Impute Missing States in Sequences — impute

Fill the gaps in incomplete sequences using a fitted context tree: each missing state is predicted from the longest matching context of the states that precede it. Filling proceeds left to right, so a just-imputed state becomes part of the context for later gaps.

Usage

impute_sequences(tree, newdata, method = c("modal", "prob"), seed = NULL)

Arguments

tree: A transitiontrees.
newdata: Sequences with gaps: a list of character vectors, a character matrix / data.frame (one row per sequence, NA or "" marking a gap), or a single character vector.
method: One of "modal" (default; fill with the most likely state) or "prob" (sample from the predicted distribution).
seed: Integer or NULL. Optional RNG seed, used only when method = "prob".

Value

The same container shape as newdata (list, matrix, data.frame, or character vector) with internal gaps filled.

Details

Only internal gaps are imputed. A run of trailing NA / "" cells (end-of-sequence padding in a wide frame) is left untouched, since there is no observed state after it to mark the sequence as continuing. A sequence that is entirely missing is returned unchanged (there is nothing to condition on).

Examples

seqs <- replicate(60, sample(c("A", "B", "C"), 8, replace = TRUE),
                  simplify = FALSE)
tree <- context_tree(seqs, max_depth = 2L)
gappy <- list(c("A", NA, "C"), c("B", "B", NA, "A"))
impute_sequences(tree, gappy)
#> [[1]]
#> [1] "A" "C" "C"
#> 
#> [[2]]
#> [1] "B" "B" "C" "A"
#>