PFWIM Workflow

Introduction

This vignette demonstrates how to use the PFWIM package to infer consumer–resource interactions from trait data, and generate hypothetical realized food webs using a power-law link distribution.

This workflow demonstrates:

1. Inferring feasible interactions with infer_edgelist().
2. Downsampling interactions into hypothetical realized webs with powerlaw_prey().
3. Customizing link distributions via the func argument.

Users can now use these realised webs for network analyses,
simulation studies, or comparisons to fossil and modern food webs.

library(dplyr)
library(tidyr)
library(pfwim)

# Load example data included in the package
data("traits", package = "pfwim")
data("feeding_rules", package = "pfwim")
data("interactions", package = "pfwim")  # internal edgelist for tests

Infer Edgelist

Infer interactions using categorical trait rules

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

head(edgelist)

## # 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

Generate Realised Webs with Power-Law

Generate 5 hypothetical realised webs

realised_webs <- powerlaw_prey(
  el = edgelist,
  n_samp = 5,
  y = 2.5
)

# Inspect first realised web
realised_webs[[1]]

##      resource   consumer
## 9    plankton        cod
## 14    plant_2       deer
## 11    plant_1       deer
## 20       seal       lynx
## 3        deer       lynx
## 16 polar_bear       orca
## 7        orca       orca
## 2         cod polar_bear
## 22       seal polar_bear
## 4        deer polar_bear
## 19        rat polar_bear
## 12    plant_1        rat
## 10   plankton       seal

Customizing the Power-Law Distribution

# Define a custom in-degree distribution function
custom_func <- function(r, M, y) (M - r + 1)^(-y)

realised_webs_custom <- powerlaw_prey(
  el = edgelist,
  n_samp = 5,
  y = 2,
  func = custom_func
)

# First custom web
realised_webs_custom[[1]]

##      resource   consumer
## 9    plankton        cod
## 14    plant_2       deer
## 18        rat       lynx
## 5        lynx       lynx
## 1         cod       orca
## 7        orca       orca
## 16 polar_bear       orca
## 21       seal       orca
## 4        deer polar_bear
## 19        rat polar_bear
## 2         cod polar_bear
## 8        orca polar_bear
## 6        lynx polar_bear
## 22       seal polar_bear
## 12    plant_1        rat
## 15    plant_2       seal