Given a vector of FOIs for all circulating years, a matrix of infection histories and the vector specifying if individuals were alive or not, returns the log probability of the FOIs given the infection histories.
calc_phi_probs(phis, infection_history, age_mask, sample_mask)a vector of FOIs
the matrix of infection histories
the age mask vector as returned by create_age_mask
the sample mask vector giving the last possible infection-time index for each individual
a single log probability for the infection histories
Other priors:
calc_phi_probs_indiv(),
calc_phi_probs_spline(),
create_prob_shifts(),
dbb_prior(),
density_beta_binom(),
find_beta_prior_mode(),
find_beta_prior_with_mean(),
find_beta_prior_with_mean_var(),
fit_beta_prior(),
fit_normal_prior(),
inf_mat_prior(),
infection_history_prior(),
prob_shifts()