Sets up an initial random infection history, where start is sampled from a prior on the total number of infections across all individuals and years
setup_infection_histories_total( titre_dat, strain_isolation_times, alpha = 1, beta = 1 )
| titre_dat | the matrix of titres data with columns for individual, sample, and titre |
|---|---|
| strain_isolation_times | vector of real times for all strains |
| alpha | alpha parameter for beta distribution to sample from |
| beta | beta parameter for beta distribution to sample from |
an infection history matrix
Other setup_infection_histories:
setup_infection_histories_old(),
setup_infection_histories_titre(),
setup_infection_histories()
data(example_titre_dat) data(example_antigenic_map) start_inf <- setup_infection_histories_total(example_titre_dat, example_antigenic_map$inf_times, 2,10)#> 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 -Inf#> Error in age_mask[i]:strain_mask[i]: NA/NaN argument