calculate_infection_history_statistics | R Documentation |
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
)
inf_chain |
the data table with infection history samples from |
burnin |
if not already discarded, discard burn in from chain (takes rows where sampno > 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. |
a list of data frames with summary statistics
Other infection_history_plots:
generate_cumulative_inf_plots()
,
plot_data()
,
plot_infection_histories_long()
,
plot_infection_histories()
,
plot_infection_history_chains_indiv()
,
plot_infection_history_chains_time()
,
plot_number_infections()
,
plot_posteriors_infhist()
,
plot_total_number_infections()
data(example_inf_chain)
data(example_antigenic_map)
data(example_titre_dat)
data(example_inf_hist)
strain_isolation_times <- example_antigenic_map$inf_times
## Find number alive in each time period
n_alive <- get_n_alive(example_titre_dat, strain_isolation_times)
## Get actual number of infections per time
n_infs <- colSums(example_inf_hist)
## Create data frame of true ARs
known_ar <- n_infs/n_alive
known_ar <- data.frame("j"=strain_isolation_times,"AR"=known_ar,"group"=1)
## Get true infection histories
known_inf_hist <- data.frame(example_inf_hist)
colnames(known_inf_hist) <- strain_isolation_times
## Need to get group specific n_alive and adjust to correct time frame
n_alive_group <- get_n_alive_group(example_titre_dat, strain_isolation_times,melt_dat = TRUE)
n_alive_group$j <- strain_isolation_times[n_alive_group$j]
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)
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