Man pages for RussellXu/rtestimate
Estimation Of Reproductive Number
| branching_model | Branching process model. Random simulation according to the... |
| branching_setup | Branching method setup |
| branching_simulation | Calling the branching simulation |
| branching_step | Set up the config of branching model |
| check_config | Epiestim config check |
| check_dates | incidence's date must be an object of class date or numeric |
| check_si_distr | Check SI model distribution |
| check_times | This only produces warnings and errors, does not return... |
| detect_extinct | Detect extinction of process of branching simulation |
| discr_si | Discretized Generation Time Distribution Assuming A Shifted... |
| dist_setup | Distribution setup |
| epiestim_rt_plot | Plot outputs of Epiestim function |
| estimate_R | Calling Epiestim function |
| estimate_R_func | Calculates the cumulative incidence over time steps, then... |
| extinct_prob | The proportion of epidemic extinction |
| inf_fn | Skew-Normal Distribution set up |
| logistic_func | Logistic function |
| make_config | Set and check parameter settings of epiestim estimation |
| modify_defaults | This function was contributed by Rich Fitzjohn. It modifies... |
| overall_infectivity | Overall infectivity |
| process_config | Epiestim config set up |
| process_I | Use incidence create a single column for the Infected person... |
| Re_estimate | Branching Rt estimation function.The core algorithm in... |
| simulate_detectable_wrapper | Simulate binary PCR results (detectables) for the line list... |
| simulate_reporting | Simulate reporting |
| simulate_seir_process_rte | Viral load simulate SEIR model |
| simulate_seir_wrapper_rte | Simulate Odin stochastic SEIR model generator and... |
| simulate_viral_loads_wrapper | Simulate observed Ct values for the line list dataset. NOTE... |
| viral_load_estimate_rt | Viral load estimate rt process |
| vnapply | vnapply function |
