inf_hist_swap_phi: Swap infection history years with phi term

In adamkucharski/serosolver: Inference Framework for Serological Data

Swap infection history years with phi term

Description

Swaps the entire contents of two columns of the infection history matrix, adhering to age and strain limitations. Also swaps the values of phi that correspond to these years

Usage

inf_hist_swap_phi(
  infection_history,
  phis,
  age_mask,
  sample_mask,
  proposal_inf_hist_indiv_swap_ratio,
  proposal_inf_hist_distance,
  n_alive
)

Arguments

infection_history	matrix of 1s and 0s to swap around representing the infection history
phis	vector of force of infection parameters for each column
age_mask	the first index in infection_history that each individual (row) could be infected in
sample_mask	the last index in infection_history that each individual (row) could be infected in ie. the time of the latest blood sample
proposal_inf_hist_indiv_swap_ratio	what proportion of infections should be swapped?
proposal_inf_hist_distance	How many time points away should be chosen as candidate swaps?
n_alive	number of individuals alive in each entry of phis

Value

a list: the same infection_history matrix, but with two columns swapped; also the swapped phis

See Also

inf_hist_swap

Other proposals: inf_hist_swap(), infection_history_symmetric(), mvr_proposal(), univ_proposal()

Examples

data(example_inf_hist)
data(example_antibody_data)
data(example_antigenic_map)
times <- example_antigenic_map$inf_times
ages <- unique(example_antibody_data[,c("birth","individual")])
age_mask <- create_age_mask(ages$birth, times)
sample_mask <- create_sample_mask(example_antibody_data, times)
phis <- runif(length(times))
n_alive <- get_n_alive(example_antibody_data,times)
new_inf_hist <- inf_hist_swap_phi(example_inf_hist, phis, age_mask,sample_mask, 1,3, n_alive)

adamkucharski/serosolver documentation built on April 13, 2024, 10:24 a.m.