ImpactMatrix: Calculate impact matrices from abundance data

In DavidGarciaCallejas/DGC: David Garcia-Callejas' functions

Description

Calculate impact matrices from abundance data

Usage

ImpactMatrix(abundance.data, sign.matrix, a.param = c(0.01, 0.01, 0.001, 0.01,
  0.01), x0 = 1, threshold = 0.001, scale.factor = c(0.1, 0.1, 0.5, 0.1,
  0.1), metric = "impact", return.type = "dataframe", my.model = NULL,
  param.list = NULL)

Arguments

abundance.data	abundances vector
sign.matrix	sign matrix
a.param	vector of 5 parameters adjusting the net interaction frequency for each type: in the following order: competition, amensalism, antagonism, mutualism, commensalism
x0	parameter for the logistic function. In principle, 1 works fine for all simulations
threshold	extinction threshold for abundance
scale.factor	factor scaling the strength of each interaction type e.g. a scaling of 1 indicates that the maximum effect of one sp. over another is of the same order of magnitude than the population growth rate. Same order as a.param
metric	which metric is returned? either "impact" (the net impact), "community" (jacobian/community matrix) or "both"
return.type	either matrix or dataframe
my.model	dynamic equations model for calculating the jacobian
param.list	list of parameters for the dynamic model

Value

either a dataframe or a list with two matrices

DavidGarciaCallejas/DGC documentation built on May 6, 2019, 1:54 p.m.