#### version 0.5 (2020-11-19)

* Rewrite of find_best_fit_solutions() function with simplified method for finding local minima in the distance heat map and new algorithm for removing solutions that are close to a better solution in the heat map grid, i.e. have similar ploidy and cellularity.

* Added filtering options as configurable settings in the Shiny app.

#### version 0.4.1 (2020-10-21)

* Fixed bug in which the MAD distance function was used regardless of what was specified in the Shiny app or when calling the find_best_fit_solutions function.
  
#### version 0.4.0 (2020-07-23)

* Added scaling of copy number values by the median segmented copy number so that these are centred on a value of 1, i.e. relative to the average copy number for the whole genome, in the Shiny app and fit_absolute_copy_numbers.R script; added as an option when extracting copy number data from a QDNAseqCopyNumbers object (RDS file) to a tab-delimited file using the extract_qdnaseq_copy_number_data.R script.

* Limiting the number of points to display for bins in the copy number plots is now optional

* Copy number plotting functions now require copy_number column in place of log2ratio column; change made so that these can be more generally used with relative and absolute copy number values as an alternative to log2 ratios.

* Improved handling of log2 ratio range in the Shiny app (increments in limits reduced to 0.25, use of 0.001 and 0.999 percentiles when not fixing the range).

* Added options to set the range of cellularities used in fitting when running the fit_absolute_copy_numbers.R script.

* Improved handling of zero-width range of ploidies or cellularities selected in the Shiny app by instead setting a small range around the set value.

#### version 0.3.0 (2020-03-29)

* Improved pruning of the distance grid to find best bit solutions by grouping candidates by the nearest whole number ploidy and iterative reduction of the multiplier of the minimum distance as a threshold for filtering.

* Improved performance in computing the distance grid by using purrr map function instead of rowwise mutate.

* Restricted the range of cellularities in the Shiny app to between 0.2 and 1.0 with option to change this range in the settings page.

* Added error dialog for attempt to set the ploidy or cellularity to a value outside the allowed range.

#### version 0.2.0 (2020-03-25)

* Added Shiny application for interactive fitting of relative copy number data to absolute copy numbers based by searching a range of ploidies and cellularities.

* Added options for setting the range of ploidies to consider in the `fit_absolute_copy_numbers.R` script.

* New functions:
    * `absolute_copy_number_distance_grid`
    * `find_best_fit_solutions`
    * `distance_heatmap`
    * `start_shiny_app`

#### version 0.1.0 (2020-03-23)

* Initial version with the following functions implemented:
    * `absolute_copy_number_distance`
    * `find_minimum`
    * `is_acceptable_ploidy_and_cellularity`
    * `genome_copy_number_plot`
    * `chromosome_copy_number_plot`
    * `copy_number_density_plot`
    * `absolute_copy_number_distance_heatmap`
    * `absolute_copy_number_scaling_factor`
    * `relative_to_absolute_copy_number`
    * `absolute_to_relative_copy_number`
    * `tumour_fraction`
    * `copy_number_density`
    * `copy_number_maxima`
    * `copy_number_segments`
    * `chromosome_offsets`
    * `convert_to_genomic_coordinates`

* Includes `fit_absolute_copy_numbers.R` script for finding best fit solutions for estimating ploidy and cellularity for scaling relative copy numbers to whole number absolute copy numbers.

* Includes `extract_qdnaseq_copy_number_data.R` script for extracting copy number data from a QDNAseqCopyNumbers object stored in an RDS file.

* Includes `copy_number_data` and `genes` data sets available using `data()` and as external data files.