Get the interspecies interaction matrix A using leave-one-out method
Source:R/utils.R
dot-estimateAFromSimulations.Rdgenerate matrix A from the comparisons between simulations with one absent species and a simulation with complete species (leave-one-out)
Usage
.estimateAFromSimulations(
simulations,
simulations2,
n_instances = 1,
t_end = NULL,
scale_off_diagonal = 0.1,
diagonal = -0.5,
connectance = 0.2
)Arguments
- simulations
A list of simulation(s) with complete species
- simulations2
A list of simulation(s), each with one absent species
- n_instances
Integer: number of instances to generate (default:
n_instances = 1)- t_end
Numeric: end time of the simulation. If not identical with t_end in params_list, then it will overwrite t_end in each simulation (default:
t_end = 1000)- scale_off_diagonal
Numeric: scale of the off-diagonal elements compared to the diagonal. Same to the parameter in function
randomA. (default:scale_off_diagonal = 0.1)- diagonal
Values defining the strength of self-interactions. Input can be a number (will be applied to all species) or a vector of length n_species. Positive self-interaction values lead to exponential growth. Same to the parameter in function
randomA. (default:diagonal = -0.5)- connectance
Numeric frequency of inter-species interactions. i.e. proportion of non-zero off-diagonal terms. Should be in the interval 0 <= connectance <= 1. Same to the parameter in function
randomA. (default:connectance = 0.2)