inf_hist_swap: Swap infection history years

In seroanalytics/serosolver: Inference Framework for Serological Data

Swap infection history years

Description

Swaps the entire contents of two columns of the infection history matrix, adhering to age and sample time limitations.

Usage

inf_hist_swap(
  infection_history,
  inf_hist_masks,
  proposal_inf_hist_indiv_swap_ratio,
  proposal_inf_hist_distance,
  proposal_ratios = NULL
)

Arguments

infection_history	matrix of 1s and 0s to swap around representing the infection history
inf_hist_masks	matrix of 1s and 0s corresponding to infection_history, with a 1 where the infection state is eligible to be updated and a 0 otherwise
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?
proposal_ratios	optional NULL. Can set the relative sampling weights of the infection state times. Should be an integer vector of length matching nrow(antigenic_map). Otherwise, leave as NULL for uniform sampling.

Value

the same infection_history matrix, but with two columns swapped

See Also

Other proposals: inf_hist_swap_phi(), 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)
new_inf_hist <- inf_hist_swap(example_inf_hist, age_mask,sample_mask, 1,3)[[1]]

seroanalytics/serosolver documentation built on Dec. 14, 2024, 5:33 a.m.