Release Notes

Planned changes for future releases

Experiment with extending the treatment knock-out (trtKO) functionality into a likelihood-ratio test for hypothesis testing. Update the tutorial on customizing statistical analyses, if needed.
Autodetect fixed-effect type, e.g., fixed-effect columns of R type “character” or “factor” are treated as two-level categorical factors, and numeric columns are treated as discrete additive effects (e.g., like a time series). Will need to update the RORB tutorial and any other tutorials which discuss time-series modeling.
Ensure any columns flagged as a time series are also treated as fixed-effects.
Add a check during the fit to see if any transition points can be replaced with a slope.
Add variable check to the loading of plot.settings in wisp. Currently only runs check_list without doing a more substantive check. Compare with the more detailed checks of MCMC.settings.
Allow MCMC.prior to be a vector of different prior distributions for each parameter. When completed, update the tutorial on customizing statistical analyses.
Ensure nested loops for matrix operations have the major axis (column) on outside.
Extracellular (out-of-soma) transcripts do not follow a Poisson distribution, and so any attempt to model them with wisp needs to account for this.

Part 2 of a major code refactor/optimization.
Finished refactoring wspc object class and its initialization method into a more organized structure.
Fixed issue in extrapolate_none.
Added option to level preprocessing coordinate transform (the cortical_coordinate_transform function) based on different layers.
Updated Roxygen2 descriptions for user-facing R functions.
Checked all tutorials to ensure they work with current version and removed auto-dating, so their current working version is properly documented. Included footnotes on saved and pre-processed code chunks.
Substantial code cleaning.

Part 1 of a major code refactor/optimization.
Improved algorithm in check_parameter_feasibility for finding nearby feasible initial parameters.
Improved placement of check_parameter_feasibility within the various fit, MCMC, and bootstrap pipelines.
Converted several large-signature stand-alone functions into wspc methods: compute_gamma_dispersion, make_extrapolation_pool, find_count_log_means, estimate_change_points, and estimate_initial_parameters.
Simplified parameter vector handling.
Wrote checks into tutorials, to ensure code changes do not change results.
Replaced some R Lists with std::vector.
Improved weight-matrix construction.
Replaced pcg with std rng, to ease licensing issues.
Removed stan variables from wspc objects.
Replaced R-style masking with numeric indexing for summed count data.
Added print.settings argument splitting_factor_colors to wisp to allow users to specify colors for the splitting factor in ratecount and timeseries plots.
Performed extensive optimization of the code, leading to a x2 or x3 speedup in running wisp.
Documentation updated, but not yet rebuilt.

Added model.settings argument max_bin to wisp which allows users to specify the largest bin number. If left at zero, the function will infer the maximum bin number from the count data.
Aligned matrix nested loops to major axis (column) to improve computational efficiency.
Updated plot.decomposition to allow for multiple contexts.
Fixed plot.timeseries to plot single-block species.
Added LRO parameter grid search option. (Very effective!)
Updated preprocessing functions for making count data.
Fixed batch size for forking.

Added model.settings argument trtKO to wisp which enables excluding treatments to run reduced models.
Replaced corrupted data file “corticallaminar_model.rds” with working version (hopefully for the last time!).
Fixed memory leak related to CI computation.

Release attached to NAR resubmission.
Redesigned plots.
Added attractor simulation functionality and benchmarking.
Includes first-draft versions of package tutorials.
Note that the package data file “corticallaminar_model.rds” was corrupted and should be pulled from the latest version or latest commit on the main branch.

Added discrete time-series modeling functionality (the timeseries variable option) and plotting (the function plot.timeseries).
Ensured code would robustly run for any data including at least count and bin columns, without need for context, species, ran, or fixed-effect variables.
Added explicit fit_only option to wisp to avoid running any parameter estimation (MCMC or bootstrapping).

Initial public release of wispack, as used in this preprint.
Defines the wisp function for implementing wisps.
Introduces one-dimensional warped sigmoidal Poisson-process mixed-effect modeling (one-dimensional wisps) for testing for functional spatial effects in spatial transcriptomics data.