Landscape Epidemiology and Evolution

Documentation for package ‘landsepi’ version 1.4.0

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Landscape Epidemiology and Evolution

-- A --

AgriLand	Landscape allocation
allocateCroptypeCultivars	Allocate cultivars to one croptype
allocateCultivarGenes	Allocate genes to a cultivar
allocateLandscapeCroptypes	Allocate croptypes to the landscape
antideriv_verhulst	Antiderivative of the Verhulst logistic function

-- C --

checkCroptypes	Check croptypes
checkCultivars	Check cultivars
checkCultivarsGenes	Check cultivars genes
checkDispersalHost	Check host dispersal
checkDispersalPathogen	Check pathogen dispersal
checkGenes	Check genes
checkInoculum	Check inoculum
checkLandscape	Check the landscape
checkOutputs	Check outputs
checkPathogen	Check pathogen
checkPI0_mat	Check the array PI0_mat when entered manually in 'loadInoculum()'.
checkSimulParams	Check simulation parameters
checkTime	Check time
checkTreatment	Check treatment
compute_audpc100S	Compute AUDPC in a single 100% susceptible field
createSimulParams	Create a LandsepiParams object.
Cultivars_list	Cultivars Type list

-- D --

demo_landsepi	Package demonstration
dispP	Dispersal matrices for rust fungi of cereal crops.
dispP_1	Dispersal matrices for rust fungi of cereal crops.
dispP_2	Dispersal matrices for rust fungi of cereal crops.
dispP_3	Dispersal matrices for rust fungi of cereal crops.
dispP_4	Dispersal matrices for rust fungi of cereal crops.
dispP_5	Dispersal matrices for rust fungi of cereal crops.

-- E --

epid_output	Generation of epidemiological and economic model outputs
evol_output	Generation of evolutionary model outputs

-- G --

getMatrixCroptypePatho	Get the "croptype/pathogen genotype" compatibility matrix.
getMatrixCultivarPatho	Get the "cultivar/pathogen genotype" compatibility matrix.
getMatrixGenePatho	Get the "resistance gene/pathogen genotype" compatibility matrix.
getMatrixPolyPatho	Get the "polygon/pathogen genotype" compatibility matrix.

-- I --

-- L --

landscapeTEST	Landscapes
landscapeTEST1	Landscapes
landscapeTEST2	Landscapes
landscapeTEST3	Landscapes
landscapeTEST4	Landscapes
landscapeTEST5	Landscapes
landsepi	Landscape Epidemiology and Evolution
LandsepiParams	Class LandsepiParams
LandsepiParams-class	Class LandsepiParams
loadCroptypes	Load Croptypes
loadCultivar	Load a cultivar
loadDispersalHost	Load a host dispersal matrix
loadDispersalPathogen	Load pathogen dispersal matrices
loadGene	Load a gene
loadInoculum	Load Inoculum
loadLandscape	Load a landscape
loadOutputs	Load outputs
loadPathogen	Load pathogen parameters
loadSimulParams	Load simulation parameters
loadTreatment	Load treatment parameters
logit	Logit function

-- M --

model_landsepi	Model for Landscape Epidemiology & Evolution
multiN	Allocation of cultivars

-- P --

periodic_cov	Periodic covariance function
plotland	Plotting the landscape
plot_allocation	Plotting allocation of croptypes in a landscape
plot_freqPatho	Plotting pathotype frequencies
price_reduction	Price reduction function
print	print
print-method	print

-- R --

-- S --

saveDeploymentStrategy	Save landscape and deployment strategy
setCroptypes	Set croptypes
setCultivars	Set cultivars
setDispersalHost	Set host dispersal
setDispersalPathogen	Set pathogen dispersal
setGenes	Set genes
setInoculum	Set inoculum
setLandscape	Set the landscape
setLansdcape	Set the landscape
setOutputs	Set outputs
setPathogen	Set the pathogen
setSeed	Set the seed
setSeedValue	setSeedValue
setTime	Set time parameters
setTreatment	Set chemical treatments
show	show
show-method	show
simul_landsepi	Simulation with input parameters as data.frames.
summary	summary
summary-method	summary
survivalProbToMatrix	Survival probability To Matrix
switch_patho_to_aggr	Switch from index of genotype to indices of agressiveness on different components

-- U --

updateReproSexProb	Update the probability of sexual reproduction
updateSurvivalProb	Update pathogen survival probability during the off-season

-- V --

Generation of a video