This function infers a co-abundance network from an abundance table.

This function infers a co-abundance network from an abundance table.

Usage

net_inference (taxa_abs, method)

Arguments

taxa_abs

An abundance table (data.frame) preprocessed with function T_collapse.

method

The method to create the network ("sparcc" or "aracne").

p

When method="sparcc", a threshold between 0-1.

Value

The function returns an igraph object representing the existing co-abundances between nodes at a certain taxonomic level.

Examples

data ("tc_dstoolA")
net_inference (tc_dstoolA, method = "aracne")
#> Warning: the standard deviation is zero
#> IGRAPH ce91ef4 UN-- 152 4 -- 
#> + attr: name (v/c)
#> + edges from ce91ef4 (vertex names):
#> [1] Tsukamurellaceae   --Gallionellaceae                              
#> [2] Hyphomonadaceae    --Armatimonadaceae                             
#> [3] Alicyclobacillaceae--ACK-M1                                       
#> [4] Nitrospiraceae     --ThermoanaerobacteralesFamilyIII.IncertaeSedis