Maximum likelihood tree search via NNI — perform_nni • scistreer

Maximum likelihood tree search via NNI

Usage

perform_nni(
  tree_init,
  P,
  max_iter = 100,
  eps = 0.01,
  ncores = 1,
  verbose = TRUE
)

Arguments

tree_init: phylo Intial tree
P: matrix Genotype probability matrix
max_iter: integer Maximum number of iterations
eps: numeric Tolerance threshold in likelihood difference for stopping
ncores: integer Number of cores to use
verbose: logical Verbosity

Value

multiPhylo List of trees corresponding to the rearrangement steps

Examples

tree_list = perform_nni(tree_upgma, P_small)
#> Iter 2 -1615.02320811357, 0.061s
#> Iter 3 -1612.77216335478, 0.059s
#> Iter 4 -1611.12211209167, 0.059s
#> Iter 5 -1609.77582445369, 0.059s
#> Iter 6 -1608.45689338819, 0.059s
#> Iter 7 -1606.49695634113, 0.059s
#> Iter 8 -1606.49695634113, 0.059s