gen_dists: Calculate genetic distance distribution

In HopkinsIDD/phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

Calculate genetic distance distribution

Description

Function calculates the distribution of genetic distances in a population of viruses with the given parameters

Usage

gen_dists(
  mut_rate,
  mean_gens_pdf,
  max_link_gens = 1,
  max_gens = NULL,
  max_dist = NULL
)

Arguments

mut_rate	mean number of mutations per generation, assumed to be Poisson distributed
mean_gens_pdf	the density distribution of the mean number of generations between cases; the index of this vector is assumed to be the discrete distance between cases
max_link_gens	the maximum generations of separation for linked pairs
max_gens	the maximum number of generations to consider, if NULL (default) value is set to the highest number of generations in mean_gens_pdf with a non-zero probability
max_dist	the maximum distance to calculate, if NULL (default) value is set to max_gens * 99.9th percentile of mut_rate Poisson distribution

Value

a data frame with distances and probabilities

Author(s)

Shirlee Wohl and Justin Lessler

See Also

Other mutrate_functions: get_optim_roc(), sens_spec_calc(), sens_spec_roc()

Examples

# ebola-like pathogen
R <- 1.5
mut_rate <- 1

# use simulated generation distributions from the provided 'genDistSim' data object
data('genDistSim')
mean_gens_pdf <- as.numeric(genDistSim[genDistSim$R == R, -(1:2)])

# get theoretical genetic distance dist based on mutation rate and generation parameters
gen_dists(mut_rate = mut_rate,
          mean_gens_pdf = mean_gens_pdf,
          max_link_gens = 1)

HopkinsIDD/phylosamp documentation built on May 28, 2023, 3:21 a.m.