Landscape Epidemiology and Evolution


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Documentation for package ‘landsepi’ version 1.1.2

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A C D E G I L M P R S V misc

landsepi-package 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

-- 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
checkSimulParams Check simulation parameters
checkTime Check time
createLandscapeGPKG createLandscapeGPKG
createSimulParams Create a LandsepiParams object.
CroptypeBDD2Params CroptypeBDD2Params
CultivarBDD2Params CultivarBDD2Params
CultivarGeneBDD2Params CultivarGeneBDD2Params

-- 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 --

GeneBDD2Params GeneBDD2Params
getGPKGArea getGPKGArea
getGPKGCroptypes getGPKGCroptypes
getGPKGCroptypesRaw getGPKGCroptypesRaw
getGPKGCultivars getGPKGCultivars
getGPKGCultivarsGenes getGPKGCultivarsGenes
getGPKGGeneIDForCultivar getGPKGGeneIDForCultivar
getGPKGGenes getGPKGGenes
getGPKGRotation getGPKGRotation
GPKGAddInputData GPKGAddInputData
GPKGAddTables GPKGAddTables

-- I --

initialize-method LandsepiParams
invlogit Inverse logit function
is.in.01 is.in.01
is.positive is.positive
is.strict.positive is.strict.positive
is.wholenumber is.wholenumber

-- 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 a pathogen dispersal matrix
loadGene Load a gene
loadLandscape Load a landscape
loadOutputs Load outputs
loadPathogen Load pathogen parameters
loadSimulParams Load simulation parameters
logit Logit function

-- M --

model_landsepi Model for Landscape Epidemiology & Evolution
multiN Allocation of cultivars

-- P --

params2CroptypeBDD params2CroptypeBDD
params2CultivarBDD params2CultivarBDD
params2GeneBDD params2GeneBDD
params2GeneListBDD params2GeneListBDD
periodic_cov Periodic covariance function
plotland Plotting the landscape
plot_allocation Plotting allocation of croptypes in a landscape
plot_freqPatho Plotting pathotype frequencies
print print
print-method print

-- R --

resetCultivarsGenes Reset cultivars genes
runShinyApp runShinyApp
runSimul Run a simulation

-- 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
show show
show-method show
simul_landsepi Simulation with input parameters as data.frames.
summary summary
summary-method summary
switch_patho_to_aggr Switch from index of genotype to indices of agressiveness on different components

-- V --

video Generation of a video

-- misc --

_PACKAGE Landscape Epidemiology and Evolution