NEWS.md
In mikemc/metacal: Bias estimation and calibration for metagenomics experiments

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
calibrate() now allows bias to be an 'mc_bias_fit' object
Add mean_efficiency() to compute mean efficiency of control or new samples
calibrate() now (by default) computes and adds the mean efficiency to the sample data

metacal 0.2.0

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).