Get the predicted genomes per person in each subpopulation

Get the predicted genomes per person in each subpopulation

Usage

get_pred_subpop_gen_per_n(
  convolve_fxn,
  n_sites,
  uot,
  ot,
  ht,
  new_i_over_n_site,
  log10_g_prior_mean,
  vl_trajectory
)

Arguments

convolve_fxn

function used to convolve infections with delay pmf. This will typically take convolve_dot_product() function from the wwinference.stan model

n_sites

integer indicating the number of sites

uot

integer indicating the days for exponential growth initialization to occur (referred to as unobserved time)

ot

integer indicating the number of days we will have observed data for in the calibration period

ht

integer indicating the time after the last observed time to

new_i_over_n_site

matrix of n_subpops rows x n total time points columns indicating the per capita infections in each subpopulation

log10_g_prior_mean

log10 scale prior on the number of genomes shed per infection

vl_trajectory

vector of simplex indicating the proportion of all shedding occuring on each day after infection

Value

A matrix of n_sites rows and ot+ ht columns indicating the predicted number of genomes per person per day in each site each day