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mikemc/metacal: metacal 0.2.0

Michael McLaren

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).
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