Man pages for BenjamenSimon/EpidemicR
Stochastic modelling and inference for epidemics.
| Avg_acc_probs | Describe the acceptance probabilities. |
| Beta_mat_form | Generate an infection rate matrix. |
| chris_integral_part | Calculate the integral part of the infection likelihood... |
| chris_integral_part_0 | Calculate the integral part of the infection likelihood... |
| chris_interval_intersect | Calculate the interval intersect (Chris' code). |
| chris_interval_intersect_0 | Calculate the interval intersect (Chris' code). |
| chris_log_likelihood | Calculate the log-likelihood for an epidemic, up to a... |
| chris_log_likelihood_0 | Calculate the log-likelihood for an epidemic, up to a... |
| chris_prod_part | Calculate the product part of the infection likelihood... |
| Dist_mat_clust | Clustered population distribution. |
| Dist_mat_edge | Clustered edge population distribution. |
| Dist_mat_latt | Lattice population distribution (with buddy). |
| Dist_mat_lines | Spreading lines population distribution. |
| Dist_mat_trials | Multiple lines population distribution. |
| Dist_mat_unif | Uniform population distribution. |
| Folded_draw | Draw a parameter from a folded Normal distribution |
| GSE_sim | An epidemic simulation |
| Hist_posteriors | Plot the trace plots of the accepted samples. |
| Initialise_2b | Initialise the parameters and infection times. |
| integral_part | Calculate the integral part of the infection likelihood. |
| interval_intersect | Calculate the interval intersect. |
| log_likelihood | Calculate the log-likelihood for an epidemic, up to a... |
| MCMC | Make inference on a General Stochastic Epidemic |
| MCMC_homo | Make inference on a homogeneous General Stochastic Epidemic. |
| MCMC_reparam | Make inference on a General Stochastic Epidemic. |
| MH_accept | Calculate the acceptance probability of a Metropolis-Hastings... |
| MH_accept_MRW | Calculate the acceptance probability of a Metropolis-Hastings... |
| Plot_epidemic | Plot a spatial epidemic. |
| Plot_trace | Plot the trace plots of the accepted samples. |
| P_mat_form | Generate an proportion of maximum infection rate matrix. |
| prod_part | Calculate the product part of the infection likelihood |
| Seed_finder | Find a seed for the desired outbreak size |
| simple_integral_part | Calculate the integral part of the infection likelihood... |
| simple_log_likelihood | Calculate the log-likelihood for an epidemic, up to a... |
| simple_prod_part | Calculate the product part of the infection likelihood... |
