Calculate FOI log probability vector

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_indiv(phis, infection_history, age_mask, sample_mask)

Arguments

phis

a vector of FOIs

infection_history

the matrix of infection histories

age_mask

the age mask vector as returned by create_age_mask

sample_mask

the sample mask vector giving the last possible infection-time index for each individual

Value

a vector of log probabilities, one for each individual

See also

Other priors: calc_phi_probs(), 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()