Man pages for jameshay218/vaxedemic
Optimal allocation of vaccination during a pandemic

addadd two things
calc_approx_final_size_distributionBritton2010 10.1016/j.mbs.2010.01.006
calc_country_attackcalculate the attack rate by country
calc_country_time_seriescalculate the number of individuals summed over compartments...
calc_incidence_time_seriescalculate the incidence over time for each country
calc_incidence_vaccinated_peak_times_attack_ratescalculate the incidence, number of vaccinated individuals,...
calc_median_ci_by_countrycalculate the mean, median and 2.5...
calc_peak_timescalculate the peak time by country
calc_peak_times_and_attack_ratescalculate the peak time and attack rate by country
calc_vaccinated_time_seriescalculate the number of vaccinated individuals over time for...
calibrating_amp_and_travelsubmit job for amp and epsilon calibration
cum_vax_pool_func_closureclosure to make vaccine production function
density_country_attack_ratesplot the density strips of the attack rate in each country...
density_country_peak_timesplot the density strips of the peak times in each country...
distribute_vax_among_age_risk_closurereturns a function which distributes vaccines between age and...
generate_age_matrixAge matrix proportions
generate_age_matrix_uniformUniform location age matrix
generate_age_mixingAge mixing manipulatoin
generate_contact_matrixAge mixing matrix generation
gen_int_sum_intgenerate n_int random integers that sum to sum_int
get_final_sizes_with_R_efffunction to simulate the final size distribution for a single...
get_func_namesreturn names of all functions in a .R file
get_user_optionsspecify user options for cluster
get_vars_from_list_with_checkextract variables from list, throwing an error if they are...
get_vaxedemic_func_optionsreturn function options for vaxedemic
initial_testInitial test function
is_integer_likecheck if a number is integer-type or close enough to an...
list2heredump variables from a list to the parent frame
list_vars_from_environmentgather variables with given names from an environment into a...
main_simulationmain simulation loop
make_arg_listmake argument list to run simulations on or off the cluster
make_y_labelmake a string to label the y-axis
model_plotsModel visualisations - MAIN FUNCTION
model_plot_simpleSimple plot
neaten_raw_output_by_countryformat the summary statistic by country over all n_runs
normalisenormalises a vector so that it sums to 1
plot_country_attack_ratesplot the median and 95 plot_country_attack_rates(dat)...
plot_country_incidenceplot incidence time series for a country
plot_country_time_seriesplot time series for a country
plot_country_vaccinatedplot vaccinated individuals time series for a country
plot_peak_timesplot the median and 95 plot_peak_times(dat) \itemdata data...
postprocessing_country_attackpostprocess simulations to plot the country attack rate and...
postprocessing_incidence_vaccinated_peak_times_attack_ratespostprocess simulations to plot the peak time and attack...
postprocessing_peak_timespostprocess simulations to plot the peak time and save...
postprocessing_peak_times_and_attack_ratespostprocess simulations to plot the peak time and attack...
postprocessing_save_country_incidencepostprocess simulations to save the daily incidence for each...
postprocessing_save_country_vaccinatedpostprocess simulations to save the daily number of...
postprocessing_simple_savejust save summary statistics from simulations as an .rds file
produce_vax_linear_with_delaylinear function of vaccine production
read_contact_datafunction to construct contact matrix from data
read_coverage_dataRead and process seasonal vaccine coverage data
read_latitude_datafunction to construct latitude matrix from data
return_all_resreturn the full results of main_simulation
round_preserve_sumrounds a numeric vector probabilistically such that its sum...
run_and_get_deaths_recoveredrun the simulation and get a vector of the number of deaths...
run_fixed_paramssubmit job with fixed parameters
run_fixed_params_and_postprocesssubmit job with fixed parameters and postprocessing
run_simulationfunction to set up simulation from inputs, then run
setup_clusterCluster setup
setup_inputsprocess inputs to run simulation
setup_populationsfunction to setup synthetic population sizes for each...
setup_populations_real_datafunction to setup population sizes for each location, age,...
setup_travel_real_datafunction to construct travel matrix from data
shorten_runsmake argument list with shorter number of runs
sum_age_risk_closurereturns a function to sum a state vector across age and risk...
sum_listsum over a list
thin_time_seriesthin a time series matrix
vaccinate_by_current_seasonal_allocallocate vaccines according to current seasonal allocation
vaccinate_by_incidenceallocate vaccines according to absolute incidence
vaccine_allocation_closureclosure to make vaccine allocation function
vcapplyvapply for characters
viapplyvapply for integers
vlapplyvapply for logicals
vnapplyvapply for numerics
jameshay218/vaxedemic documentation built on July 29, 2018, 12:43 p.m.