Man pages for pspc-data-science/branchsim
Gamma negative binomial branching process simulation of epidemics
| add_layer | Builds the next generation of nodes in a tree. |
| as_tidygraph | Convert a tree to a 'tidygraph' object. |
| asymptotic_plot | A gradient plot of the Malthusian parameter as a function of... |
| average_component_size | The average component size of paths that go extinct. |
| branchsim-package | branchsim: Gamma negative binomial branching process... |
| build_tree | Simulate a single epidemic path |
| calc_avg_path | Compute average epidemic path |
| calc_mu | Expectation of the logarithmic distribution |
| calc_R0 | Calculate R0 implied from the model |
| char_function | The characteristic function of the branching process. |
| component_size_plot | A gradient plot of the average compenent size if extinction... |
| derivative_generating_function | The derivative of the generating function of the branching... |
| dMu | A function for the infinitesimal expectation in births:... |
| equalize_paths | Make all paths end at a fixed time |
| extinct_plot | A gradient plot of the extincition probability as a function... |
| find_gamma_parameters | Get the shape and rate parameter of a gamma distribution... |
| find_kappa | Find Gamma rate parameter |
| find_p | A function for obtaining the p parameter of the log-series... |
| find_p_from_quantile | Find logarithmic distribution parameter from a quantile value |
| G | A function for the expecation for the number of individuals... |
| generating_function | The generating function of the branching process f(s) = sum_k... |
| get_extinct_prob | A function for obtaining the extinction probability over all... |
| get_malthusian | A function for obtaining the Malthusian parameter of the CMJ... |
| make_first_layer | Initialize the tree |
| plot_dendrogram | Plot dendrogram for a single path |
| plot_exp | Plot the time between infectious events |
| plot_gamma | Plot the Gamma density for the communicable window |
| plot_gamma_dist | The plot of communicable window's distribution. |
| plot_log | Plot the number of individuals infected per infectious event |
| plot_paths | Plot epidemic paths |
| plot_R0 | Contour plot of R_eff for different values of lambda and mu. |
| plot_single_mother_dist | The plot of a single mother's distribution function for her... |
| plot_single_path | Show infection counts (cumulative and ongoing) for a single... |
| prob_distribution_2 | The probability distribution of births from a single mother... |
| renewal_function | Renewal equation solution to the expectation of the... |
| renewal_plot | Plot the solution to the renewal equation solution for... |
| run_sims | Multiple path simulations over a range of input parameters |
| single_mother_distribution | The probability distribution of births from a single mother... |
| treelist_to_paths | Compute paths from a list of trees |
