Building a Metaweb • pfwim

Introduction

A metaweb represents the set of all potential consumer–resource interactions in a system. In the context of paleoecology, the metaweb captures interactions that are trait-compatible, even if they may not all occur simultaneously in a realised community.

The PFWIM workflow allows users to infer these potential interactions from species trait data and categorical feeding rules.

This vignette demonstrates how to: * Infer a metaweb edgelist using infer_edgelist() * Convert the edgelist into an igraph network * Visualise the resulting food web

library(pfwim)
library(dplyr)
library(igraph)

data("traits", package = "pfwim")
data("feeding_rules", package = "pfwim")

Inferring the Metaweb

The function infer_edgelist() evaluates trait compatibility between species according to a set of categorical feeding rules. It returns an edgelist, where each row represents a feasible interaction.

metaweb_el <- infer_edgelist(
  data = traits,
  cat_combo_list = feeding_rules,
  col_taxon = "species",
  certainty_req = "all",
  hide_printout = TRUE
)

head(metaweb_el)

## # A tibble: 6 × 2
##   taxon_resource taxon_consumer
##   <chr>          <chr>         
## 1 cod            orca          
## 2 cod            polar_bear    
## 3 deer           lynx          
## 4 deer           polar_bear    
## 5 lynx           lynx          
## 6 lynx           polar_bear

Typical edgelists contain:

consumer – the feeding species
resource – the prey species

These edges define the structure of the potential food web.

Converting the Edgelist to an igraph Network

The edgelist can be directly converted into an igraph object, which allows users to compute network statistics and generate visualisations.

metaweb_graph <- graph_from_data_frame(
  metaweb_el,
  directed = TRUE
)

metaweb_graph

## IGRAPH 7dfae95 DN-- 10 22 -- 
## + attr: name (v/c)
## + edges from 7dfae95 (vertex names):
##  [1] cod       ->orca       cod       ->polar_bear deer      ->lynx      
##  [4] deer      ->polar_bear lynx      ->lynx       lynx      ->polar_bear
##  [7] orca      ->orca       orca      ->polar_bear plankton  ->cod       
## [10] plankton  ->seal       plant_1   ->deer       plant_1   ->rat       
## [13] plant_1   ->seal       plant_2   ->deer       plant_2   ->seal      
## [16] polar_bear->orca       polar_bear->polar_bear rat       ->lynx      
## [19] rat       ->polar_bear seal      ->lynx       seal      ->orca      
## [22] seal      ->polar_bear

Visualising the Metaweb

Food webs are directed networks where edges flow from resource → consumer.

set.seed(66)

plot(
  metaweb_graph,
  vertex.size = 35,
  vertex.label.cex = 0.6,
  edge.arrow.size = 0.3,
  layout = layout_with_fr(metaweb_graph),
  main = "Metaweb"
)

This visualisation represents the potential trophic structure of the community based purely on trait compatibility.

Because all feasible interactions are included, metawebs are typically much denser than observed ecological networks.