Function reference • squire.page

All functions

afg_fit: Nimue fit to reported deaths for Afghanistan

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 times it changes into a time-series of the parameter values.

dp_plot(): Plot daily model deaths.

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 squire:::sample_pmcmc()

get_WHO_region(): Get the WHO Regions for a given set of iso3 codes

get_covax_iso3c(): Get iso3 codes of recipient countries in COVAX

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_end_date(<excess_nimue_simulation>): S3 Method to get final date in the data from a model

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_end_date_inner(<excess_nimue_simulation>): S3 Method to get start date of the final time-period in the data from a model

get_data_end_date_inner(<nimue_simulation>): S3 Method to get start date of the final time-period in the data from a model

get_data_end_date_inner(<rt_optimised>): S3 Method to get start date of the final time-period in the data from 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 data of a model

get_dates(<nimue_simulation>): S3 Method to get all the start dates of time-periods in the data of a model

get_dates(<rt_optimised>): S3 Method to get all the start dates of time-periods in the data of a model

get_dates_greater(<excess_nimue_simulation>): S3 Method to get all the end dates of time-periods in the data of a model

get_dates_greater(<nimue_simulation>): S3 Method to get all the end dates of time-periods in the data of a model

get_dates_greater(<rt_optimised>): S3 Method to get all the end dates of time-periods in the data of a model

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 immune

get_immunity_ratios(<default>): An S3 method to calculate the proportion of the population immune

get_immunity_ratios(<rt_optimised>): An S3 method to calculate the proportion of the population immune

get_income_group(): Get the World Bank Income Categories for a given set of iso3 codes

get_parameters(<default>): S3 Method to get total susceptible population

get_parameters(<rt_optimised>): S3 Method to get total susceptible population

loadCounterfactualData(): A function to load and summarise the deaths averted data

nimue_booster_model(): nimue model creation.

nimue_format(): Nimue format that returns just compartments/summaries requested

plot(<excess_nimue_simulation>): Add some adjustments for excess data in plotting nimue simulations.

plot(<rt_optimised>): Essentially just does squire::plot_pmcmc_sample. Not intended for use otherwise.

plot(<rt_optimised_trimmed>): Calls plot.rt_optimised and adds excluded fits . Not intended for use otherwise.

projections(): Provide projections from calibrated simulations by changing RO, contact matrices or bed availability.

rt_optimise(): Fit nimue to a given set of death data via the particle and optimisation exploration approach.

setup_parameters(<default>): If no particular method we default to calling the parameter function attached to the model

setup_parameters(<nimue_model>): If no particular method we default to calling the parameter function attached to the model

trim_rt_optimise(): Trim an Rt Optimised output