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 |
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