Tidytacos - v1.0.7

What's changed

• Fix clr abundance bug where the create_tidytacos would not allow negative counts
• Fix bug in tacoplot_prevalence threshold filter

New Contributors

• @TomEile made their first contribution in https://github.com/LebeerLab/tidytacos/pull/74

Full Changelog: https://github.com/LebeerLab/tidytacos/compare/v1.0.6...v1.0.7

Scientific Software - Peer-reviewed - R
Published by TheOafidian 10 months ago

Tidytacos - v1.0.6

What's Changed

• Adds option to keep empty samples when calculating alpha metrics as suggested by #68
• Adds LDA analysis methods
  

Full Changelog: https://github.com/LebeerLab/tidytacos/compare/v1.0.3...v1.0.6

Scientific Software - Peer-reviewed - R
Published by TheOafidian about 1 year ago

Tidytacos - v1.0.3

What's Changed

• Minor changes to tests and mentioning default tax ranks in documentation by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/62

Full Changelog: https://github.com/LebeerLab/tidytacos/compare/v1.0.2...v1.0.3

Scientific Software - Peer-reviewed - R
Published by TheOafidian over 1 year ago

Tidytacos - v1.0.2

What's Changed

• Rank name detection and empty sample checks by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/40
• Add all function arguments to documentation pages
• Add examples of core functionalities by
• Unifrac Distance method

Full Changelog: https://github.com/LebeerLab/tidytacos/compare/v1.0.1...v1.0.2

Scientific Software - Peer-reviewed - R
Published by TheOafidian over 1 year ago

Tidytacos - v1.0.1

What's Changed

• Add different alpha diversity metrics and a plotting function by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/18
• Aggregate taxonomy on trimming by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/20
• Additional diversity metrics by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/21
• Add permanova test to possible pcoa annotations by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/22
• Add bootstrap, pvalues and fdr to networking by @TheOafidian in https://github.com/LebeerLab/tidytacos/pull/23

Full Changelog: https://github.com/LebeerLab/tidytacos/compare/v1.0.0...v1.0.1

Scientific Software - Peer-reviewed - R
Published by TheOafidian almost 2 years ago

Tidytacos - v1.0.0

What's Changed

• Improved function documentation
• Add Mantel test, anosim and interactive option for venndiagram by in https://github.com/LebeerLab/tidytacos/pull/17
• Allow >3 dimensions with add_ord

Full Changelog: https://github.com/LebeerLab/tidytacos/compare/v0.3.0...v1.0.0

Scientific Software - Peer-reviewed - R
Published by TheOafidian about 2 years ago

Tidytacos - tidytacos version 0.3.0

This is the official release of version 0.3.0 of the tidyamplicons package, now renamed to tidytacos! :taco: :tada: :taco:

This version constitutes a major update of the entire package, with many breaking changes. In addition, the package has been renamed to tidytacos (tidy TAxonomic COmpositionS). The package was originally developed by Stijn Wittouck at the Lebeer Lab, but fellow lab members Tim Van Rillaer and Wenke Smets joined the developer team. Together, we streamlined the package, created better documentation and implemented more features. For this reason, in addition to the name change, the package has been moved to the GitHub profile of the Lebeer Lab.

For people familiar with tidyamplicons: the names of some functions, arguments, tables and column names have changed. A notable example is the "abundances" table, which was renamed to "counts". Similarly, the "abundance" column name was renamed to "count". Many similar changes were implemented to make names clearer and more consistent. In addition, many redundant functions were removed. An overview of all tidytacos functions can be found here. Finally, we want to emphasize that tidytacos still follows the familiar tidy philosophy of the tidyverse and tidyamplicons, and no features have been removed.

If you find bugs or have suggestions for new features, don't hesitate to post issues!

For new users of the package, but also for people familiar with tidyamplicons, we recommend to checkout the quick start guide in our brand new wiki.

Have fun diving into your favorite microbial communities!

Scientific Software - Peer-reviewed - R
Published by SWittouck over 2 years ago