metacal (development version)

  • build_matrix() now works correctly on grouped tibbles

  • pairwise_ratios() now correctly handles phyloseq objects with just 1 sample or taxon, and is properly exported

  • estimate_bias() now allows observed to have extra samples and taxa not in actual, by automatically subsetting to those in actual

metacal 0.2.0

New features

New estimation and calibration functions

estimate_bias() and calibrate() provide easy-to-use high-level interfaces to the original metacal bias-estimation and calibration method. Their use is illustrated in the new tutorial.

New utility functions

  • pairwise_ratios() allows computing ratios between pairs of taxa and/or samples.

  • perturb() applies a compositional perturbation to all observations in an abundance matrix (or phyloseq object).

Support for phyloseq objects

The new functions estimate_bias(), perturb(), calibrate(), and pairwise_ratios() all work with objects from the phyloseq package as well as plain matrices. Phyloseq is now a required dependency, though may be made optional in the future.

New tutorial

The new tutorial demonstrates the new estimation and calibration functions on a new dataset from Leopold and Busby (2020).

Minor fixes

  • Fixed failure of coocurrence_matrix() when names were missing (#5).

metacal 0.1.0

Direct implementation of the methods described in McLaren MR, Willis AD, Callahan BJ (2019) and used for the analysis of that paper.