make_postPois_KDE {ontophylo}

Make posterior distribution of NHPP

Description

Produces a posterior distribution from a given list of statistics calculated with the 'posterior_lambda_KDE' function.

Usage

make_postPois_KDE(Edge.KDE.stat, lambda.post, lambda.post.stat = "Mean")

Arguments

Edge.KDE.stat

list. A list with the estimated normalized or loess smoothing KDEs for each edge.

lambda.post

list. A list with the distribution statistics calculated with the 'posterior_lambda_KDE' function.

lambda.post.stat

character. A value with the statistic to be used.

Value

A list with the distribution of the selected statistic for each edge.

Author(s)

Sergei Tarasov

Examples

data("hym_stm_amalg", "hym_kde")
# Get a sample of ten stochastic maps from head.
tree_list <- hym_stm_amalg$head[1:10]
tree_list <- merge_tree_cat_list(tree_list)
# Calculate posterior poisson statistics.
lambda_post <- posterior_lambda_KDE(tree_list)
# Get smoothing of normalized edge KDE data for mean rates.
Edge_KDE <- hym_kde$head
Edge_KDE_stat <- Edge_KDE$Maps.mean.loess.norm
# Make posterior poisson distribution.
Edge_KDE$lambda.mean <- make_postPois_KDE(Edge_KDE_stat, lambda_post, lambda.post.stat = "Mean")
# Check posterior poisson of some arbitrary branch.
plot(density(Edge_KDE$lambda.mean[[5]]), main = "", xlab = "Rates")