Skip to contents

greatR 1.1.0

CRAN release: 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 timepoint 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.

greatR 1.0.0

CRAN release: 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 depedency.
  • Updated list of exported functions:

Improvements

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).

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

  • 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().

greatR 0.1.0

CRAN release: 2022-01-12

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