NEWS

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dar 1.7.1

dar 1.5.6

• CHANGED: Mark step_metagenomeseq as defunct and remove its implementation and related references.

dar 1.5.5

• CHANGED: Migration from Maaslin2 to maaslin3

dar 1.5.4

• FIXED: Resolved a crash occurring on servers with >128 cores by limiting connection setup based on available R connections.
• CHANGED: Refactored parallel execution to use with(..., local = TRUE). This ensures the internal parallel plan is temporary and does not overwrite the user's global future configuration.

dar 1.5.3

Bug Fixes

• https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues/117

dar 1.1.3

• setp_ancom temporally deactivation

dar 1.1.2

Bug Fixes

• data_import.Rmd

dar 0.99.13

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

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

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.