Man pages for mrc-ide/squire.page
Functions used in global-lmic-reports-orderly and other repos
| afg_fit | Nimue fit to reported deaths for Afghanistan |
| ar_plot | Plot the attack rate from the model |
| beta_est.booster_min_model | An S3 method for getting Beta for a model |
| beta_est.booster_model | An S3 method for getting Beta for a model |
| beta_est.default | An S3 method for getting Beta for a model |
| bhu_fit | Nimue fit to excess mortality for Bhutan |
| block_interpolate | Convert a vector of parameter values and a vector of the... |
| calc_loglikelihood_booster | Likelihood function for reported deaths with boosters Not for... |
| calc_loglikelihood_variant | Likelihood function for reported deaths with VoC adjustments... |
| cdp_plot | Plot the cumulative deaths from the model |
| compare_adjustment_plot | A diagnostic plot for looking at the infections-based fitting |
| country_immunity_plot | Plot the Rt trends for a country accounting for immunity |
| dp_plot | Plot daily model deaths. |
| excess_log_likelihood | Likelihood function for excess mortality data Not for... |
| excess_log_likelihood_vaccine | Likelihood function for excess mortality with fitted vaccine... |
| extend_vaccine_inputs | Updates vaccine inputs into the future. I.e. prevents... |
| generate_draws | Generate Draws from a model fit. |
| generate_draws.default | Generate Draws from pmcmc run |
| generate_draws.rt_optimised | Generate Draws from pmcmc run |
| generate_parameters | Generate parameter draws from a pmcmc run Code take from... |
| get_covax_iso3c | Get iso3 codes of recipient countries in COVAX |
| get_data_end_date.excess_nimue_simulation | S3 Method to get final date in the data from a model |
| get_data_end_date_inner.excess_nimue_simulation | S3 Method to get start date of the final time-period in the... |
| get_data_end_date_inner.nimue_simulation | S3 Method to get start date of the final time-period in the... |
| get_data_end_date_inner.rt_optimised | S3 Method to get start date of the final time-period in the... |
| get_data_end_date.nimue_simulation | S3 Method to get final date in the data from a model |
| get_data_end_date.rt_optimised | S3 Method to get final date in the data from a model |
| get_data.excess_nimue_simulation | S3 Method to get all the data of a model |
| get_data.nimue_simulation | S3 Method to get all the data of a model |
| get_data.rt_optimised | S3 Method to get all the data of a model |
| get_data_start_date.excess_nimue_simulation | S3 Method to get the start date of the data in a model |
| get_data_start_date.nimue_simulation | S3 Method to get the start date of the data in a model |
| get_data_start_date.rt_optimised | S3 Method to get the start date of the data in a model |
| get_dates.excess_nimue_simulation | S3 Method to get all the start dates of time-periods in the... |
| get_dates_greater.excess_nimue_simulation | S3 Method to get all the end dates of time-periods in the... |
| get_dates_greater.nimue_simulation | S3 Method to get all the end dates of time-periods in the... |
| get_dates_greater.rt_optimised | S3 Method to get all the end dates of time-periods in the... |
| get_dates.nimue_simulation | S3 Method to get all the start dates of time-periods in the... |
| get_dates.rt_optimised | S3 Method to get all the start dates of time-periods in the... |
| get_future_Rt | Calculates the Rt used in the short term scenarios |
| get_gavi_iso3c | Get iso3 codes of recipient countries in GAVI |
| get_global_fund_iso3c | Get iso3 codes of recipient countries in TheGlobalFund |
| get_immunity_ratios | An S3 generic to calculate the proportion of the population... |
| get_immunity_ratios.default | An S3 method to calculate the proportion of the population... |
| get_immunity_ratios.rt_optimised | An S3 method to calculate the proportion of the population... |
| get_income_group | Get the World Bank Income Categories for a given set of iso3... |
| get_parameters.default | S3 Method to get total susceptible population |
| get_parameters.rt_optimised | S3 Method to get total susceptible population |
| get_Rt | Methods to calculate Rt over time from each model type |
| get_WHO_region | Get the WHO Regions for a given set of iso3 codes |
| loadCounterfactualData | A function to load and summarise the deaths averted data |
| nimue_booster_min_model | nimue model creation. |
| nimue_booster_model | nimue model creation. |
| nimue_format | Nimue format that returns just compartments/summaries... |
| pipe | Pipe operator |
| plot.excess_nimue_simulation | Add some adjustments for excess data in plotting nimue... |
| plot.rt_optimised | Essentially just does squire::plot_pmcmc_sample. Not intended... |
| plot.rt_optimised_trimmed | Calls plot.rt_optimised and adds excluded fits . Not intended... |
| pmcmc_drjacoby | Runs an parallel tempering MCMC (drjacoby) on the specified... |
| pmcmc_excess | Runs an adaptive metropolis hasting MCMC on the specified... |
| projections | Provide projections from calibrated simulations by changing... |
| rt_optimise | Fit nimue to a given set of death data via the particle and... |
| rt_plot_immunity | Plot the Rt trends accounting for immunity |
| run_booster | Run the vaccine model |
| sero_plot | Plot the seroprevalence from the model Under some assumptions |
| setup_parameters.booster_min_model | If no particular method we default to calling the parameter... |
| setup_parameters.default | If no particular method we default to calling the parameter... |
| setup_parameters.nimue_model | If no particular method we default to calling the parameter... |
| squire.page-package | squire.page: Functions used in global-lmic-reports-orderly... |
| trim_rt_optimise | Trim an Rt Optimised output |
| update_Rt | Applies new Rt to the data |
