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Changelog

Source: NEWS.md

dar 0.99.12

Bug Fixes

  • Remove humann example form data import vignette

dar 0.99.10

New Features

  • Reimplementing step_corncob after the return of corncob package to cran

dar 0.99.9

Bug Fixes

  • Set workers parameter to 4 in order to avoid issues with BBS builds

dar 0.99.8

Improvements

  • Reducing examples computation time

dar 0.99.7

Improvements

  • Reducing examples computation time

dar 0.99.6

Improvements

dar 0.99.5

Improvements

  • Reducing vignettes computation time

dar 0.99.4

Improvements

  • Reducing tests and examples computation time

Bug Fixes

  • Fixing bug in Github Actions on Linux with rlang installation.

dar 0.99.3

New Features

  • The dar package now accepts both phyloseq class objects and TreeSummarizedExperiment as inputs.
  • The tutorial has been refocused to become a tutorial on how to import biom, qiime, mothur, metaphlan, and humann into TreeSummarizedExperiment and phyloseq class objects.
  • The Recipe and PrepRecipe classes have been introduced, replacing the previous recipe and prep_recipe classes.
  • The subset and filter operations have been updated to allow all steps of the recipe to be defined in a chainable manner.
  • The functions step_filter_by_abundance, step_filter_by_prevalence, step_filter_by_rarity, and step_filter_by_variance have been added to enhance filtering functionality.

Improvements

  • The R version dependency has been updated to 4.4.0.
  • The dependency on data.table has been removed.
  • The re-export of %>% and := has been removed. Now code examples and vignettes use |>.
  • The required_deps function is no longer exported.
  • The package now recommends more commonly used installation methods, such as BiocManager::install() or install.packages().
  • A warning message is now displayed whenever the rarefy = TRUE option is used, informing users that a fixed seed is being used and how it could impact their results.
  • The package coverage has increased to 82.33%.

Bug Fixes

  • Unconventional package installation methods have been avoided, for example, pak::pkg_install.
  • The setting of a seed within a function (run_aldex) has been addressed.
  • The name of the data in the R/data.R documentation has been corrected from NA.

dar 0.99.0

  • Initial Bioconductor submission.