setOutputs {landsepi}

Set outputs

Description

Updates a LandsepiParams object with a list of output parameters.

Usage

setOutputs(params, output_list)

Arguments

params

a LandsepiParams object.

output_list

a list of outputs to be generated and parameters for output generation. It can be generated manually or, alternatively, via loadOutputs. This list is composed of:

• epid_outputs = epidemiological outputs to compute (see details)

• evol_outputs = evolutionary outputs to compute (see details)

• thres_breakdown = an integer (or vector of integers) giving the threshold (i.e. number of infections) above which a pathogen genotype is unlikely to go extinct, used to characterise the time to invasion of resistant hosts (several values are computed if several thresholds are given in a vector).

• audpc100S = the audpc in a fully susceptible landscape (used as reference value for graphics).

Details

"epid_outputs" is 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:

• "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 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 - 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" is 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 LandsepiParams object.

See Also

loadOutputs

Examples

## Not run: 
simul_params <- createSimulParams()
simul_params <- setOutputs(simul_params, loadOutputs())
simul_params@Outputs

## End(Not run)