gen_dists {phylosamp} | R Documentation |
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 |
max_dist |
the maximum distance to calculate, if |
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)