sparccboot: Bootstrap SparCC

In zdk123/SpiecEasi: Sparse Inverse Covariance for Ecological Statistical Inference

Bootstrap SparCC

Description

Get bootstrapped estimates of SparCC correlation coefficients. To get empirical p-values, pass this output to pval.sparccboot.

Usage

sparccboot(
  data,
  sparcc.params = list(),
  statisticboot = function(data, indices) triu(do.call("sparcc", c(list(data[indices, ,
    drop = FALSE]), sparcc.params))$Cor),
  statisticperm = function(data, indices) triu(do.call("sparcc",
    c(list(apply(data[indices, ], 2, sample)), sparcc.params))$Cor),
  R,
  ncpus = 1,
  ...
)

Arguments

data	Community count data
sparcc.params	named list of parameters to pass to sparcc
statisticboot	function which takes data and bootstrap sample indices and results the upper triangle of the bootstapped correlation matrix
statisticperm	function which takes data and permutated sample indices and results the upper triangle of the null correlation matrix
R	number of bootstraps
ncpus	number of cores to use for parallelization
...	additional arguments that are passed to boot::boot

zdk123/SpiecEasi documentation built on Oct. 20, 2023, 6:49 a.m.