setCultivars: Set cultivars

In landsepi: Landscape Epidemiology and Evolution

Set cultivars

Description

Updates a LandsepiParams object with cultivars parameters

Usage

setCultivars(params, dfCultivars)

Arguments

params	a landsepiParams object.
dfCultivars	a data.frame defining the cultivars (see details). It can be generated manually or, alternatively, via loadCultivar.

Details

dfCultivars is a dataframe of parameters associated with each host genotype (i.e. cultivars, lines) when cultivated in pure crops. Columns of the dataframe are:

• cultivarName: cultivar names (cannot accept space),

• initial_density: host densities (per square meter) at the beginning of the cropping season as if cultivated in pure crop,

• max_density: maximum host densities (per square meter) at the end of the cropping season as if cultivated in pure crop,

• growth rate: host growth rates,

• reproduction rate: host reproduction rates,

• yield_H: theoretical yield (in weight or volume units / ha / cropping season) associated with hosts in sanitary status H as if cultivated in pure crop,

• yield_L: theoretical yield (in weight or volume units / ha / cropping season) associated with hosts in sanitary status L as if cultivated in pure crop,

• yield_I: theoretical yield (in weight or volume units / ha / cropping season) associated with hosts in sanitary status I as if cultivated in pure crop,

• yield_R: theoretical yield (in weight or volume units / ha / cropping season) associated with hosts in sanitary status R as if cultivated in pure crop,

• planting_cost = planting costs (in monetary units / ha / cropping season) as if cultivated in pure crop,

• market_value = market values of the production (in monetary units / weight or volume unit).

The data.frame must be defined as follow (example):

cultivarName	initial_density	max_density	growth_rate	reproduction_rate	yield_H	yield_L	yield_I	yield_R	planting_cost	market_value
Susceptible	0.1	2.0	0.1	0.0	2.5	0.0	0.0	0.0	225	200
Resistant1	0.1	2.0	0.1	0.0	2.5	0.0	0.0	0.0	225	200
Resistant2	0.1	2.0	0.1	0.0	2.5	0.0	0.0	0.0	225	200

Value

a LandsepiParams object

See Also

loadCultivar

Examples

## Not run: 
simul_params <- createSimulParams()
cultivar1 <- loadCultivar(name = "Susceptible", type = "growingHost")
cultivar2 <- loadCultivar(name = "Resistant", type = "growingHost")
cultivars <- data.frame(rbind(cultivar1, cultivar2), stringsAsFactors = FALSE)
simul_params <- setCultivars(simul_params, cultivars)
simul_params@Cultivars

## End(Not run)

landsepi documentation built on July 26, 2023, 5:36 p.m.