Most Predictively Divergent Pathways

Returns the top n pathways by Kullback-Leibler divergence from their (k-1)-suffix. These are the pathways whose extended history adds the most predictive information over the shorter one. Pathways whose most likely next state actually flips between orders are marked in the changes_prediction column.

Usage

divergent_pathways(tree, top = 10L, min_count = 1L, flips_only = FALSE)

Arguments

tree

A transitiontrees.

top

Integer. Number of pathways to return. Default 10.

min_count

Integer. Drop pathways with fewer than this many occurrences. Default 1.

flips_only

Logical. If TRUE, return only pathways that flip the most likely next state between orders. Default FALSE.

Value

A data.frame, same columns as tree_pathways, sorted by divergence descending.

Examples

# \donttest{
seqs <- replicate(50, sample(c("A","B","C"), 12, replace = TRUE),
                  simplify = FALSE)
tree <- context_tree(seqs, max_depth = 3)
divergent_pathways(tree, top = 6)
#>       pathway depth count likely_next next_probability divergence
#> 1 A -> A -> B     3    12           A        0.5825833  0.5737596
#> 2 C -> A -> B     3    19           C        0.5263158  0.2240645
#> 3 A -> B -> A     3    14           B        0.5714286  0.2173227
#> 4 B -> C -> A     3    17           A        0.5882353  0.1732741
#> 5 B -> B -> A     3    17           A        0.4705882  0.1606417
#> 6 C -> C -> B     3    12           B        0.5000000  0.1107270
#>   changes_prediction
#> 1               TRUE
#> 2               TRUE
#> 3               TRUE
#> 4              FALSE
#> 5              FALSE
#> 6              FALSE
divergent_pathways(tree, flips_only = TRUE)
#>        pathway depth count likely_next next_probability divergence
#> 1  A -> A -> B     3    12           A        0.5825833 0.57375959
#> 2  C -> A -> B     3    19           C        0.5263158 0.22406455
#> 3  A -> B -> A     3    14           B        0.5714286 0.21732269
#> 7  C -> A -> A     3    21           A        0.4761905 0.10217770
#> 8  A -> C -> A     3    21           B        0.4285714 0.09413230
#> 11 B -> A -> C     3    13           B        0.5384615 0.06615899
#> 12 C -> B -> A     3    13           C        0.4615385 0.06590266
#> 15 C -> B -> C     3    18           A        0.4444444 0.05257821
#> 17 A -> A -> A     3    20           B        0.4000000 0.04762184
#> 18 B -> C -> B     3    23           C        0.4347826 0.04672169
#>    changes_prediction
#> 1                TRUE
#> 2                TRUE
#> 3                TRUE
#> 7                TRUE
#> 8                TRUE
#> 11               TRUE
#> 12               TRUE
#> 15               TRUE
#> 17               TRUE
#> 18               TRUE
# }