Man pages for emmalouisedavis/TTI-branching-process
TTI COVID-19 branching process model
| adhere | A function to calculate adherence times |
| box_plot_max_weekly_cases | Create box plots of maximum weekly cases by scenario |
| detect_extinct | Calculate proportion of outbreaks that went extinct |
| dist_setup | Create partial function to sample from gamma distributions |
| extinct_prob | Calculate proportion of runs that have controlled outbreak |
| inf_fn | Samples the serial interval for given incubation period... |
| make_figure_2 | Constructs figure 2 from the manuscript |
| make_figure_2a | Makes Figure 2a from manuscript |
| make_figure_3a | Construct Figure 3a from manuscript |
| make_figure3b | Generate a figure comparing the effective reproduction no... |
| make_figure_4 | Construct Figure 4 from the manuscript |
| make_figure_S1 | Construct Figure S1 from the supplementary material |
| make_figure_S2 | Construct Figure S2 from the supplementary material |
| make_figure_S3 | Construct Figure S3 from the supplementary material |
| make_figure_S6 | Both plot functions no longer relevant (plotting for... |
| make_figure_S7 | Plots the impact of dispersion on the distribution of new... |
| outbreak_model | Run a single instance of the branching process model |
| outbreak_setup | Set up initial cases for branching process |
| outbreak_step | Move forward one generation in the branching process |
| parameter_sweep | Sweep across parameters |
| pipe | Pipe operator |
| rename_variables_for_plotting | Rename variables for plotting |
| scenario_sim | Run a specified number of simulations with identical... |
| sub_plot | Create sub-plot for supplementary figures |
