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Route between#232

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dsheldon wants to merge 5 commits intomainfrom
route-between
Open

Route between#232
dsheldon wants to merge 5 commits intomainfrom
route-between

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Implements route_between() which generates synthetic migration routes
conditioned on known locations at specific times using an HMM
forward-filtering-backward-sampling approach.

Also adds forward_filter() (R/forward_filter.R) as a shared internal
helper, to be reused by predict_between() when implemented.

Supports hard observations (x_coord/y_coord/date) and soft observation
potentials (n_active x n_obs matrix). Includes statistical correctness
tests verifying that sampled route marginals match predict() output.
Implements predict_between() which computes marginal probability
distributions at each timestep conditioned on observed locations,
using a HMM forward-backward algorithm.

Also adds backward_filter() (R/backward_filter.R) as an internal
helper, and a vignette (vignettes/route_between.Rmd) demonstrating
both route_between() and predict_between().

Supports hard observations (x_coord/y_coord/date) and soft observation
potentials (n_active x n_obs matrix). Returns log-likelihood of
observations as attribute log_z. Documentation inherits shared parameter
descriptions from route_between().
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