters
max	list of maximum values for the parameters
params	list of parameters with the correct structure

Details

###################################################### ## Finite parameters ? ######################################################

is.finite.params.BM <- function(params) if (params$root.state$random) return(is.finite.params.BM.randroot(params)) else return(is.finite.params.BM.fixedroot(params))

is.finite.params.BM.randroot <- function(params) if (is.finite(params$variance) && is.finite(params$root.state$exp.root) && is.finite(params$root.state$var.root) ) return(TRUE) else return(FALSE)

is.finite.params.BM.fixedroot <- function(params) if ( is.finite(params$variance) && is.finite(params$root.state$value.root) ) return(TRUE) else return(FALSE)

is.finite.params.OU <- function(stationary.root, shifts_at_nodes, alpha_known) if (stationary.root && shifts_at_nodes && alpha_known) return(is.finite.params.OU.specialCase) else if (stationary.root && shifts_at_nodes) return(is.finite.params.OU.stationary.root_AND_shifts_at_nodes) else stop("The EM algorithm for the OU is only defined (for the moment) for a stationary root and shifts at nodes !")

is.finite.params.OU.specialCase <- function(params) if (is.finite(params$variance) && is.finite(params$root.state$exp.root) && is.finite(params$root.state$var.root) ) return(TRUE) else return(FALSE)

is.finite.params.OU.stationary.root_AND_shifts_at_nodes <- function(params) if (is.finite(params$variance) && is.finite(params$root.state$exp.root) && is.finite(params$root.state$var.root) && is.finite(params$selection.strength)) return(TRUE) else return(FALSE)

This function is used to test the convergence of the algorithm.

Value

boolean

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.