efficiency_matrix: Create an efficiency_matrix object to use in a trophic...

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

Description

An 'efficiency_matrix' object stores the efficiency of energy conversion between a given pair of species. It has two components: average values and standard deviations and is a sub-component of a trophic_dynamics object

Usage

build_efficiency_matrix(efficiency_mean, efficiency_sd = NULL, nsp = NULL,
  ...)

is.efficiency_matrix(x)

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

Arguments

efficiency_mean	a scalar, vector, or matrix denoting average trophic efficiencies between species pairs
efficiency_sd	a scalar, vector, or matrix denoting the standard deviation of trophic efficiencies
nsp	a scalar denoting the number of species in the associated food_web object; only required if efficiency is a scalar
...	further arguments passed to or from other methods
x	an object to print or test as an efficiency object

Value

An object of class efficiency

Note

Scalar value efficiencies are assumed to be constant (on average) for all species. Vector efficiencies are are assumed to apply to prey (not predators) under an assumption that conversion efficiencies are a property of the food not the feeder. Matrix efficiencies are treated identically to food_web interaction matrices but note that efficiency_matrix objects are not checked for loops or cannibalism (so any values on the diagonal or upper triangular of the matrix are ignored).

Examples

library(trophic)

# Load a pre-compiled food_web object

# Construct the efficiency object
test_efficiency_scalar <- build_efficiency_matrix(efficiency_mean = 0.1,
                                                  efficiency_sd = 0.05,
                                                  nsp = 10)

# Vector example
efficiency_vector <- data(example_efficiency_vector)
test_efficiency_vector <- build_efficiency_matrix(efficiency_mean = efficiency_mean[1, ],
                                                  efficiency_sd = 0.05)

# Matrix example 1: fixed standard deviation
test_efficiency_matrix <- build_efficiency_matrix(efficiency_mean = efficiency_mean,
                                                  efficiency_sd = 0.05)

# Matrix example 2: changing standard deviation
test_efficiency_matrix <- build_efficiency_matrix(efficiency_mean = efficiency_mean,
                                                  efficiency_sd = (0.5 * efficiency_mean))

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

## End(Not run)

# Print information about the 'efficiency_matrix' object

## Not run: 
print(x)

## End(Not run)

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