Make an xds Object to Study Human / Host Cohort Dynamics

Source: R/xds_setup.R

A modified version of xds_setup to setup up studies of cohort dynamics.

The xds object defines frame = class(frame) = 'cohort' but there is no cohort case for xds_solve. Instead, cohort dynamics are studied using xds_solve_cohort, which was designed to compare the outcomes for cohorts of different ages when exposure is changing.

The interface includes options to configure a function describing F_eir as a function of time, with seasonal components and a trend. Exposure in a cohort is a function of its age, including a function that modifies exposure by age.

xds_setup_cohort(
  eir = 1,
  F_season = F_flat,
  F_trend = F_flat,
  F_age = F_flat,
  xds = "ode",
  Xname = "SIS",
  Xopts = list(),
  Xday = 1,
  HPop = 1000,
  searchB = 1,
  model_name = "unnamed"
)

Arguments

eir

is the entomological inoculation rate

F_season

a function describing a seasonal pattern over time

F_trend

a function describing a temporal trend over time

F_age

a assigning a biting weight by age

xds

is ode or dde or dts for ordinary OR delay differential OR difference equations

Xname

is a character string specifying an X Component module

Xopts

a list to configure the X Component module

Xday

is the run-time time step for X Component (in days): integer or 1/integer

HPop

is the number of humans in each stratum

searchB

is a vector of search weights for blood feeding

model_name

is a name for the model (arbitrary)

Value

an xds object