| add | add two things |
| apply_named_args | a version of apply. if MARGIN = 1, the values in each column... |
| calc_approx_final_size_distribution | Britton2010 10.1016/j.mbs.2010.01.006 |
| calc_country_attack | calculate the attack rate by country |
| calc_country_time_series | calculate the number of individuals summed over compartments... |
| calc_cumulative_deaths_time_series | calculate the cumulative number of deaths over time for each... |
| calc_incidence_peak_times_attack_rates_deaths | calculate the incidence, peak times, attack rates and deaths... |
| calc_incidence_time_series | calculate the incidence over time for each country |
| calc_incidence_vaccinated_peak_times_attack_rates | calculate the incidence, number of vaccinated individuals,... |
| calc_incidence_vaccinated_peak_times_attack_rates_deaths | calculate the incidence, number of vaccinated individuals,... |
| calc_median_ci_by_country | calculate the mean, median and 2.5... |
| calc_peak_times | calculate the peak time by country |
| calc_peak_times_and_attack_rates | calculate the peak time and attack rate by country |
| calc_vaccinated_time_series | calculate the number of vaccinated individuals over time for... |
| calibrating_amp_and_travel | submit job for amp and epsilon calibration |
| cum_vax_pool_func_closure | closure to make vaccine production function |
| density_country_attack_rates | plot the density strips of the attack rate in each country... |
| density_country_peak_times | plot the density strips of the peak times in each country... |
| distribute_vax_among_age_risk_closure | returns a function which distributes vaccines between age and... |
| generate_age_matrix | Age matrix proportions |
| generate_age_matrix_uniform | Uniform location age matrix |
| generate_age_mixing | Age mixing manipulatoin |
| generate_contact_matrix | Age mixing matrix generation |
| gen_int_sum_int | generate n_int random integers that sum to sum_int |
| get_final_sizes_with_R_eff | function to simulate the final size distribution for a single... |
| get_func_names | return names of all functions in a .R file |
| get_user_options | specify user options for cluster |
| get_vars_from_list_with_check | extract variables from list, throwing an error if they are... |
| get_vaxedemic_func_options | return function options for vaxedemic |
| initial_test | Initial test function |
| is_integer_like | check if a number is integer-type or close enough to an... |
| list2here | dump variables from a list to the parent frame |
| list_vars_from_environment | gather variables with given names from an environment into a... |
| main_simulation | main simulation loop |
| make_arg_list | make argument list to run simulations on or off the cluster |
| make_y_label | make a string to label the y-axis |
| Map_vapply | a version of Map() where we specify the format of the output |
| model_plots | Model visualisations - MAIN FUNCTION |
| model_plot_simple | Simple plot |
| neaten_raw_output_by_country | format the summary statistic by country over all n_runs |
| normalise | normalises a vector so that it sums to 1 |
| num2str | turn number(s) into string for filename, replacing decimal... |
| plot_country_attack_rates | plot the median and 95 plot_country_attack_rates(dat)... |
| plot_country_incidence | plot incidence time series for a country |
| plot_country_time_series | plot time series for a country |
| plot_country_vaccinated | plot vaccinated individuals time series for a country |
| plot_peak_times | plot the median and 95 plot_peak_times(dat) \itemdata data... |
| postprocessing_country_attack | postprocess simulations to plot the country attack rate and... |
| postprocessing_deaths | postprocess simulations to save the cumulative number of dead... |
| postprocessing_incidence_peak_times_attack_rates_deaths | postprocess simulations to plot the peak time and attack... |
| postprocessing_incidence_vaccinated_peak_times_attack_rates | postprocess simulations to plot the peak time and attack... |
| postprocessing_incidence_vaccinated_peak_times_attack_rates_deaths | postprocess simulations to plot the peak time and attack... |
| postprocessing_peak_times | postprocess simulations to plot the peak time and save... |
| postprocessing_peak_times_and_attack_rates | postprocess simulations to plot the peak time and attack... |
| postprocessing_save_country_incidence | postprocess simulations to save the daily incidence for each... |
| postprocessing_save_country_vaccinated | postprocess simulations to save the daily number of... |
| postprocessing_simple_save | just save summary statistics from simulations as an .rds file |
| produce_vax_linear_with_delay | linear function of vaccine production |
| read_contact_data | function to construct contact matrix from data |
| read_coverage_data | Read and process seasonal vaccine coverage data |
| read_latitude_data | function to construct latitude matrix from data |
| return_all_res | return the full results of main_simulation |
| round_preserve_sum | rounds a numeric vector probabilistically such that its sum... |
| run_and_get_deaths_recovered | run the simulation and get a vector of the number of deaths... |
| run_fixed_params | submit job with fixed parameters |
| run_fixed_params_and_postprocess | submit job with fixed parameters and postprocessing |
| run_simulation | function to set up simulation from inputs, then run |
| scientific_10x | Format numbers to scientific notation (10^#) |
| setup_cluster | Cluster setup |
| setup_inputs | process inputs to run simulation |
| setup_populations | function to setup synthetic population sizes for each... |
| setup_populations_real_data | function to setup population sizes for each location, age,... |
| setup_travel_real_data | function to construct travel matrix from data |
| shorten_runs | make argument list with shorter number of runs |
| sum_age_risk_closure | returns a function to sum a state vector across age and risk... |
| sum_list | sum over a list |
| thin_time_series | thin a time series matrix |
| vaccinate_by_current_seasonal_alloc | allocate vaccines according to current seasonal allocation |
| vaccinate_by_incidence | allocate vaccines according to absolute incidence |
| vaccine_allocation_closure | closure to make vaccine allocation function |
| vcapply | vapply for characters |
| viapply | vapply for integers |
| vlapply | vapply for logicals |
| vnapply | vapply for numerics |
