Changes in version 1.1.2                        

Bug Fixes

  - data_import.Rmd

                       Changes in version 0.99.13                       

Bug Fixes

  - Remove humann example form data import vignette

                       Changes in version 0.99.10                       

New Features

  - Reimplementing step_corncob after the return of corncob package to
    cran

                       Changes in version 0.99.9                        

Bug Fixes

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

                       Changes in version 0.99.8                        

Improvements

  - Reducing examples computation time

                       Changes in version 0.99.7                        

Improvements

  - Reducing examples computation time

                       Changes in version 0.99.6                        

Improvements

  - Suggest using BiocManager::install() to install dar dependencies

                       Changes in version 0.99.5                        

Improvements

  - Reducing vignettes computation time

                       Changes in version 0.99.4                        

Improvements

  - Reducing tests and examples computation time

Bug Fixes

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

                       Changes in version 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.

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission.