Changes in version 0.1.2                        

  - Set the coverage to 200 instead of 100 for figures examining the
    overall performance in the sensitivity analysis.

                        Changes in version 0.1.1                        

New vignettes

  - New vignette("example_real_data") illustrates how to use the package
    on your own real data sets.
  - New vignette("sensitivity_analysis_discrete") describes the
    sensitivity analysis for the discrete methods.
  - New vignette("sensitivity_analysis_continuous") describes the
    sensitivity analysis for the continuous methods.
  - New vignette("simulator_details") explains how data is simulated.

New features

  - New bootstrap_ci() function can be used to compute a bootstrapped
    confidence interval for COI estimates (#24, #25).
  - An autoplot and plot method have been written for simulated data
    (#22).
  - Simulated data have been restructured and are now assigned a class
    sim (#22).
  - The default sequence error threshold has been set to 1%.
  - Our methods now can estimate the COI without grouping data points
    into buckets (#17).
  - Within sample minor allele frequencies are now weighed by read
    coverage. If no coverage is supplied, the coverage is assumed to be
    uniform across all loci (#16.)
  - New theme_coiaf() creates a custom theme for this package.

Bug Fixes

  - Midpoint calculation for buckets has been improved. Previously, if
    buckets consisted of a single value, we would combine the bucket
    with another bucket. We no longer do so and let buckets consist of
    only a single value (#19).
  - In our estimation methods, each bucket is now weighed by the number
    of points in each bucket (#15).
  - The Frequency Method is undefined for a COI less than two. When we
    suspect the COI should be less than two, we return NaN. We
    additionally return a note indicating that the COI may be one. If we
    are able to compute the COI, we also return the COI estimated by our
    methods (#14, #21, #23).

Maintenance

  - Fix broken links.
  - Deprecate arguments in favor of newer methods to estimate the COI.
    Arguments deprecated include: comparison, distance, use_bins, and
    bin_size (#26).
  - PLAF has been renamed to PLMAF to indicate the focus is the minor
    allele (#13).
  - WSAF has been renamed to WSMAF to indicate the focus is the minor
    allele (#13).
  - Fix partial argument match warnings.
  - Update license year.
  - The number of dependencies has been reduced.
  - {patchwork} is used instead of {ggpubr} for combining plots.
  - {cli} is now used for messages, warnings, and errors.
  - Superseded functions have been replaced with their alternatives
    (#6).
  - Functions now exit implicitly and visibly (#8).
  - Internal documentation has been improved.
  - COI methods have been renamed for improved clarity. "Method 1" has
    been renamed to "Variant Method" and "Method 2" has been renamed to
    "Frequency Method" (#9).

                        Changes in version 0.1.0                        

  - Initial public release.