Man pages for sjfox/rtZIKVrisk
Accompanies: "Real-time risk assessment for Zika in the United States"
| all_max_cum_infect | Get all final cumulative infected numbers from sims |
| county_epi_prob_by_d | Epidemic probability for counties |
| county_prob_detect_x | County Detection probability |
| county_risk_data | County Risk spreadsheet |
| cumcases_by_detects | Cumulative cases for detects for single simulation run |
| cum_detect_local | Returns cumulative vector of locally detected cases |
| dying_arrows | Dying outbreak arrow data |
| epi_prob_by_reported_data | Epidemic probability by reported cases data |
| ex_dying_epidemic_data | Dying outbreak example |
| ex_growing_epidemic_data | Growing outbreak example |
| ex_outbreak_sims | Simulated stochastic outbreak data |
| exp_triggers_data | County surveillance triggers |
| freq_above_thresh | Get frequency cases above cum threshold and prev threshold... |
| freq_above_thresh_vec | Vectorizes the freq_above_thresh for the number of detected |
| get_county_parms | Get County-specific parameters |
| get_cumcases_by_detects_all | Get all cumcases and prevalence by detects |
| get_epidemic_prob_by_d | Get the epidemic probability as a function of number of... |
| growing_arrows | Growing outbreak arrow data |
| last_cuminfect_local | Get single final cumulative infected numbers from sims |
| major_city_loc | Texas Major city location |
| max_local_prev | Get single maximum of local prevalence |
| plot_epi_prob | Plot epidemic risk |
| plot_fig1 | Plot Fig 1 from Zika risk assessment |
| plot_fig2 | Plot Fig 2 from Zika risk assessment |
| plot_fig3 | Plot Fig 3 from Zika risk assessment |
| plot_fig4 | Plot Fig 4 from Zika risk assessment |
| plot_final_sizes | Plot histogram of the final sizes of zika outbreaks |
| plot_zika_outbreaks | Plot outbreaks |
| prev_by_reported_data | Prevalence by reported cases data |
| run_n_zika_sims | Run multiple zika simulations |
| run_zika_sim | Runs a single zika simulation |
| texas_county_shp | Texas county map |
| track_infectious | Track movement through infectious classes |
| update_state | Update state movement |
| update_states | Update multiple state's movement |
| zika_def_parms | Default Zika parameters for sims |
