NEWS

dar 0.99.13

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.

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%.

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.