Man pages for mrc-ide/gonovax
Deterministic Compartmental Model of Gonorrhoea with Vaccination
| adjust_baseline | adjust model run in absence of vaccination so diagnoses are... |
| aggregate | aggregate model runs by vaccination group x vaccine strata |
| compare | Calculate the log likelihood of the data given the parameters... |
| compare_baseline | compare model runs with vaccination to a baseline runs |
| compare_baseline_xpvwrh | compare model runs with vaccination to a baseline run for the... |
| compare_basic | Calculate the log likelihood of the data given the parameters |
| create_diagnosis_waning_map | Create mapping for movement between strata due to diagnosis... |
| create_uptake_map | Creates uptake mapping array with dimensions n_group x n_vax... |
| create_uptake_map_xpvwrh | Creates uptake mapping for the branching XPVWRH model where... |
| create_uptake_map_xvw | Creates uptake mapping array with dimensions n_group x n_vax... |
| create_uptake_map_xvwr | Creates uptake mapping array with dimensions n_group x n_vax... |
| create_uptake_map_xvwv | Creates uptake mapping array with dimensions n_group x n_vax... |
| create_vax_map | Create mapping for movement between strata due to vaccination |
| create_vax_map_branching | Create mapping for movement between strata due to vaccination... |
| create_waning_map | Create mapping for movement between strata due to vaccine... |
| create_waning_map_branching | Create mapping for movement between strata due to vaccine... |
| create_waning_map_trial | Create mapping for movement between strata due to vaccine... |
| dbetabinom | pdf of a betabinomial parametrised in terms of probability... |
| extract_flows | extract flows used for run_grid |
| extract_flows_trial | extract flows for the XVW trial model |
| extract_flows_xpvwrh | extract flows used for run_grid when the branching xpvwrh... |
| gen_erlang_labels | generates the appropriate strata labels for the number of... |
| gen_labels | generates the appropriate strata labels for the number of... |
| gen_trial_labels | generates the appropriate strata labels for the number of... |
| gono_params | Posterior parameters of gonorrhoea natural history |
| gono_params_trial | Posterior parameters of gonorrhoea natural history |
| gonovax_data | Get gonovax data |
| gonovax_year | Convert a year into the number of years after 2009 |
| gonovax_year_as_year | Convert a gonovax year into calendar years |
| initial_params | Initial conditions for the model |
| initial_params_trial | Initial conditions for the model trial where the entire... |
| initial_params_xpvwrh | Initial conditions for the model |
| initial_params_xvwrh | Initial conditions for the model |
| initial_params_xvw_trial | Initial conditions for the model in a vaccine trial |
| mcmc | Run a mcmc sampler |
| mcmc_combine | Combine mcmc samples |
| mcmc_thin | Thin a mcmc chain |
| model | Model of gonorrhoea with dual vaccines This is an odin model. |
| model_params | Parameters for the dualvax model |
| model_params_trial | Parameters for the vaccination trial model |
| model_params_xpvwrh | Parameters for the dualvax model |
| restart_hes | uses XPVWRH model run in the absence of vaccination or... |
| restart_params | Create initial conditions to start the model from the end of... |
| run | Run odin model of gonorrhoea with or without vaccination |
| run_grid | run model from equilibrium with single vaccine at the input... |
| run_onevax_xpvwrh | run model with a two-dose vaccine for input parameter sets,... |
| run_onevax_xvw | Run model with single vaccine for input parameter sets,... |
| run_onevax_xvwr | run model with single vaccine for input parameter sets,... |
| run_onevax_xvwrh | run model with single vaccine for input parameter sets,... |
| run_onevax_xvw_trial | Run model with single vaccine for input parameter sets,... |
| run_onevax_xvwv | run model with single vaccine for input parameter sets,... |
| run_trial | Run odin model of gonorrhoea vaccine trial with or without... |
| run_xpvwrh | Run odin model of gonorrhoea with or without vaccination |
| set_protection | generates vector which tells the model which strata are under... |
| set_strategy | Translate each named vaccine strategy into a format... |
| stratum_index_xpvwrh | Generate the indices of all xpvwrh strata |
| stratum_index_xvw | Generate the indices of all xvwv trial strata |
| stratum_index_xvwr | Generate the indices of all xvwr trial strata |
| stratum_index_xvwrh | Generate the indices of all xvwrh trial strata |
| stratum_index_xvw_trial | Generate the indices of all xvw trial strata |
| stratum_index_xvwv | Generate the indices of all xvwv trial strata |
| transform | Transform fitted parameters into gonovax params |
| transform_fixed | Transform fitted parameters into non-time-varying gonovax... |
| vax_params0 | create vaccination parameters for use in novax model (null) |
| vax_params_xpvwrh | create vaccination parameters for use in onevax_xpvwrh model |
| vax_params_xvw | Create vaccination parameters for use in onevax_xvw model |
| vax_params_xvwr | create vaccination parameters for use in onevax_xvwr model |
| vax_params_xvwrh | create vaccination parameters for use in onevax_xvwrh model |
| vax_params_xvw_trial | Create vaccination parameters for use in onevax_xvw_trial... |
| vax_params_xvwv | create vaccination parameters for use in onevax_xvwv model |
