Swap infection history years with phi term

Source: R/proposal_infection_history.R

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

inf_hist_swap_phi(
  infection_history,
  phis,
  age_mask,
  strain_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
strain_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_titre_dat)
data(example_antigenic_map)
times <- example_antigenic_map$inf_times
ages <- unique(example_titre_dat[,c("DOB","individual")])
age_mask <- create_age_mask(ages$DOB, times)
strain_mask <- create_strain_mask(example_titre_dat, times)
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phis <- runif(length(times))
n_alive <- get_n_alive(example_titre_dat,times)
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new_inf_hist <- inf_hist_swap_phi(example_inf_hist, phis, age_mask,strain_mask, 1,3, n_alive)