Man pages for jameshay218/zikaProj
zikaInfer
| average_buckets | Averages a vector based on bucket sizes |
| b.calc | Bite rate calculation |
| calc_deviance | Deviance |
| calc_post_mean | Posterior mean |
| calc_post_var | Posterior variance |
| calculate_AR | Attack rate |
| calculate_BIC | BIC calculation |
| calculate_DIC | DIC |
| calculate_gamma_mode | Gamma mode |
| combine_chains | Combine MCMC chains |
| convert_name_to_location | Location conversion |
| convert_name_to_location_factor | Convert name to factor |
| createLocationParTable | MCMC location-specific parameter table creation |
| createParTable | MCMC parameter table creation |
| create_posterior | Simplify posterior call |
| cumul_true | Cumulative true |
| density.calc | Density calculation |
| density_plot_func | Microcephaly parameter density plot |
| density_plot_state | Posterior density plot |
| exampleParTab | Example parameter table |
| extra_microceph_calculations | Post calculations |
| find_peak_times | Find peak times |
| forecast_CRS | Model function for CRS prediction |
| forecast_microceph | Microcephaly incidence forecast |
| fromUnitScale | Converts to linear scale |
| generateAllowableParams | Generate allowable starting parameters |
| generate_foi | FOI calculation |
| generate_micro_curve | Generate microceph curve |
| generate_multiple_data | Simulation multi-state microcephaly and incidence data |
| generate_plot_date_labels | Generate date labels |
| generate_probM | Time varying microcephaly risk |
| generate_probM_aux | Time varying microcephaly risk AUX |
| generate_probM_forecast | Time varying microcephaly risk not aborted |
| generate_probM_forecast_OLD | Time varying microcephaly risk AUX |
| generate_riskI | Risk of infection |
| generate_riskS | Cumulative susceptible probability |
| generateStartingParTab | MCMC start parTab |
| generate_y0s | Generates y0s |
| get_best_pars | Best pars |
| get_correct_order | Location order |
| getDaysPerMonth | Get days per month of the year |
| get_epidemic_locations | Subset epidemic locations |
| get_index_pars | Index pars |
| get_lower_micro_bound | Lower microcephaly risk bound |
| get_max_micro | Max micro risk |
| get_max_micro_day | Max micro risk day |
| get_microceph_range | Microcephaly risk range |
| get_upper_micro_bound | Upper microbound |
| incidence_likelihood | Incidence likelihood (binomial) |
| incidence_likelihood_norm | Incidence likelihood (normal) |
| isolate_location | Isolate location from chain |
| likelihood_probM | Likelihood function for time-varying microcephaly |
| likelihood_probM_norm | Likelihood function for time-varying microcephaly |
| load_mcmc_chains | Load MCMC chains |
| locationInfo | Location information table |
| make_micro_dat | Format MCMC chain |
| median.quantile | Median and quantiles |
| microceph_v1 | Microcephaly risk V1 |
| microceph_v2 | Microcephaly risk V2 |
| microceph_v3 | Microcephaly risk V3 |
| microceph_v4 | Microcephaly risk V4 |
| mvr_proposal | Multivariate proposal function |
| parTabSetup | Parameter setup |
| parTabSetup_aux | MCMC parameter setup |
| plot_best_trajectory_multi | Plot all best trajectoroes |
| plot_best_trajectory_single | Plot single best trajectory |
| plot_MCMC | Plot MCMC chains |
| plot_micro_bounds | Plot microcephaly curves with bounds |
| plot_random_microceph_curves | Plot microceph curves |
| plot_setup_data | Get plot data |
| posterior_complex_buckets | Posterior function for the simple SEIR model with bucketed... |
| posterior_CRS | Posterior function for CRS prediction |
| posterior_inc | Posterior function for the simple SEIR model with incidence... |
| posterior_known_inc | Posterior function for forecast |
| posterior_known_inc_seir | Posterior function for forecasting analysis |
| posterior_simple_buckets | Posterior function for the simple SEIR model with bucketed... |
| print_version_names | Risk window names |
| proposalfunction | MCMC proposal function |
| r0.calc | R0 calculation |
| r0.vector | R0 vector calculation |
| read_all_data | Read all data |
| read_inipars | Read partab |
| rm_scale | Step size scaler |
| run_metropolis_MCMC | Adaptive Metropolis-within-Gibbs Random Walk Algorithm. |
| scaletuning | Scale step sizes |
| setupListPars | Default parameter list setup |
| setupLocationParTable | Setup location specific parameter table |
| setupParsLong | Default simulation parameters |
| setupParsODE | Defaults ODE parameters |
| simeq | Attack rate simeq |
| solveSEIRModel | Solve simple SEIR model |
| solveSEIRModel_lsoda | Solve simple SEIR model (lsoda) |
| solveSEIRModel_rlsoda | Solve simple SEIR model (rlsoda) |
| sum_buckets | Sums a vector based on bucket sizes |
| summarise_chain | Summarise MCMC chain |
| sum_n_vector | Sums nth elements |
| to.png | PNG - Rich's function to print to device without potential... |
| to.svg | SVG - Rich's function to print to device without potential... |
| toUnitScale | Converts to unit scale |
| zikaInfer | zikaInfer |
