Get posterior information infection histories

Source: R/plots.R

Finds the median, mean and 95

calculate_infection_history_statistics(
  inf_chain,
  burnin = 0,
  years = NULL,
  n_alive = NULL,
  known_ar = NULL,
  group_ids = NULL,
  known_infection_history = NULL,
  solve_cumulative = FALSE
)

Arguments

inf_chain

the data table with infection history samples from serosolver
burnin

if not already discarded, discard burn in from chain (takes rows where samp_no > burnin)
years

vector of the epochs of potential circulation
known_ar

data frame of known attack rates, if known.
known_infection_history

data frame of known infection histories.
solve_cumulative

if TRUE, finds the cumulative infection histories for each individual. This takes a while, so is left FALSE by default.

Value

a list of data frames with summary statistics

See also

Other infection_history_plots: generate_cumulative_inf_plots(), plot_data(), plot_infection_histories(), plot_infection_history_chains_indiv(), plot_infection_history_chains_time(), plot_number_infections(), plot_posteriors_infhist(), plot_total_number_infections()

Examples

data(example_inf_chain)
data(example_antigenic_map)
data(example_titre_dat)
data(example_inf_hist)
strain_isolation_times <- example_antigenic_map$inf_times
## Find number alive in each time period
n_alive <- get_n_alive(example_titre_dat, strain_isolation_times)
#> Warning: no non-missing arguments to max; returning -Inf
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## Get actual number of infections per time
n_infs <- colSums(example_inf_hist)
## Create data frame of true ARs
known_ar <- n_infs/n_alive
known_ar <- data.frame("j"=strain_isolation_times,"AR"=known_ar,"group"=1)
#> Error in data.frame(j = strain_isolation_times, AR = known_ar, group = 1): arguments imply differing number of rows: 0, 48, 1
## Get true infection histories
known_inf_hist <- data.frame(example_inf_hist)
colnames(known_inf_hist) <- strain_isolation_times

## Need to get group specific n_alive and adjust to correct time frame 
n_alive_group <- get_n_alive_group(example_titre_dat, strain_isolation_times,melt_dat = TRUE)
#> Warning: no non-missing arguments to max; returning -Inf
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#> Error in melt(n_alive, id.vars = c("group")): could not find function "melt"
n_alive_group$j <- strain_isolation_times[n_alive_group$j]
#> Error in eval(expr, envir, enclos): object 'n_alive_group' not found
results <- calculate_infection_history_statistics(example_inf_chain, 0, strain_isolation_times,
                                                  n_alive=n_alive_group, known_ar=known_ar,
                                                  known_infection_history=known_inf_hist)
#> Padding inf chain...
#> Error in fsetdiff(expanded_values, inf_chain[, c("i", "j", "samp_no", "chain_no",     "group")]): could not find function "fsetdiff"