Package: medfate 4.4.0
Miquel De Cáceres
medfate: Mediterranean Forest Simulation
Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Authors:
medfate_4.4.0.tar.gz
medfate_4.4.0.tar.gz(r-4.5-noble)medfate_4.4.0.tar.gz(r-4.4-noble)
medfate_4.4.0.tgz(r-4.4-emscripten)medfate_4.4.0.tgz(r-4.3-emscripten)
medfate.pdf |medfate.html✨
medfate/json (API)
| # Install 'medfate' in R: |
| install.packages('medfate', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/emf-creaf/medfate/issues
- SFM_metric - Standard fuel models
- SpParamsDefinition - Data tables with species parameter definitions and values
- SpParamsMED - Data tables with species parameter definitions and values
- exampleforest - Description of a forest stand.
- exampleforest2 - Description of a forest stand.
- examplemeteo - Example daily meteorology data
- exampleobs - Example observed data
- poblet_trees - Example forest inventory data
Last updated 2 months agofrom:f36fcd3b96. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 23 2024 |
| R-4.5-linux-x86_64 | OK | Aug 23 2024 |
Exports:aspwbaspwb_dayaspwbInputbiophysics_irradianceToPhotonFluxbiophysics_leafTemperaturebiophysics_leafTemperature2biophysics_leafVapourPressurebiophysics_radiationDiurnalPatternbiophysics_temperatureDiurnalPatternbiophysics_waterDynamicViscositycarbon_carbonCompartmentscarbon_leafStarchCapacitycarbon_leafStructuralBiomasscarbon_osmoticWaterPotentialcarbon_relativeSapViscositycarbon_sapwoodStarchCapacitycarbon_sapwoodStructuralBiomasscarbon_sapwoodStructuralLivingBiomasscarbon_sugarConcentrationcarbon_sugarStarchDynamicsLeafcarbon_sugarStarchDynamicsStemdefaultControldefaultManagementArgumentsdefaultManagementFunctiondefaultSoilParamsdroughtStressemptyforestevaluation_metricevaluation_plotevaluation_statsevaluation_tableextractfire_barkThermalDiffusivityfire_FCCSfire_leafThermalFactorfire_necrosisCriticalTemperaturefire_necrosisHeightfire_plumeTemperaturefire_radialBoleNecrosisfire_RothermelfireHazardfordynforest_mapShrubTableforest_mapTreeTableforest_mapWoodyTablesforest_mergeShrubsforest_mergeTreesforest_reduceToDominantforest2abovegroundforest2belowgroundforest2growthInputforest2spwbInputfuel_FCCSfuel_stratificationfuel_windAdjustmentFactorgrowthgrowth_daygrowthInputherb_foliarBiomassherb_fuelLoadingherb_LAIhydraulics_averagePsihydraulics_averageRhizosphereResistancePercenthydraulics_correctConductanceForViscosityhydraulics_E2psiAbovegroundhydraulics_E2psiBelowgroundhydraulics_E2psiNetworkhydraulics_E2psiTwoElementshydraulics_E2psiVanGenuchtenhydraulics_E2psiXylemhydraulics_E2psiXylemUphydraulics_ECrithydraulics_EVanGenuchtenhydraulics_EXylemhydraulics_findRhizosphereMaximumConductancehydraulics_initSperryNetworkshydraulics_K2Psihydraulics_maximumSoilPlantConductancehydraulics_maximumStemHydraulicConductancehydraulics_proportionDefoliationSigmoidhydraulics_proportionDefoliationWeibullhydraulics_psi2Khydraulics_psi2Weibullhydraulics_psiCrithydraulics_referenceConductivityHeightFactorhydraulics_regulatedPsiTwoElementshydraulics_regulatedPsiXylemhydraulics_rootxylemConductanceProportionshydraulics_soilPlantResistanceshydraulics_supplyFunctionAbovegroundhydraulics_supplyFunctionBelowgroundhydraulics_supplyFunctionNetworkhydraulics_supplyFunctionOneXylemhydraulics_supplyFunctionPlothydraulics_supplyFunctionThreeElementshydraulics_supplyFunctionTwoElementshydraulics_taperFactorSavagehydraulics_terminalConduitRadiushydraulics_vanGenuchtenConductancehydraulics_vulnerabilityCurvePlothydraulics_xylemConductancehydraulics_xylemPsihydrology_herbaceousTranspirationhydrology_infiltrationAmounthydrology_infiltrationBoughtonhydrology_infiltrationGreenAmpthydrology_infiltrationRepartitionhydrology_interceptionPlothydrology_rainfallIntensityhydrology_rainInterceptionhydrology_snowMelthydrology_soilEvaporationhydrology_soilEvaporationAmounthydrology_soilWaterBalancehydrology_waterInputsinitSureauNetworkslight_cohortAbsorbedSWRFractionlight_cohortSunlitShadeAbsorbedRadiationlight_directionalExtinctionCoefficientlight_instantaneousLightExtinctionAbsortionlight_layerDiffuseIrradianceFractionlight_layerDirectIrradianceFractionlight_layerSunlitFractionlight_leafAngleBetaParameterslight_leafAngleCDFlight_longwaveRadiationSHAWlight_PARcohortlight_PARgroundlight_SWRgroundmodifyCohortParamsmodifyInputParamsmodifySpParamsmoisture_apoplasticPsimoisture_apoplasticRWCmoisture_leafWaterCapacitymoisture_pressureVolumeCurvePlotmoisture_sapwoodWaterCapacitymoisture_symplasticPsimoisture_symplasticRWCmoisture_tissueRWCmoisture_turgorLossPointmortality_dailyProbabilitymultiple_runsoptimization_evaluation_functionoptimization_evaluation_multicohort_functionoptimization_functionoptimization_multicohort_functionpheno_leafDevelopmentStatuspheno_leafSenescenceStatuspheno_updateLeavespheno_updatePhenologyphoto_electronLimitedPhotosynthesisphoto_GammaTempphoto_JmaxTempphoto_KmTempphoto_leafPhotosynthesisFunctionphoto_leafPhotosynthesisFunction2photo_multilayerPhotosynthesisFunctionphoto_photosynthesisphoto_photosynthesisBaldocchiphoto_rubiscoLimitedPhotosynthesisphoto_sunshadePhotosynthesisFunctionphoto_VmaxTempplant_basalAreaplant_characterParameterplant_coverplant_crownBaseHeightplant_crownLengthplant_crownRatioplant_densityplant_equilibriumLeafLitterplant_equilibriumSmallBranchLitterplant_foliarBiomassplant_fuelLoadingplant_heightplant_IDplant_individualAreaplant_LAIplant_largerTreeBasalAreaplant_parameterplant_phytovolumeplant_speciesplant_speciesNameplant_waterplot.fordynplot.forestplot.growthplot.growth_dayplot.pwbplot.pwb_dayplot.spwbplot.spwb_dayprint.summary.forestpwbregeneration_recruitmentregeneration_resproutingregeneration_seedmortalityregeneration_seedproductionregeneration_seedrefillresetInputsresistancesroot_coarseRootLengthsroot_coarseRootLengthsFromVolumeroot_coarseRootSoilVolumeroot_coarseRootSoilVolumeFromConductanceroot_conicDistributionroot_fineRootAreaIndexroot_fineRootBiomassroot_fineRootHalfDistanceroot_fineRootRadiusroot_fineRootSoilVolumeroot_horizontalProportionsroot_individualRootedGroundArearoot_ldrDistributionroot_rhizosphereMaximumConductanceroot_specificRootSurfaceAreasemi_implicit_integrationshinyplotshinyplot.fordynshinyplot.forestshinyplot.growthshinyplot.growth_dayshinyplot.pwbshinyplot.pwb_dayshinyplot.spwbshinyplot.spwb_dayshrub2forestsoilsoil_campbellParamsClappHornbergersoil_capacitancesoil_conductivitysoil_psisoil_psi2cVGsoil_psi2kVGsoil_psi2thetaSXsoil_psi2thetaVGsoil_redefineLayerssoil_retentionCurvePlotsoil_rockWeight2Volumesoil_saturatedConductivitySXsoil_saturatedWaterDepthsoil_temperatureChangesoil_temperatureGradientsoil_thermalCapacitysoil_thermalConductivitysoil_thetasoil_theta2psiSXsoil_theta2psiVGsoil_thetaFCsoil_thetaSATsoil_thetaSATSXsoil_thetaWPsoil_unsaturatedConductivitySXsoil_USDATypesoil_vanGenuchtenParamsCarselsoil_vanGenuchtenParamsTothsoil_watersoil_waterExtractablesoil_waterFCsoil_waterPsisoil_waterSATsoil_waterWPspecies_basalAreaspecies_characterParameterspecies_coverspecies_densityspecies_foliarBiomassspecies_fuelLoadingspecies_LAIspecies_parameterspwbspwb_dayspwbInputstand_basalAreastand_dominantTreeDiameterstand_dominantTreeHeightstand_dominantTreeSpeciesstand_foliarBiomassstand_fuelLoadingstand_hartBeckingIndexstand_LAIstand_meanTreeHeightstand_quadraticMeanTreeDiameterstand_shrubVolumestand_treeDensitysummary.fordynsummary.forestsummary.growthsummary.pwbsummary.soilsummary.spwbtrait_family_meanstransp_maximumTranspirationModeltransp_profitMaximizationtransp_stomatalRegulationPlottransp_transpirationGraniertransp_transpirationSperrytransp_transpirationSureautree2forestvprofile_fuelBulkDensityvprofile_leafAreaDensityvprofile_PARExtinctionvprofile_rootDistributionvprofile_SWRExtinctionvprofile_windExtinctionwaterUseEfficiencywind_canopyTurbulencewind_canopyTurbulenceModelwoodformation_growRingwoodformation_initRingwoodformation_relativeExpansionRatewoodformation_relativeGrowthRatewoodformation_temperatureEffect
Dependencies:abindarealassertthatbase64encbslibcachemCFtimeclassclassIntclicolorspacecommonmarkcpp11crayoncubelyrDBIdigestdplyre1071fansifarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclelubridatemagrittrMASSMatrixmemoisemeteolandmgcvmimemunsellncdfgeomncmetanlmepillarpkgconfigpromisesproxypurrrR6rappdirsRColorBrewerRcpprlangRNetCDFs2sassscalessfshinysourcetoolsstarsstringistringrtibbletidyrtidyselecttimechangeunitsutf8vctrsviridisLitewithrwkxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Control parameters for simulation models | defaultControl |
| Default forest management actions | defaultManagementArguments defaultManagementFunction |
| Default soil parameters | defaultSoilParams |
| Drought stress indicators | droughtStress |
| Creation of an empty forest | emptyforest |
| Evaluation of simulations results | evaluation evaluation_metric evaluation_plot evaluation_stats evaluation_table |
| Example daily meteorology data | examplemeteo |
| Example observed data | exampleobs |
| Extracts model outputs | extract |
| Fire behaviour functions | fire_behaviour fire_FCCS fire_Rothermel |
| Fire hazard | fireHazard |
| Forest dynamics | fordyn |
| Description of a forest stand. | exampleforest exampleforest2 forest |
| Map forest plot data | forest_mapShrubTable forest_mapTreeTable forest_mapWoodyTables |
| Forest complexity reduction | forest_mergeShrubs forest_mergeTrees forest_reduceToDominant forest_simplification |
| Fuel stratification and fuel characteristics | fuel_FCCS fuel_properties fuel_stratification |
| Forest growth | growth |
| Single-day simulation | growth_day spwb_day |
| Input for simulation models | growthInput modelInput spwbInput |
| Modify parameters | modifyCohortParams modifyInputParams modifyParams modifySpParams |
| Multiple model runs and function factories for optimization routines | multiple_runs optimization optimization_evaluation_function optimization_evaluation_multicohort_function optimization_function optimization_multicohort_function |
| Parameter average values | trait_family_means |
| Plot forest attributes | plot.forest shinyplot.forest |
| Plots simulation results | plot.fordyn plot.growth plot.pwb plot.spwb |
| Plots simulation results for one day | plot.growth_day plot.pwb_day plot.spwb_day |
| Example forest inventory data | poblet_trees |
| Reset simulation inputs | resetInputs |
| Soil-plant resistances | resistances |
| Standard fuel models (Albini 1976, Scott & Burgan 2005) | SFM_metric |
| Shiny app with interactive plots | shinyplot shinyplot.fordyn shinyplot.growth shinyplot.growth_day shinyplot.pwb shinyplot.pwb_day shinyplot.spwb shinyplot.spwb_day |
| Soil initialization | soil summary.soil |
| Redefine soil layer widths | soil_redefineLayers |
| Data tables with species parameter definitions and values | SpParams SpParamsDefinition SpParamsMED |
| Soil-plant water balance | pwb spwb |
| Summary of forest structure | print.summary.forest summary.forest |
| Summarize simulation results | summary.fordyn summary.growth summary.pwb summary.spwb |
| Single-cohort forests | shrub2forest tree2forest |
| Water use efficiency | waterUseEfficiency |
