Swaps the entire contents of two columns of the infection history matrix, adhering to age and strain limitations.
inf_hist_swap( infection_history, age_mask, strain_mask, proposal_inf_hist_indiv_swap_ratio, proposal_inf_hist_distance, proposal_ratios = NULL )
| infection_history | matrix of 1s and 0s to swap around representing the infection history |
|---|---|
| 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? |
| 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. |
the same infection_history matrix, but with two columns swapped
Other proposals:
inf_hist_swap_phi(),
infection_history_symmetric(),
mvr_proposal(),
univ_proposal()
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)#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Inf#> Warning: no non-missing arguments to max; returning -Infnew_inf_hist <- inf_hist_swap(example_inf_hist, age_mask,strain_mask, 1,3)[[1]]