tapnet (version 0.3)

simnetfromtap: Simulates a network from parameters, abundances, traits and phylogeny provided

Description

The workhorse function of this package, called by various other functions to construct a bipartite interaction network

Usage

simnetfromtap(
  traits,
  abuns,
  paramsList,
  pems,
  tmatch_type_pem,
  tmatch_type_obs
)

Arguments

traits

a named ("low"/"high") list of species-named trait data matrices for lower and higher trophic level;

abuns

a named ("low"/"high") list of species-named abundance vectors for lower and higher trophic level;

paramsList

a list of parameter values with six elements: [[1]] and [[2]]: two vectors of linear combination parameters (importance values, one vector for each trophic level); [[3]]: a single shift parameter added to linear combination of higher trophic level PEMs; [[4]]: a single trait matching parameter for the PEMs; [[5]]: a vector of trait matching parameters for observed traits; [[6]]: a non-negative scalar delta to weight the importance of abundances

pems

a named ("low"/"high") list of two species-named data frames (PEMs of lower and higher trophic level);

tmatch_type_pem

type of trait matching function for latent traits (any name accepted by tmatch, currently "normal" and "shiftlnorm");

tmatch_type_obs

type of trait matching function for observed traits (see previous argument).

Value

A named interaction matrix.

Details

Details in here!

References

Benadi et al. in prep