Infer networks using SpiecEasi, Spearman or gCoda
callTools(alldata, klemmadj, toolnames, setname, x, n, absolute = FALSE, mode = "env")
| 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 |
Returns nothing, but saves .rds files of networks and statistics
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.