Optimal allocation of vaccination during a pandemic

add | add two things |

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_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_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 |

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 |

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_incidence_vaccinated_peak_times_attack_rates | 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 |

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 |

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