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coiaf 0.1.2

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

coiaf 0.1.1

New vignettes

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  • Superseded functions have been replaced with their alternatives (#6).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).

coiaf 0.1.0

  • Initial public release.