R/mcmc_help.R
setup_infection_histories_old.RdGiven a matrix of titre data, proposes plausible initial infection histories from which to begin MCMC sampling. NOTE - MIGHT NEED TO UPDATE THIS FOR GROUPS
setup_infection_histories_old( titre_dat, strain_isolation_times, sample_prob, titre_cutoff = 3 )
| titre_dat | the matrix of titres data with columns for individual, sample, and titre |
|---|---|
| strain_isolation_times | vector of real times for all strains |
| sample_prob | given an infection seems likely based on titre, suggest infection with 1 minus this probability |
| titre_cutoff | specifies how high the titre must be to imply an infection |
an nxm matrix of infection histories containing 1s and 0s, where n is the number of individuals and m is the number of potential infecting strains
Other setup_infection_histories:
setup_infection_histories_titre(),
setup_infection_histories_total(),
setup_infection_histories()
data(example_titre_dat) data(example_antigenic_map) start_inf <- setup_infection_histories_old(example_titre_dat, example_antigenic_map$inf_times, 0.2, 3)#> 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[indiv]:strain_mask[indiv]: NA/NaN argument