Changes in version 2.1.0 (2026-05-04)                  

Changes

  - Aligned num_spline_params used in compare_H1_and_H2() BIC
    calculation with the spline model (5 parameters per curve).
  - calculate_distance() now imputes query expression on the registered
    time grid with impute_query_exp_value() (linear interpolation via
    stats::approxfun()); spline-based imputation remains available as
    impute_query_exp_value_from_spline() for comparison workflows.
  - get_timepoint_comb_data() gains optional cross_join_all to support
    four-quadrant time-point combinations (reference-reference,
    query-query, etc.); ref_ / query_ prefixes are only applied in that
    mode so the default path keeps numeric time points.
  - calculate_distance() and plot.dist_greatR() now handle numeric and
    label-formatted time-point tables more robustly (pre-aggregation
    relabelling removed from distance calculation; plot-side label
    stripping is conditional).

Tooling & Documentation

  - Added maintainer script dev/scripts/rebuild_brapa_registration_rds.R
    (plus notes under dev/) to regenerate
    inst/extdata/brapa_arabidopsis_registration.rds after registration
    changes.
  - dev/full_pipeline_example.Rmd: runnable full pipeline (CSV →
    register() → summaries, curves, distances) for smoke-testing from a
    source checkout.
  - Added here under Suggests for the rebuild script; updated
    Config/roxygen2/version for current {roxygen2}.

Tests

  - Updated unit test expectations for BIC_diff and calculate_distance()
    to match current outputs.

                 Changes in version 2.0.0 (2024-04-09)                  

  - Added {patchwork} as a dependency.
  - Updated {greatR} logo.
  - Updated default optimisation_method in register() to be "lbfgsb"
    (LBFSG-B) instead of "nm" (Nelder-Mead).
  - Added sample SOC1 arabidopsis_SOC1_data.csv and brapa_SOC1_data.csv
    extdata.
  - Refactored optimise_registration_parameters argument in register()
    to use_optimisation.
  - Updated register() to return object of S3 class res_greatR.
  - Updated calculate_distance() to return object of S3 class
    dist_greatR.
  - Refactored summarise_registration() as summary.res_greatR() S3
    method.

Improvements

  - Deprecate use of time_delta variable in registration process.
  - Added fun_args (a list of arguments used when calling the function)
    in register() results.
  - Updated summary.res_greatR() to return NA instead of [NA, NA] when
    all genes are non-registered.
  - Added reg_params (table containing distribution of registration
    parameters) to results list in summary.res_greatR() method.
  - Simplified calc_overlapping_percent() calculation.
  - Take into consideration overlapping_percent when applying manual
    registration.
  - Updated logic of calc_variance() for data with no replicates to
    consider expression_value.
  - Updated get_stretch_search_space_limits() and
    get_shift_search_space_limits() to exclude unexplorable regions in
    search space.
  - Improved calculate_distance() and aux get_timepoint_comb_*_data()
    functions to eliminate column selection and renaming inside lapply()
    calls, reducing execution time by up to 25%.
  - Added type ("registered" or "all") and genes_list arguments to
    calculate_distance() to filter genes.
  - Added new unit tests.
  - Updated unit tests, and added S3 class checks where apropriate.
  - Updated vignettes and README diagrams and figures.
  - Updated vignettes with additional examples, comments on arguments,
    and full coverage of all plot() methods.

Bug fixes

  - Fixed get_shift_search_space_limits() to adjust shift space limits
    accordingly to removal of time_delta variable (see 48c943cd).
  - Fixed default overlapping_percent = 0.5 (instead of 50) in
    register_manually().
  - Fixed get_stretch_search_space_limits() to correctly determine lower
    and upper limits when single stretch value is provided.
  - Fixed issue in get_shift_search_space_limits() where range variables
    were not available when calc_mode == "bound".

New functions

  - bind_results() auxiliary function to merge results from register().
  - theme_greatR() function and greatR_palettes list.
  - transform_input() S3 generic to accept different types of input in
    register().
  - plot.res_greatR() S3 method to replace plot_registration_results().
  - plot.dist_greatR() S3 method to replace plot_heatmap().
  - plot.summary.res_greatR() S3 method inspired by
    WVPlots::ScatterHistC().

                 Changes in version 1.1.0 (2024-01-09)                  

  - Added {furrr} and {future} as dependencies.
  - Added num_cores parameter to register() to allow users to run
    registration in parallel.
  - Added exp_sd parameter to register() to allow users to manually set
    up experimental gene expression variance.
  - Updated scaling_method parameter in register() and scale_data() to
    allow no scaling ("none", default), Z-score scaling ("z-score"), and
    min-max scaling ("min-max"), and updated unit tests accordingly.

Improvements

  - Updated register() to perform 3 sequential registrations when using
    Nelder-Mead, this improves the results of optimal stretch and shift
    parameters.
  - Updated calc_loglik() to use sigma_squared in every time point in
    the sum.
  - Updated scaled_data() and preprocess_data() to return all_data
    object only, instead of a list() containing all_data.
  - Updated compare_H1_and_H2() to return BIC_diff column (BIC_combined
    - BIC_separate), instead of BIC_combined and BIC_separate on their
    own.
  - Updated explore_manual_search_space() to use BIC_diff instead of
    BIC_combined to calculate best_params from model_comparison table.
  - Updated register() to perform 3 sequential registrations when using
    Nelder-Mead, this improves the results of optimal stretch and shift
    parameters. This may be reverted by tweaking neldermead() parameters
    to ensure correct convergence.
  - Added optional stretch_init and shift_init to
    get_search_space_limits(), and updated optimise() to allow for
    different space_lims calculation settings: automatic, given boundary
    box, and given initial coords (new).
  - Removed unused mean_data calculation from preprocess_data() and
    argument from scale_data().
  - Moved "Will process N genes" message from register() to
    preprocess_data() after running filter_*() functions.
  - Ensure results_list$data is arranged/ordered correctly in
    register().
  - Updated get_H*_model_curves() functions to ensure model curves are
    smooth.
  - Updated parse_gene_facets() to display BIC_diff in facet strips.
  - Added plot_mean_data parameter to plot_registration_results().
  - Updated overlapping_percent parameter in register() so it goes
    from 0 to 100 (it's later normalised in the function to avoid
    breakages down the line).
  - Added scaling_method as an attribute in data results from
    register(), this is used in plot_registration_results() to build the
    y-axis label according the the scaling method used.
  - Updated brapa_arabidopsis_registration.rds file with new pipeline
    results.
  - Split get_search_space_limits() into separate aux functions for
    stretch and shift, which allows more stretch and shift input
    combinations.
  - Updated validate_params(..., registration_type = "optimisation") to
    allow more stretch and shift input combinations.

Bug fixes

  - Improved get_timepoint_comb_original_data() and
    get_timepoint_comb_registered_data() to perform cross_join() on a
    single gene_id at a time using lapply(), this fixes "Error: vector
    memory exhausted (limit reached?)" error.
  - Updated match_names() to do double setdiff() to ensure name matching
    is done two ways, and updated corresponding unit test.

New functions

  - filter_incomplete_accession_pairs() to filter out genes that are
    missing one accession.
  - calc_variance() to preprocess data variance inside preprocess_data()
    instead of calc_loglik().
  - Aux register_single_gene_*() functions inside register() to simplify
    and generalise the pipeline for parallel registration.

                 Changes in version 1.0.0 (2023-07-19)                  

  - Rewrote registration pipeline from scratch, deprecating unnecessary,
    and redundant auxiliary functions.
  - Added L-BFGS-B and Nelder-Mead (now default) optimisation methods to
    {greatR}.
  - Switched to manual calculation of log likelihood via calc_loglik()
    instead of stats::logLik().
  - Reduced computation time up to 1000 times, (x30 speed-up from
    package rewrite, and x35 speed-up from switching default
    optimisation method).
  - Removed {dplyr}, {magrittr}, {purrr}, {rlang}, and {stringr} as
    package dependencies.
  - Added {neldermead} as a package dependency.
  - Updated list of exported functions:
      - register()
      - summarise_registration()
      - get_approximate_stretch()
      - plot_registration_results()
      - plot_heatmap()
      - calculate_distance()

Improvements

  - Simplified parameters of main register() function, and added
    scaling_method.
  - Simplified structure of output object of register().
  - Simplified parameters of summarise_registration(),
    plot_registration_results(), plot_heatmap(), calculate_distance() to
    simply require results object from register(), vastly simplifying
    usage.
  - Improved messages, errors, and progress indicators with {cli}.
  - Added correct pluralisation in {cli} messages.
  - Rewrote unit tests to use {data.table} exclusively for data
    manipulation.
  - Added unit tests for calc_loglik_H1(), calc_loglik_H2(),
    calc_overlapping_percent(), calculate_distance(), cross_join(),
    get_search_space_limits_from_params(), get_search_space_limits(),
    objective_fun(), optimise(), plot_heatmap(),
    plot_registration_results(), preprocess_data(), register_manually(),
    register(), summary_registration(), validate_params().

Bug fixes

  - Fixed match_names() call when validating accession names in
    register()
  - Fixed use of deprecated aes_string() by parsing timepoint_var using
    !!ggplot2::sym() call.
  - Fixed preds left join in plot_registration_results().
  - Fixed issue in plot_registration_results() not working when all
    genes are unregistered with type = "registered".
  - Fixed calculation of time_delta in preprocess_data() to ensure it's
    grouped by gene_id and accession (not just accession).

                 Changes in version 0.2.0 (2022-06-08)                  

  - Added Alex Calderwood as package co-author.
  - Added vignette for optimisation process.
  - Refactored num_shifts and shift_extreme parameters by simplified
    shifts parameter.

Improvements

  - Improved default parameter values in exported functions.
  - Added {optimization}, {purrr} as package dependencies.
  - Removed {cowplot}, {ggpubr}, {ggrepel}, {Rtsne}, and {viridis} as
    package dependencies.
  - Cleaned up {cli} messages.
  - Removed legacy AIC references, as it is no longer used.
  - Updated calculate_between_sample_distance() to use
    registration_results as primary parameter instead of mean_df,
    mean_df_sc, and imputed_mean_df.
  - Added warning if there is no comparable time points found using
    users' pre-defined parameters.
  - Refactored optimise_shift_extreme as
    maintain_min_num_overlapping_points, properly defined and corrected
    the boundary box if number overlapping points whether needed to be
    maintained or not.

Bug fixes

  - Check that input accessions exist in the input data in
    get_approximate_stretch().
  - Manually create time point sorting levels for x_sample and y_sample
    columns according in plot_heatmap().
  - Properly handle - character in accession names in plot_heatmap() so
    that time points are parsed correctly.

New features

  - Added optional parameter optimisation process using Simulated
    Annealing through optimise_registration_params().

New functions

  - preprocess_data() to simplify scale_and_register_data() code and
    reuse logic elsewhere.
  - get_best_stretch_and_shift_simplified().
  - get_BIC_from_registering_data().
  - get_boundary_box().
  - optimise_registration_params_single_gene().
  - optimise_registration_params() as wrapper of
    optimise_registration_params_single_gene() for multiple genes.
  - get_best_stretch_and_shift_after_optimisation().

                 Changes in version 0.1.0 (2022-01-12)                  

  - Initial release.
  - Added a NEWS.md file to track changes to the package.