loadInoculum: Load Inoculum

Description

Loads an inoculum for the beginning of the simulation (t=0), with controlled localisation (polygons), infected cultivars and pathogen genotypes. Note that landscape, gene, cultivar and croptype parameters must be set before loading the inoculum.

Usage

loadInoculum(
  params,
  pI0_all = NULL,
  pI0_host = NULL,
  pI0_patho = NULL,
  pI0_poly = NULL,
  pI0_mat = NULL
)

Value

a 3D array of dimensions (1:Nhost,1:Npatho,1:Npoly)

Arguments

params: a LandsepiParams object.
pI0_all: a numeric indicating the (same) probability to infect a host for all pathogen genotypes, all cultivars and in all polygons
pI0_host: a vector of length Nhost indicating the probabilities to infect an host, for each cultivar (for all pathogen genotypes and all polygons).
pI0_patho: a vector of length Npatho indicating the probabilities to infect an host, for each pathogen genotype (for all cultivars and all polygons).
pI0_poly: a vector of length Npoly indicating the probabilities to infect an host, for each polygon (for all pathogen genotypes and all cultivars).
pI0_mat: a 3D array of dimensions (1:Nhost,1:Npatho,1:Npoly) indicating the probability to infect an host, for each cultivar, pathogen genotype and polygon. Note that pI0_all, pI0_host, pI0_patho and pI0_poly are not accounted if pI0_mat is filled.

Details

The different options enable different types of inoculum (localisation, infected cultivars and pathogen genetic diversity, see different options in Examples).
Unless the array pI0_mat is filled, the probability for a host to be infected at the beginning of the simulation is computed in every polygon (poly), cultivar (host) and pathogen genotype (patho) with pI0[host, patho, poly] = pI0_all * pI0_patho[patho] * pI0_host[host] * pI0_poly[poly].
Before loading the inoculum, one can use getMatrixGenePatho(), getMatrixCultivarPatho() and getMatrixCroptypePatho() to acknowledge which pathogen genotypes are adapted to which genes, cultivars and croptypes.
Once setInoculum() is used, one can call inoculumToMatrix() to get the inoculum as a 3D array (1:Nhost,1:Npatho,1:Npoly)

Examples

Run this code

if (FALSE) {
simul_params <- createSimulParams()
simul_params <- setTime(simul_params, Nyears = 1, nTSpY = 80)
basic_patho_param <- loadPathogen(disease = "rust")
simul_params <- setPathogen(simul_params, patho_params = basic_patho_param)
simul_params <- setLandscape(simul_params, loadLandscape(id = 1))
simul_params <- setDispersalPathogen(simul_params, loadDispersalPathogen(id = 1)[[1]])
gene1 <- loadGene(name = "MG 1", type = "majorGene")
gene2 <- loadGene(name = "MG 2", type = "majorGene")
genes <- data.frame(rbind(gene1, gene2), stringsAsFactors = FALSE)
simul_params <- setGenes(simul_params, genes)
cultivar1 <- loadCultivar(name = "Susceptible", type = "wheat")
cultivar2 <- loadCultivar(name = "Resistant", type = "wheat")
cultivars <- data.frame(rbind(cultivar1, cultivar2), stringsAsFactors = FALSE)
simul_params <- setCultivars(simul_params, cultivars)
simul_params <- allocateCultivarGenes(simul_params, "Resistant", c("MG 1", "MG 2"))
croptypes <- loadCroptypes(simul_params, names = c("Susceptible crop", "Resistant crop"))
croptypes <- allocateCroptypeCultivars(croptypes, "Susceptible crop", "Susceptible")
croptypes <- allocateCroptypeCultivars(croptypes, "Resistant crop", c("Resistant"))
simul_params <- setCroptypes(simul_params, croptypes)
simul_params <- allocateLandscapeCroptypes(simul_params, rotation_period = 0
, rotation_sequence = croptypes$croptypeID
, prop = c(1/2,1/2), aggreg = 1, graphic = FALSE)

#### Definition of the inoculum ####

### Scenario 1. Only the avirulent pathogen on the susceptible cultivar ###
# In this situation, the susceptible cultivar must be entered
# at the first line of the table cultivars

## Global inoculum (i.e. in the whole landscape)
# Option 1: simply use the default parameterisation
simul_params <- setInoculum(simul_params, 5E-4)

# Option 2: use loadInoculum()
Npatho <- prod(simul_params@Genes$Nlevels_aggressiveness)
Nhost <- nrow(simul_params@Cultivars)
pI0 <- loadInoculum(simul_params,
                    pI0_all=5E-4,
                    pI0_host=c(1,rep(0, Nhost-1)),
                    pI0_patho=c(1,rep(0, Npatho-1)))
simul_params <- setInoculum(simul_params, pI0)
inoculumToMatrix(simul_params)

## Local inoculum (i.e. in some random polygons only)
Npatho <- prod(simul_params@Genes$Nlevels_aggressiveness)
Nhost <- nrow(simul_params@Cultivars)
Npoly <- nrow(simul_params@Landscape)
Npoly_inoc <- 5  ## number of inoculated polygons
## whether the avr pathogen can infect the polygons
compatible_poly <- getMatrixPolyPatho(simul_params)[,1]
## random polygon picked among compatible ones
id_poly <- sample(grep(1, compatible_poly), Npoly_inoc)
pI0_poly <- as.numeric(1:Npoly %in% id_poly)  
pI0 <- loadInoculum(simul_params,
                    pI0_all=5E-4,
                    pI0_host=c(1,rep(0, Nhost-1)),
                    pI0_patho=c(1,rep(0, Npatho-1)), 
pI0_poly=pI0_poly)
simul_params <- setInoculum(simul_params, pI0)
inoculumToMatrix(simul_params)

### Scenario 2. Diversity of pathogen genotypes in the inoculum ###
# in this example,  Nhost=2 cultivars, Npatho=4

## Global inoculum (i.e. in all polygons of the landscape)
pI0 <- loadInoculum(simul_params, pI0_patho=c(1E-3,1E-4,1E-4,1E-5), pI0_host=c(1,1))
simul_params <- setInoculum(simul_params, pI0)
inoculumToMatrix(simul_params)[,,1:5]

## Local inoculum (i.e. in some polygons only) ##
Npoly <- nrow(simul_params@Landscape)
Npoly_inoc <- 5  ## number of inoculated polygons 
id_poly <- sample(1:Npoly, Npoly_inoc)  ## random polygon 
pI0_poly <- as.numeric(1:Npoly %in% id_poly) 
pI0 <- loadInoculum(simul_params, pI0_patho=c(1E-3,1E-4,1E-4,1E-5),
pI0_host=c(1,1), pI0_poly=pI0_poly)
simul_params <- setInoculum(simul_params, pI0)
inoculumToMatrix(simul_params)
}