greatR 1.0.0

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 depedency.
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().
Simplfied parameters of summarise_registration(), plot_registration_results(), plot_heatmap(), calculate_distance() to simply require results object from register(), vastly simplifing 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().

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).

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

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.

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.

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

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().