Changelog

Source: NEWS.md

flocker 1.1-1

  • Fixed single-visit event formatting dropping the dimensions of its index table.
  • Added deterministic characterization tests for packing and reconstruction ahead of the version 2 schema rewrite.

flocker 1.1-02026-10-16

  • Added the twolevel_single model family for single-season occupancy models in which groups of closure units may themselves be structurally absent. Users specify the grouping factor with level2_group, may supply a separate table of group-level predictors with level2_covs, and model group-level occupancy with f_meta.
  • Refactored the data-augmented model as a special case of the general two-level model, with shared data formatting, likelihood, fitting, and post-processing machinery.
  • Breaking change for augmented models: every species supplied in the original obs array must have at least one detection. Never-observed pseudospecies must instead be added through n_aug.
  • Breaking change for augmented models: get_Z() now returns a list containing unit states for species-site combinations and level2 states for species. Generic two-level models use the same return structure. Joint samples from the two levels are mutually consistent.
  • Two-level outputs from get_Z(), log_lik_flocker(), and loo_flocker() now retain user-supplied group names. Augmented models similarly retain supplied species names and assign stable names to augmented pseudospecies.
  • Improved the numerical stability of two-level log-likelihood calculations by evaluating occupancy mixtures in log space.
  • Corrected backward smoothing and backward sampling of latent states from multiseason models so that both use the appropriate transition probabilities and future-data likelihoods.
  • Corrected history-conditioned get_Z() calculations for augmented models and when using new_data, including rep-constant models. Augmented group-level probabilities now marginalize over unit occupancy and incorporate the fitted group-level occupancy probability.
  • Fixed expansion of user-supplied unit and event covariates in simulate_flocker_data() so that values are shared across species at each unit or visit, and allowed make_flocker_data() to accept data-frame observation inputs as documented.
  • Fixed reconstruction of maximally ragged observation and covariate arrays, including multiseason data with a final season that is unobserved in every series, and made post-processing robust when exactly one posterior draw is requested.
  • Fitted models and formatted data objects are now tagged with the version of flocker that created them. Two-level packing metadata is stored separately from the underlying brmsfit data.

flocker 1.0-22026-06-22

  • fixed a bug that resulted in incorrect log likelihoods returned by log_lik_flocker for the data augmented model. Model fitting was not affected, and posteriors were correct.
  • log-likelihood computations now enabled over new data.
  • dramatically improved efficiency in certain post-processing functions for multiseason models
  • CI runs properly
  • backend hygiene improvements
  • updated compatibility with upcoming changes to loo_compare() output structure in the loo package (> 2.9.0), which now returns a data frame instead of a matrix and includes additional diagnostic columns.

flocker 1.0-1

  • fixed a bug that was throwing an uninformative error when making predictions in multiseason models where history_condition is TRUE
  • dramatic efficiency improvements to get_positions as applied to multiseason models.
  • groundwork laid for enabling log-likelihood computations over new data.

flocker 1.0-02024-02-05

  • Initial CRAN submission.
  • Fixed bug in mixed predictive checking.
  • Fixed bug that prevented post-processing with new data with different numbers of visits/seasons than original data.
  • Substantially more thorough unit testing.
  • Removed testing dependency on cmdstanr (not on CRAN)
  • Refactored to avoid shipping large objects as package data