NEWS.md
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
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.
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).
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.
The new tutorial demonstrates the new estimation and calibration functions on a new dataset from Leopold and Busby (2020).
coocurrence_matrix() when names were missing (#5).Direct implementation of the methods described in McLaren MR, Willis AD, Callahan BJ (2019) and used for the analysis of that paper.