loadOutputs {landsepi}

Load outputs

Description

Creates an output list

Usage

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

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.

Value

a list of outputs and parameters for output generation

See Also

setOutputs, compute_audpc100S

Examples

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