generate_random_community: Pseudo-random community generator

In ecolTest: Community Ecology Tests

Description

This function generates a random community sample dataset that has a user-specified Shannon diversity index, species number, and total abundance.

Usage

generate_random_community(
  H_index,
  shannon.base = exp(1),
  sp_num,
  ntotal,
  tol = 1e-04,
  maxiter = 100,
  silent = FALSE
)

Arguments

H_index	The value of the generated communty Shannon diversity index H'.
shannon.base	A numeric value indicating the logarithm base for the Shanon indices. Defaults to e.
sp_num	Numeric. The number of species in the generated community sample.
ntotal	Numeric. The total number of individuals in the generated community sample.
tol	Numeric. The tolerance of the diffrence of the diversity index of the generated community relative abundance and the H_index argument. Defaults to 0.0001.
maxiter	Numeric. The maximum number of iterations to be performed. Defaults to 100.
silent	Logical. Indicates if convergence success or failure messages are omitted. Defaults to FALSE.

Details

This function generates random community sample data: a numeric vector whose elements represent a sample. The generated sample data is composed of a number of species with a total number of individuals set by the user, such that the community has a Shannon diversity index approximately equal to a user-specified argument.

Value

A list containing the following components:

• community: If convergence is successful, a numeric vector with the abundance of each species, else NA

• n_ite: If convergence is successful, the number of iterations used to achieve convergence, else NA

Author(s)

David Ramirez Delgado [e-mail]

Hugo Salinas [e-mail]

Examples

# Generate a community with diversity index 2, composed of 20 species
# and 200 total individuals sampled
set.seed(26)
result <- generate_random_community(H_index = 2.7, sp_num = 20, ntotal = 200,
 maxiter = 300)
random_community <- result$community

#Compute H index
total <- sum(random_community)
-sum(random_community/total*log(random_community/total))

#Default maxiter argument will not converge
set.seed(26)
generate_random_community(H_index = 2.7, sp_num = 20, ntotal = 200)

ecolTest documentation built on Feb. 15, 2021, 5:06 p.m.