Man pages for landsepi
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 |
| antideriv_verhulst | Antiderivative of the Verhulst logistic function |
| 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... |
| 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 |
| demo_landsepi | Package demonstration |
| dispP | Dispersal matrices for rust fungi of cereal crops. |
| epid_output | Generation of epidemiological and economic model outputs |
| evol_output | Generation of evolutionary model outputs |
| getMatrixCroptypePatho | Get the "croptype/pathogen genotype" compatibility matrix. |
| getMatrixCultivarPatho | Get the "cultivar/pathogen genotype" compatibility matrix. |
| getMatrixGenePatho | Get the "resistance gene/pathogen genotype" compatibility... |
| getMatrixPolyPatho | Get the "polygon/pathogen genotype" compatibility matrix. |
| initialize-methods | LandsepiParams |
| inoculumToMatrix | Inoculum To Matrix |
| 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 |
| landsepi-package | Landscape Epidemiology and Evolution |
| LandsepiParams | 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 |
| model_landsepi | Model for Landscape Epidemiology & Evolution |
| multiN | Allocation of cultivars |
| periodic_cov | Periodic covariance function |
| plot_allocation | Plotting allocation of croptypes in a landscape |
| plot_freqPatho | Plotting pathotype frequencies |
| plotland | Plotting the landscape |
| price_reduction | Price reduction function |
| print-methods | |
| 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 |
| 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-methods | show |
| simul_landsepi | Simulation with input parameters as data.frames. |
| summary-methods | summary |
| survivalProbToMatrix | Survival probability To Matrix |
| switch_patho_to_aggr | Switch from index of genotype to indices of agressiveness on... |
| updateReproSexProb | Update the probability of sexual reproduction |
| updateSurvivalProb | Update pathogen survival probability during the off-season |
| video | Generation of a video |
