dot-estimateAFromSimulations: Get the interspecies interaction matrix A using leave-one-out...
In microbiome/miaSim: Microbiome Data Simulation

.estimateAFromSimulations

R Documentation

Get the interspecies interaction matrix A using leave-one-out method

Description

generate 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`)