Changelog • coiaf

coiaf 0.1.2

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

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 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.

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).

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Superseded functions have been replaced with their alternatives (#6).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