The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.