Function reference • coiaf

Complexity of Infection

Determine the complexity of infection (COI) of a sample

optimize_coi(): Optimize the COI

likelihood(): Likelihood of a COI

compute_coi(): Predict the COI

compute_coi_regression(): Compute COI based on residuals of all loci against theoretical curves

optimize_coi_regression(): Compute COI based on all points fitted to best fitting curve for COI

theoretical_coi(): Theoretical COI

bootstrap_ci(): Generate bootstrapped CI

Real Data

Process and run real data

process_real(): Process real data

example_real_data: Example real data

Simulation

Simulate data and run algorithm

sim_biallelic(): Simulate biallelic data

process_sim(): Process simulated data

disc_sensitivity(): Discrete Sensitivity analysis

cont_sensitivity(): Continuous sensitivity analysis

Visualize

autoplot(<sim>) plot(<sim>): Plot simulated data

error_plot(): Error plot

sensitivity_plot(): Sensitivity plot

world_map(): World map plot

theme_coiaf(): Custom ggplot2 theme