Function reference • sircovid

All functions
`add_trajectory_incidence()` `drop_trajectory_incidence()`	Add incidence to trajectories
`basic`	The basic sircovid model
`basic_compare()`	Compare observed and modelled data for the basic model
`basic_index()`	Index of basic model
`basic_initial()`	Initial conditions for the basic model
`basic_parameters()`	Parameters for the basic model
`check_sircovid_model()`	Check a model type
`combine_rt()`	Combine Rt estimates
`combine_rt_epiestim()`	Combine Rt estimates from EpiEstim
`combine_trajectories()`	Combine trajectories
`compile_gpu()`	Create GPU model
`get_sample_rank()`	Get the ranking of sample by a given variable, e.g. infections
`inflate_state_strains()`	Inflate strains in model state
`inflate_state_vacc_classes()`	Inflate vacc classes in model state
`lancelot`	The lancelot sircovid model
`lancelot_Rt()`	Compute "Rt"
`lancelot_Rt_trajectories()`	Compute Rt for a set of trajectories
`lancelot_check_data()`	Check data for particle filter
`lancelot_check_severity()`	Check severity parameters
`lancelot_compare()`	Compare observed and modelled data for the lancelot model
`lancelot_ifr_excl_immunity()`	Compute "IFR" excluding immunity
`lancelot_index()`	Index of lancelot model
`lancelot_initial()`	Initial conditions for the lancelot model
`lancelot_parameters()`	Parameters for the lancelot model
`lancelot_parameters_observation()`	Lancelot observation parameters
`lancelot_parameters_progression()`	Lancelot progression parameters
`lancelot_parameters_sens_and_spec()`	Lancelot sensitivity and specificity parameters
`lancelot_parameters_severity()`	Lancelot severity parameters
`lancelot_rt_trajectories_epiestim()`	Compute Rt using EpiEstim for a set of trajectories
`modify_severity()`	Modify severity and transmission of variants
`regions()`	Regions
`reorder_rt_ifr()`	Reorder Rt or IFR trajectories
`reorder_sample()`	Reorder samples
`rotate_strains()`	Rotate strains
`sircovid_date()` `sircovid_date_as_date()` `as_sircovid_date()` `as_date()`	Date handling for sircovid
`sircovid_models()`	Available sircovid Models
`sircovid_parameters_expand_step()`	Expand beta steps
`sircovid_parameters_piecewise_constant()`	Construct piecewise constant array
`sircovid_parameters_piecewise_linear()`	Construct piecewise linear array
`sircovid_parameters_severity()`	Process severity data
`upgrade_state()`	Upgrade model state after change
`vaccine_eligibility()`	Create vaccine eligibility vector
`vaccine_priority_proportion()` `vaccine_priority_population()`	Compute vaccination order
`vaccine_remap_state()`	Remap state to include vaccination
`vaccine_schedule()`	Create vaccine schedule
`vaccine_schedule_from_data()`	Create historical vaccine schedule
`vaccine_schedule_future()`	Create vaccination schedule
`vaccine_schedule_scenario()`	High-level vaccine scenario creation

Reference

All functions