Man pages for mrc-ide/YFestimation
Estimate ecological niche and two transmission models for yellow fever in Africa.
| add_1940_1950 | internal fucntion to add early years to population data |
| calc_incidence_vac_general | calculate the first instance of vaccine coverage |
| calc_pop_moments | calculate population moments |
| calc_pop_moments_agg | calculate the population moments for aggregated data |
| calc_t0_vac_africa | get time of first vaccination |
| calculate_bootstrap_Bayes | Calculate Bayes factors and bootstrap for uncertainty |
| calculate_hpd | Calculating the High probability density regions for all... |
| create_pop30_agg_vc30_agg | get aggregated population and vaccination across observation... |
| create_pop_at_survey | get the population at the survey times and places |
| create_R0_lookup | function to calculate aggregated seroprevalence at survey in... |
| fit_glm | fit the glm |
| foi_calculate_seroprevalence | function to calculate aggregated seroprevalence at survey in... |
| fun_calc_pdetect_multi_both | calculate the probability of detection for both models |
| fun_calcPred | calculate predicitions from glm |
| fun_calc_transmission_Africa | calculate the probability of detection for both models |
| get_chains | Import and bind chains for estimation |
| get_pop_data_3d | function to import and get pop data in array |
| GLMlike | likelihood for the GLM parameters |
| GLM_MCMC | mcmc for the GLM parameters |
| GLM_MCMC_step | mcmc step for the GLM parameters |
| GLMprior | Prior distributions for the GLM parameters |
| GLMproposal | Proposal distribution for GLM |
| hpd_out | Internal function to get hpd |
| import_pop_data_LS2014 | old popualtion data import function |
| import_pop_data_LS2017 | population data import function |
| launch_env_dat | load environmental data from path |
| Make_aggregate_pop_vc | aggregating population and vaccination data for serological... |
| Make_aggregate_pop_vc_3d | Aggregate the population and vaccination data into an array |
| Make_pop3d_Ptot2d_Pprop3d | function to reorganise population data |
| mean_fun | Internal mean function |
| plot_glm_map | plot a map of glm output alongside map of data |
| plot_prior_post | Plot the prior and posterior deinsities |
| plot_sero_predictions | plot the seroprevalence predictions with data and credible... |
| plot_transmission_intensity | calculate and plot the transmission intensity across the... |
| process_serology | extract key information from serological data |
| R0_calculate_seroprevalence | function to calculate aggregated seroprevalence at survey in... |
| R0_recurrence_seroprev | function to calculate seroprevalence by recurrence relation... |
| R0_recurrence_seroprev_survey | function to calculate seroprevalence at survey by recurrence... |
| R0_recurrence_seroprev_whole | function to calculate seroprevalence everywhere by recurrence... |
| Sero_Gibbs_MCMC | MCMC for Sero |
| Sero_Gibbs_MCMC_model_step | MCMC model step for Sero |
| Sero_Gibbs_MCMC_parameter_step | MCMC parameter step for Sero |
| Sero_Gibbs_MCMC_step | MCMC step for Sero |
| SEROlike | Likelihood distribution for Sero |
| SEROlike_onesurvey | likelihood for one serological survey in either model |
| SEROprior | Prior distribution for Sero |
| SEROproposal | Proposal distribution for Sero |
| SEROpseudoprior | Pseudo prior probability |
| setup_modelprior | function estimate a value for the model prior in order to... |
| setup_pseudoprior | function estimate a value for the pseudo prior in order to... |
| transform_into_vc3d | get vaccine data into an array |
| YFestimation | YFestimation: Estimate ecological niche and two transmission... |
