Run ODE

Run ordinary differential equation model

Usage

run_det_ode(
  init.inf = 1,
  herd.size = 500,
  r0 = 1.2,
  fever.duration = 1.15,
  milk.loss.dur = 7,
  cow.prod.lifespan = 365.25 * 2,
  include.prod.lifespan = FALSE,
  base.milk.prod = 100,
  sympt.milk.prod = 100 - 25,
  recovered.milk.prod = 80,
  discard.sick.prod = FALSE,
  disease.induced.mortality = 0,
  prop.cull = 0,
  sim.length = 365,
  gamma_multiplier = 0,
  beta_multiplier = 0,
  intervention_date = NULL,
  intervention_stop = sim.length,
  sigmoid_fun = FALSE,
  add_milk = TRUE
)

Arguments

init.inf

integer, the number of initial infection

herd.size

integer, the size of the herd

r0

positive number, the basic reproduction number

fever.duration

a positive number, the days of fever (infectious)

milk.loss.dur

a positive number, the days of milk loss

cow.prod.lifespan

a positive number, the productive lifespan of a cow in days.

include.prod.lifespan

a logical, should background demographics be considered with a default of FALSE

base.milk.prod

a positive number, the baseline milk production

sympt.milk.prod

a positive number, the milk production when the cow is symptomatic

recovered.milk.prod

a positive number, the production among recovered cows.

discard.sick.prod

a logical, discard infected milk from production

disease.induced.mortality

a positive number between 0 and 1 representing the mortality rate from disease.

prop.cull

a positive number between 0 and 1 representing the proportion of cows who recover from infection who are sent to market

sim.length

a positive number, number of days to run the simulation

gamma_multiplier

a number, representing the impact on the recovery rate where values greater than 0 represent faster removal and values less than 0 represent longer recovery times.

beta_multiplier

a number, represent the impact on the contact rate rate where values less than 0 indicate less contact while values greater than 0 indicate more contact.

intervention_date

a positive number represent the day number of an an intervention with a default of NULL representing no intervention taking place.

intervention_stop

a positive number representing the day that the intervention in the beta_multiple stops. Removal rates are assumed to continue after the intervention and stop dates.

sigmoid_fun

a logical, if true a sigmoid function will be utilized to phase in the gamma mulipltier based on the intervention date.

add_milk

a logical, if true milk production will be added to the simulation.