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Construct an EDA agent

edaAgent.Rd

Returns a validated agent specification used by EDA. Each agent is written to its own per-agent input file on disk and listed in the main extension file's EDAInputFiles block.

Usage

edaAgent(
  name,
  SHIMode = "mean",
  StartYear = NULL,
  EndYear = NULL,
  TransmissionRate = NULL,
  AcquisitionRate = NULL,
  InitialEpidemMap = NULL,
  DispersalType = "STATIC",
  DispersalKernel = "PowerLaw",
  DispersalMaxDist = NULL,
  AlphaCoef = NULL,
  EDASpeciesParameters = NULL,
  DisturbanceModifiers = NULL,
  IgnoredSpecies = NULL,
  extraClimateLines = character(0)
)

Arguments

name

Character. Agent name (no spaces).

SHIMode

Character. One of "mean" or "max".

StartYear, EndYear

(Optional) Integer. Outbreak window.

TransmissionRate

Numeric (beta0). Mean rate at which an infected cell infects another cell per timestep.

AcquisitionRate

Numeric (rD). Rate of acquisition of detectable symptoms per timestep.

InitialEpidemMap

(Optional) Character. Relative path to the initial-outbreak raster.

DispersalType

Character. One of "STATIC" or "DYNAMIC".

DispersalKernel

Character. One of "PowerLaw" or "NegExp".

DispersalMaxDist

Numeric. Cut-off distance (m) for the dispersal kernel.

AlphaCoef

Numeric. Exponent of the dispersal kernel.

EDASpeciesParameters

data.frame with required columns: Species, LowAge, LowScore, MediumAge, MediumScore, HighAge, HighScore, VulnLowAge, VulnLowMortProb, VulnMediumAge, VulnMediumMortProb, VulnHighAge, VulnHighMortProb, CFSConifer, MortalityPlot.

DisturbanceModifiers

(Optional) data.frame with columns SHIModifier, Duration, Type.

IgnoredSpecies

(Optional) Character vector of species codes to exclude from the SHI calculation.

extraClimateLines

(Optional) Character vector of raw lines for the climate-input section (e.g. ClimateVariables table). Inserted verbatim, before the transmission block.

Value

A list of class "EDAAgent".

Details

Climate-related blocks (ClimateVariables, DerivedClimateVariables, WeatherIndexVariables, AnnualWeatherIndex, formula blocks, etc.) vary widely between pathogens; supply them verbatim via extraClimateLines rather than modelling each one as an active binding.

See also

Other EDA helpers: EDA, insertEDADisturbanceModifiers(), insertEDAIgnoredSpecies(), insertEDAInputFiles(), insertEDASpeciesParameters(), writeEDAAgentFile()