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landsepi (version 1.5.1)

loadOutputs: Load outputs

Description

Creates an output list

Usage

loadOutputs(epid_outputs = "all", evol_outputs = "all", disease = "rust")

Value

a list of outputs and parameters for output generation

Arguments

epid_outputs

a character string (or a vector of character strings if several outputs are to be computed) specifying the type of epidemiological and economic outputs to generate (see details):

  • "audpc" : Area Under Disease Progress Curve (average number of diseased host individuals per time step and square meter)

  • "audpc_rel" : Relative Area Under Disease Progress Curve (average proportion of diseased host individuals relative to the total number of existing hosts)

  • "gla" : Green Leaf Area (average number of healthy host individuals per time step and square meter)

  • "gla_rel" : Relative Green Leaf Area (average proportion of healthy host individuals relative to the total number of existing hosts)

  • "eco_yield" : total crop yield (in weight or volume units per ha)

  • "eco_cost" : operational crop costs (in monetary units per ha)

  • "eco_product" : total crop products (in monetary units per ha)

  • "eco_margin" : Margin (products - operational costs, in monetary units per ha)

  • "contrib": contribution of pathogen genotypes to LIR dynamics

  • "HLIR_dynamics", "H_dynamics", "L_dynamics", "IR_dynamics", "HLI_dynamics", etc.: Epidemic dynamics related to the specified sanitary status (H, L, I or R and all their combinations). Graphics only, works only if graphic=TRUE.

  • "all" : compute all these outputs (default)

  • "" : none of these outputs will be generated.

evol_outputs

a character string (or a vector of character strings if several outputs are to be computed) specifying the type of evolutionary outputs to generate :

  • "evol_patho": Dynamics of pathogen genotype frequencies

  • "evol_aggr": Evolution of pathogen aggressiveness

  • "durability": Durability of resistance genes

  • "all": compute all these outputs (default)

  • "": none of these outputs will be generated.

disease

a disease name, among "rust" (default), "mildew", "sigatoka" and "no pathogen"

See Also

setOutputs, compute_audpc100S

Examples

Run this code
outputList <- loadOutputs(epid_outputs = "audpc", evol_outputs = "durability")
outputList

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