YFestimation: YFestimation: Estimate ecological niche and two transmission...

In mrc-ide/YFestimation: Estimate ecological niche and two transmission models for yellow fever in Africa.

Description

The YFestimation package estimates ecological niche model (GLM) and two transmission models (SERO) for yellow fever. The GLM is estimated using conventional MCMC and the two transmission models are estimated with product space MCMC allowing the user to find the model evidence for one relative to the other. Models are based on Garske et al. (2014) and Jean et al. (2019). The estimation approaches are detailed in Gaythorpe et al. (2019).

YFestimation functions

GLM_MCMC GLM_MCMC_step GLMlike GLMprior GLMproposal Make_aggregate_pop_vc Make_aggregate_pop_vc_3d R0_calculate_seroprevalence R0_recurrence_seroprev R0_recurrence_seroprev_survey R0_recurrence_seroprev_whole SEROlike SEROlike_onesurvey SEROprior SEROproposal SEROpseudoprior Sero_Gibbs_MCMC Sero_Gibbs_MCMC_model_step Sero_Gibbs_MCMC_parameter_step Sero_Gibbs_MCMC_step add_1940_1950 calc_incidence_vac_general calc_pop_moments calc_pop_moments_agg calc_t0_vac_africa calculate_bootstrap_Bayes calculate_hpd create_R0_lookup create_pop30_agg_vc30_agg create_pop_at_survey fit_glm foi_calculate_seroprevalence fun_calcPred fun_calc_pdetect_multi_both fun_calc_transmission_Africa get_chains get_pop_data_3d hpd_out import_pop_data_LS2014 import_pop_data_LS2017 launch_env_dat plot_glm_map plot_prior_post plot_sero_predictions plot_transmission_intensity process_serology setup_modelprior setup_pseudoprior transform_into_vc3d

mrc-ide/YFestimation documentation built on March 13, 2021, 1:40 p.m.