Coabundance analysis using mb as implemented in SpiecEasi

Source: R/correlate.R

This is a wrapper arround function SpiecEasi::spiec.easi with argument method = "mb".

correlate_mb(
  data,
  pulsar.params = list(thresh = 0.05, subsample.ratio = 0.8, ncores =
    getOption("mc.cores"), rep.num = 20, seed = 1337),
  ...
)

Arguments

data

integer matrix of abundance count data. One sample per row and one taxon per column
pulsar.params

list of options passed to pulsar.params
...

further options passed to spiec.easi

References

Kurtz ZD, M?ller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA (2015). “Sparse and compositionally robust inference of microbial ecological networks.” PLoS Comput Biol, 11(5), e1004226.

Meinshausen N, Bühlmann P, others (2006). “High-dimensional graphs and variable selection with the lasso.” The annals of statistics, 34(3), 1436--1462.