callTools: Call tools to infer networks

In ramellose/NetworkUtils: Network analysis utitilities for "From hairballs to hypotheses: biological insights from microbial networks"

Description

Infer networks using SpiecEasi, Spearman or gCoda

Usage

callTools(alldata, klemmadj, toolnames, setname, x, n, absolute = FALSE,
  mode = "env")

Arguments

alldata	list of datasets with simulated counts
klemmadj	list of Klemm matrices
toolnames	list of toolnames
setname	name of simulation
x	vector specificying environmental strength or removed species
n	number of replicates
absolute	if true: only check for edge presence, not matching sign
mode	"env" or "abundance", env takes environmental strength into account while "abundance" includes species removal

Details

Calls on original implementations of SpiecEasi and gCoda or the CoNet implementation of Spearman. The wrapper also ensures that adjacency matrices are returned that are compatible with other functions.

Value

Returns nothing, but saves .rds files of networks and statistics

ramellose/NetworkUtils documentation built on May 26, 2019, 12:34 a.m.