bioenergmod

The bioenergmod package contains a set of functions developed for bioenergetics modeling, to compare the daily energy requirements of a wildlife population of interest to the daily energy supply available, taking into account dynamic habitat availability and consumption in previous time steps. This was primarily developed with wetland-dependent shorebirds in mind, to account for variation in the proportion of potential habitat that is flooded (i.e. has open water) and variation in the proportion of the open water that is accessible (i.e. shallow enough for use by foraging shorebirds).

References

For details on the model’s structure:
Dybala KE, Reiter ME, Hickey CM, Shuford WD, Strum KM, Yarris GS. 2017. A bioenergetics modeling approach to setting conservation objectives for non-breeding shorebirds in California’s Central Valley. San Francisco Estuary and Watershed Science 15(1). Available from: https://doi.org/10.15447/sfews.2017v15iss1art2

Features

• Accommodates multiple land cover types with differing availability and foraging value
• Accommodates tracking energy supply in all available habitat vs. accessible habitat (e.g. if only a proportion of available habitat is also accessible)
• Includes option for Monte Carlo simulation
• Includes plotting function

Installation

You can install this package directly from R using the devtools package:

devtools::install_github("kdybala/bioenergmod")

Example

library(bioenergmod)

## 1. Calculate daily energy requirements for a shorebird from population size
##   (n), average individual body mass (kg), and assimilation efficiency.
energy.need = calculate_energy_demand(
  n = c(5000, 7000, 10000), bodymass = c(0.1, 0.08, 0.05), 
  metabolism='FMR', assimilation=0.73, plot=FALSE)

## 2. Specify foraging value (kJ/ha) of each land cover type:
energy.density = data.frame(
  habitat = c('A', 'B', 'C'), 
  value = c(20, 15, 12))

## 3. Quantify dynamics of foraging habitat availability:
##    --total area of each land cover type (ha)
total.area = data.frame(
  habitat = c('A', 'B', 'C'), 
  area = c(70000, 150000, 100000))

##    --proportion of total area that is available at each time step 
##      (e.g., flooded)
prop.openwater = data.frame(
  habitat = c(rep('A', 3), rep('B', 3), rep('C', 3)), 
  yday = rep(c(1:3), 3), 
  value = c(0.9, 0.85, 0.95, 
            0.2, 0.5, 0.8, 
            0.5, 0.9, 0.7))

##    --proportion of available area that is accessible at each time step 
##      (e.g. suitable depth)
prop.accessible = data.frame(
  habitat = c(rep('A', 3), rep('B', 3), rep('C', 3)), 
  yday = rep(c(1:3), 3), 
  value = rep(0.9, 9))

## 4. Calculate daily change in foraging habitat availability:
change = calculate_habitat_change(
  tothabitat = total.area, flood = prop.openwater, time = 'yday',
  value = 'value', accessible = prop.accessible, wetsplit = F)

## 5. Run bioenergetics model:
results = run_bioenergmod_loop(
  energyneed = energy.need, 
  energydens = energy.density, 
  habitat.available = change$openwater, 
  habitat.accessible = change$accessible,
  habitat.added = change$added, 
  habitat.returned = change$returned,
  prop.accessible = change$prop.accessible)

## 6. Plot accessible energy supply against daily energy requirement at each 
##    time step:
plot_bioenergmod(
  results$energy.accessible, scale = 1000000, ylab = 'kJ (millions)', 
  der = energy.need, palette = c('#3682C7', '#64AD34', '#F38118')) +
  ggplot2::theme(legend.position = 'right')