phylosamp

• Added a NEWS.md file to track changes to the package.
• Added relR_* functions to the package to allow for sample size and power calculations when estimating differential transmission between groups

What's Changed

• Added functions, vignettes, and unit tests to perform sample size calculations related to the frequency of a pathogen variant, related to this preprint: Sample Size Calculations for Variant Surveillance in the Presence of Biological and Systematic Biases (Wohl, Lee, Diprete, and Lessler 2022)
• Soft deprecation of original functions by replacing them with new function names that match the structure of the newly-added functions.
• Some parameter names in original functions were changed in new function versions
• Users that rely on original functions and old parameter names will receive deprecation warnings
• Added deprecation unit tests to original functions
• Updated unit tests to rely on testthat v3
• Updated README and pkgdown site to describe new manuscript's functions

Full Changelog: https://github.com/HopkinsIDD/phylosamp/compare/v0.1.6...v1.0.0

Updating documentation as requested by CRAN

Citation functionality and updates to documentation.

This release contains minor edits to allowable values in function arguments and edits to documentation, test cases, and vignettes.

First alpha release of the 'phlyosamp' R package. This package implements novel tools that estimate the probability of true transmission between two cases given phylogenetic linkage and the expected number of true transmission links in a sample. The package also contains functions that calculate the sample size needed to correctly identify true pairs at some particular rate.