biomass_estimates: Estimate biomass for each node in a food web

In jdyen/trophic: Trophic Models of Energetics to Estimate Carrying Capacity

Description

Estimation converts production estimates to biomass estimates

Usage

estimate_biomass(production_estimates, pb_ratio)

is.biomass_estimates(x)

## S3 method for class 'biomass_estimates'
print(x, ...)

## S3 method for class 'biomass_estimates'
plot(x, nodes = NULL, settings = list(), ...)

extract_nodes(x, nodes = NULL, FUN = summary, ...)

Arguments

production_estimates	a production_estimates object calculated with production_estimates
pb_ratio	a production:biomass ratio object created with pb_ratio
x	a biomass_estimates object
...	further arguments passed to or from other methods
nodes	integer, character, integer vector, or character vector of nodes to plot (indexed by name or food_web row)
settings	plot settings passed directly to plot
FUN	function used to summarise information extracted from a biomass_estimates object

Value

An object of class biomass_estimates

Examples

library(trophic)
library(future)
plan(multiprocess)

# Construct the component objects
test_fw <- build_food_web(interaction_matrix = food_web)
test_efficiency_matrix <- build_efficiency_matrix(efficiency_mean = efficiency_mean,
                                                  efficiency_sd = 0.01)
test_dominance <- build_dominance_matrix(dominance = dominance_matrix)
test_primary_producers <- build_primary_producers(production_mean = c(1, 2),
                                                  production_sd = c(0.5, 0.5))

# Construct the trophic_dynamics object
test_trophic_dynamics <- build_trophic_dynamics(food_web = test_fw,
                                                efficiency_matrix = test_efficiency_matrix,
                                                dominance_matrix = test_dominance)

# Estimate production values from constructed trophic_dynamics object
production_estimates <- estimate_production(test_trophic_dynamics,
                                            test_primary_producers)

# Create a pb_ratio object
test_pb_ratio <- build_pb_ratio(range = c(0.25, 5.75),
                                probs = c(5, 20, 10, 3, 1, 1, 1))

# Convert production to biomass estimates
biomass_estimates <- estimate_biomass(production_estimates, test_pb_ratio)

# Test if object is of the type 'biomass_estimates'
  
## Not run: 
is.biomass_estimates(x)

## End(Not run)

# Print information about the 'biomass_estimates' object

## Not run: 
print(x)

## End(Not run)

# Plot a 'biomass_estimates' object

## Not run: 
plot(x)

## End(Not run)

# Extract information on one or several nodes from a 'biomass_estimates' object

## Not run: 
extract_nodes(x, nodes = c(5:7), FUN = mean)

## End(Not run)

jdyen/trophic documentation built on May 15, 2019, 3:19 p.m.