Description Usage Arguments Value
Calculate impact matrices from abundance data
1 2 3 4 | 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)
|
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 |
either a dataframe or a list with two matrices
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