flocker 1.1-0

• 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 1.0-2

• 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 1.0-0

• 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