|
add_target_use()
|
Find nearest LLIN target use to match to NPC outputs |
|
adjust_net_efficiency()
|
After 2023, net distribution switches to the most efficient observed country for all countries |
|
age_specific_coverage()
|
Age specific coverage |
|
annual_net_distibuted()
|
Annual nets distributed |
|
annual_net_distibuted_gts()
|
Annual nets distributed |
|
any_vc_coverage()
|
Add coverage of either net or IRS. These are modelled as -ve correlated so
the coverage is their sum (to max of 100%) |
|
approx_target_use()
|
Linear interpolation for eq_npc use |
|
back_adjust_iccm()
|
Split out iccm coverage from treatment coverage |
|
case_weighting
|
Case weighting. |
|
cases()
|
Add clinical cases |
|
commodities_and_services()
|
Commodity and service estimates |
|
coverage_options()
|
Create set of binary coverage options |
|
create_coverage()
|
Modify GP intervention data.frame for coverage options |
|
create_intervention_option_matrix()
|
Create matrix of coverage options |
|
create_names()
|
Create the replenishment naming scheme indicating which interventions are on and off during the replenishment period |
|
create_optim_matrices()
|
Create optimisation matrices |
|
create_optimisation_data()
|
Create dataset for optimisation |
|
daly_components()
|
Add DALY components |
|
dalys_cast_forward()
|
Dalys case forward |
|
deaths()
|
Add deaths |
|
dominant()
|
Filter non-dominant solutions |
|
dominant2()
|
Filter non-dominant solutions |
|
elim_threshold()
|
Elimination threshold |
|
epi_post_processing()
|
Epidemiological post processing |
|
extend()
|
Extend any inputs that do not span the full modelled time horizon |
|
final_format()
|
Final formatting |
|
fixed_post()
|
Continue coverage in post replenishment period |
|
forward_adjust_iccm()
|
Combine iccm coverage with treatment coverage |
|
get_weighting()
|
Get case weighting |
|
gf_aggregate()
|
Aggregate output |
|
gf_countries
|
List of countries to model for the GF |
|
gf_public
|
Proportion of treatment public sector |
|
gf_select()
|
Select output for GF |
|
half_life()
|
Half life net loss function |
|
hh
|
Average HH size |
|
interventions_rename()
|
Rename interventions |
|
life_years()
|
Add Life years lived |
|
link_data()
|
Link simulation output with input data |
|
model_output_to_long()
|
Raw output to long |
|
mortality_rate()
|
Add mortality rate (dependent on severe case incidence and treatment coverage) |
|
multi_optimisation()
|
Run multiple optimisations |
|
net_loss()
|
Net loss function |
|
non_malarial_fevers()
|
Add non-malarial fevers (NMFs). |
|
outcome_uncertainty()
|
Add case and death uncertainty |
|
par()
|
Add age disaggregated population at risk |
|
population_indicators()
|
Add some population-level indicators |
|
population_projections
|
Population projections |
|
ppf
|
Proportion pf |
|
process_raw()
|
Raw output pre-processing wrapper |
|
proportion_overlap()
|
Proportion overlap |
|
prune()
|
Keep only required columns - helps for memory issues with large countries |
|
render_report()
|
Create country summary report |
|
replace_missing()
|
Replaces -999 values in outputs |
|
replenishment_options()
|
Make replenishment options |
|
severe_cases()
|
Add severe cases |
|
single_optimisation()
|
Perform optimisation for a single budget line |
|
treatment_unit_costs
|
Treatment unit costs |
|
unit_costs
|
Unit costs |
|
use_npc
|
Use to npc |
|
who_burden
|
WHO burden estimates (callibrated to) |
|
year_summary()
|
Isolate annual summary |
|
yll_cast_forward()
|
Sum of deaths in last "lifetime left" years |