loadOutputs: Load outputs

In landsepi: Landscape Epidemiology and Evolution

Load outputs

Description

Creates an output list

Usage

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

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"

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

landsepi documentation built on Sept. 23, 2024, 5:11 p.m.