phylosamp - phylosamp v1.0.1 (CRAN release)

• 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

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Published by shwohl almost 3 years ago

phylosamp - phylosamp v1.0.0

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

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Published by eclee25 about 3 years ago

phylosamp - phylosamp version 0.1.6

Updating documentation as requested by CRAN

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Published by gilesjohnr over 4 years ago

phylosamp - phylosamp version 0.1.5

Citation functionality and updates to documentation.

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Published by gilesjohnr over 4 years ago

phylosamp - phylosamp alpha release v0.1.3

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

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Published by gilesjohnr over 5 years ago

phylosamp - phylosamp alpha release v0.1.1

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.

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Published by gilesjohnr over 5 years ago