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greatR 0.2.0

CRAN release: 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

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().

greatR 0.1.0

CRAN release: 2022-01-12

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