setOutputs.RdUpdates a LandsepiParams object with a list of output parameters.
setOutputs(params, output_list)a LandsepiParams object.
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).
a LandsepiParams object.
"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.
if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setOutputs(simul_params, loadOutputs())
simul_params@Outputs
}