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Summary and Parameter Estimation for BetNet Output

Source: R/summary_betnet.R
summary_betnet.Rd

Processes MCMC output from BetNet, generates convergence plots, calculates posterior means for parameters, reconstructs the most likely transmission network, and identifies direct transmission events.

Usage

summary_betnet(
  betnet_output_file,
  snp_file,
  time_file,
  burnin = 0.1,
  genome_size = 1e+06,
  plot = TRUE
)

Arguments

betnet_output_file

String. Path to the CSV output from BetNet.

snp_file

String. Path to the CSV file containing observed SNP differences.

time_file

String. Path to the CSV file containing onsite and removal times.

burnin

Numeric. Proportion of initial iterations to discard (default 0.1).

genome_size

Numeric. Size of the genome in base pairs (default 1,000,000).

plot

Logical. If TRUE, displays MCMC trace plots.

Value

A list containing:

  • theta: Posterior mean of the theta parameter.

  • mu: Posterior mean of the mutation rate.

  • infrate: Posterior mean of the infection rate.

  • transmission: A data frame of the reconstructed transmission network.