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 |
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