tapnet (version 0.3)

make_tapnet: Constructs an object of type "tapnet"

Description

Collates networks, traits and phylogenies into a consistent data structure used for all other tapnet functions

Usage

make_tapnet(
  tree_low,
  tree_high,
  networks,
  abun_low = NULL,
  abun_high = NULL,
  traits_low = NULL,
  traits_high = NULL,
  npems_lat = NULL,
  use.all.pems = FALSE
)

Arguments

tree_low

phylogenetic tree of lower trophic level; required;

tree_high

phylogenetic tree of higher trophic level; required;

networks

a single or list of interaction network (as matrix); required;

abun_low

named abundance vector(s) for lower trophic level (single vector or list of vectors); optional;

abun_high

named abundance vector(s) for higher trophic level; optional;

traits_low

lower trophic level traits (species x traits matrix with row and column names); optional;

traits_high

higher trophic level traits (species x traits matrix with row and column names; optional;

npems_lat

number of phylogenetic eigenvectors to be used to construct latent traits. If NULL, all eigenvectors will be used.

use.all.pems

option to force the function to use all phylogenetic eigenvectors, not only those useful for describing the specific network's species.

Value

A tapnet object, i.e. an thoroughly organised list with the inputs as entries. If multiple networks are provided, each has its own list entry, with PEMs, traits and abundances given for each network separately, in addition to the overall phylogenetic eigenvectors across all networks. See example for, well, for an example.

Details

Tapnet objects are the starting point for almost all other tapnet functions. They contain the information on the species and the (quantitative) interaction network data.

References

Benadi et al. in prep

Examples

# NOT RUN {
data(Tinoco)
tapnet_web1 <- make_tapnet(tree_low = plant_tree, tree_high = humm_tree, networks = networks[1], 
               traits_low = plant_traits, traits_high = humm_traits, npems_lat = 4)
str(tapnet_web1) # show tapnet structure

# }