landsepi-package | Landscape Epidemiology and Evolution |
AgriLand | Landscape allocation |
allocateCroptypeCultivars | Allocate cultivars to one croptype |
allocateCultivarGenes | Allocate genes to a cultivar |
allocateLandscapeCroptypes | Allocate croptypes to the landscape |
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 |
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. |
epid_output | Generation of epidemiological and economic model outputs |
evol_output | Generation of evolutionary model outputs |
GeneBDD2Params | GeneBDD2Params |
getGPKGArea | getGPKGArea |
getGPKGCroptypes | getGPKGCroptypes |
getGPKGCroptypesRaw | getGPKGCroptypesRaw |
getGPKGCultivars | getGPKGCultivars |
getGPKGCultivarsGenes | getGPKGCultivarsGenes |
getGPKGGeneIDForCultivar | getGPKGGeneIDForCultivar |
getGPKGGenes | getGPKGGenes |
getGPKGRotation | getGPKGRotation |
GPKGAddInputData | GPKGAddInputData |
GPKGAddTables | GPKGAddTables |
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 |
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 |
model_landsepi | Model for Landscape Epidemiology & Evolution |
multiN | Allocation of cultivars |
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-method |
resetCultivarsGenes | Reset cultivars genes |
runShinyApp | runShinyApp |
runSimul | Run a simulation |
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 |
video | Generation of a video |
_PACKAGE | Landscape Epidemiology and Evolution |