Bed Nets

library(ramp.xds)
library(ramp.control)

Every bed net model has six configurable functions, each one dispatched and configured by a different object.

The bednets model object:

bednets

$distribute_mod
$owner_mod
$user_mod
$effects_mod
$coverage_mod
coverage
$ef_sz_mod
- [[1]] - for species 1
- …

The models get called at two different points:

VectorControl dispatches on class(model$vector_control) == "dynamic"
- BedNet dispatches on class(model$bednets) == "dynamic"
  - DistributeBedNets dispatches on class(model$bednets$distribute_mod) is there to model mass distribution of ITNs that should sharply increase bednet ownership
  - OwnBedNets dispatches on class(model$bednets$owner_mod) is a model that can account for background net replacement and loss
  - UseBedNets dispatches on class(model$bednets$user_mod) is a model for bed net usage
  - BedNetEffects dispatches on class(model$bednets$effects_mod) is a function that modifies search weights
VectorControlEffectSizes dispatches on class(model$bednets) == "dynamic"
- BedNetCoverage dispatches on class(model$bednets$coverage_mod)
- After evaluating BedNetCoverage, values are stored at model$bednets$coverage
- BedNetEffectSizes dispatches on class(model$bednets$ef_sz_mod[[s]]) for the $s^{th}$ species

To set all this up, we call a function with a name that calls a setup function and as set of options to set it up, passed as a list:

setup_bednets = function(..., 
                        distribute_name = 'none', distribute_opts = list(),
                        own_name = 'none', own_opts = list(),
                        use_name = 'none', use_opts = list(),
                        effects_name = 'none', effects_opts = list(),
                        coverage_name = 'none', coverage_opts = list(),
                        effect_sizes_name = 'none', effect_sizes_opts = list(), 
                        ...

Coverage

In the simplest models, we can simply set coverage

mod <- xds_setup(MYname = "SI")

mod <- setup_vector_control(mod)
mod <- xds_solve(mod)

cov_opts <- list(
  F_season = function(t)
    {ifelse(t < 0, 0, (sin(2*pi*(t-365/4) / 365) + 1))}
)

tt = seq(0:730)
with(cov_opts, plot(tt, F_season(tt), type = "l"))

mod <- setup_bednets(mod,
     coverage_name = "func", coverage_opts = cov_opts, 
     effect_sizes_name = "lemenach")

tt = seq(0:730)
show_bednet_coverage(tt, mod)

Coverage

Effect Sizes