greatR 0.2.0

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.

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().