FitMatching {cassandRa}

Fit Latent Trait (Matching Model)

Description

Repeatedly fits a latent trait model to a binary interaction network to return a probability matrix

Usage

FitMatching(
  list,
  N_runs = 10,
  maxit = 10000,
  method = "Nelder-Mead",
  ExtraSettings = NULL
)

Arguments

list

Network List

N_runs

Number of start points for k2 and lambda to try. The best (maximum likelihood) half will be used to construct the probability matrix

maxit

Default = 10'000

method

Passed to optim, default = 'Nelder-Mead'

ExtraSettings

Other control settings to pass to optim()

Details

The optimiser is started at values derived from the row-sums and column-sums of a CCA analysis, which correspond closely to latent traits by matching closely related species together.

The k2 and lambda parameters are started from points drawn from a uniform distribution 0:1.

Value

Network list with added 'M_par',the best fitting parameters, 'M_ProbsMatrix', the probability matrix