PhylogeneticEM (version 1.8.0)

merge_alpha_grids: Merge PhyloEM fits on various grids of alpha values

Description

merge_alpha_grids takes several fits from PhyloEM, and merge them so as to take into account all alpha values. This can be used to break down computations into smaller chunks to be run independently.

Usage

merge_alpha_grids(...)

Value

An object of class PhyloEM, result of the merge.

Arguments

...

objects of class PhyloEM fitted on the same dataset with the same parameters, but different grids of alpha values.

Examples

if (FALSE) {
## Load Data
data(monkeys)
## First fit with coarse grid
res1 <- PhyloEM(Y_data = monkeys$dat,
                phylo = monkeys$phy,
                process = "scOU",
                random.root = TRUE,
                stationary.root = TRUE,
                K_max = 10,
                alpha = c(0.2, 0.3),
                parallel_alpha = TRUE,
                Ncores = 2)
## Second fit with finer grid
res2 <- PhyloEM(Y_data = monkeys$dat,
                phylo = monkeys$phy,
                process = "scOU",
                random.root = TRUE,
                stationary.root = TRUE,
                K_max = 10,
                alpha = c(0.22, 0.24),
                parallel_alpha = TRUE,
                Ncores = 2)
## Thrid fit with redundancies
res3 <- PhyloEM(Y_data = monkeys$dat,
                phylo = monkeys$phy,
                process = "scOU",
                random.root = TRUE,
                stationary.root = TRUE,
                K_max = 10,
                alpha = c(0.26, 0.3),
                parallel_alpha = TRUE,
                Ncores = 2)

## Merge the three
res_merge <- merge_alpha_grids(res1, res2, res3)
## Plot the selected result
plot(res_merge)
## Plot the model selection criterion
plot_criterion(res_merge)
}