Package: medfate 4.8.0

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:Miquel De Cáceres [aut, cre, cph], Nicolas Martin-StPaul [aut], Víctor Granda [aut], Antoine Cabon [aut], Jordi Martínez-Vilalta [ctb], Maurizio Mencuccini [ctb], Julien Ruffault [ctb], François Pimont [ctb], Hervé Cochard [ctb], Aitor Améztegui [ctb], Shengli Huang [ctb], Léa Veuillen [ctb], John Burkardt [cph]

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medfate.pdf |medfate.html✨
medfate/json (API)

# Install 'medfate' in R:

install.packages('medfate', repos = c('https://emf-creaf.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emf-creaf/medfate/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

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

On CRAN:

7.55 score 11 stars 1 packages 173 scripts 571 downloads 321 exports 81 dependencies

Last updated 10 days agofrom:b09a3859bf. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024
R-4.5-win-x86_64	OK	Nov 13 2024
R-4.5-linux-x86_64	OK	Nov 13 2024
R-4.4-win-x86_64	OK	Nov 13 2024
R-4.4-mac-x86_64	OK	Nov 13 2024
R-4.4-mac-aarch64	OK	Nov 13 2024
R-4.3-win-x86_64	OK	Nov 13 2024
R-4.3-mac-x86_64	OK	Nov 13 2024
R-4.3-mac-aarch64	OK	Nov 13 2024

Exports:aspwb aspwb_day aspwb_day_inner aspwbInput biophysics_irradianceToPhotonFlux biophysics_leafTemperature biophysics_leafTemperature2 biophysics_leafVapourPressure biophysics_radiationDiurnalPattern biophysics_temperatureDiurnalPattern biophysics_waterDynamicViscosity carbon_carbonCompartments carbon_leafStarchCapacity carbon_leafStructuralBiomass carbon_osmoticWaterPotential carbon_relativeSapViscosity carbon_sapwoodStarchCapacity carbon_sapwoodStructuralBiomass carbon_sapwoodStructuralLivingBiomass carbon_sugarConcentration carbon_sugarStarchDynamicsLeaf carbon_sugarStarchDynamicsStem copy_model_output defaultControl defaultManagementArguments defaultManagementFunction defaultSoilParams droughtStress emptyforest evaluation_metric evaluation_plot evaluation_stats evaluation_table extract fire_barkThermalDiffusivity fire_FCCS fire_leafThermalFactor fire_necrosisCriticalTemperature fire_necrosisHeight fire_plumeTemperature fire_radialBoleNecrosis fire_Rothermel fireHazard fordyn forest_mapShrubTable forest_mapTreeTable forest_mapWoodyTables forest_mergeShrubs forest_mergeTrees forest_reduceToDominant forest2aboveground forest2belowground forest2growthInput forest2spwbInput fuel_FCCS fuel_stratification fuel_windAdjustmentFactor general_communication_structures growth growth_day growth_day_inner growthInput herb_foliarBiomass herb_fuelLoading herb_LAI hydraulics_averagePsi hydraulics_averageRhizosphereResistancePercent hydraulics_correctConductanceForViscosity hydraulics_E2psiAboveground hydraulics_E2psiBelowground hydraulics_E2psiNetwork hydraulics_E2psiTwoElements hydraulics_E2psiVanGenuchten hydraulics_E2psiXylem hydraulics_E2psiXylemUp hydraulics_ECrit hydraulics_EVanGenuchten hydraulics_EXylem hydraulics_findRhizosphereMaximumConductance hydraulics_initSperryNetworks hydraulics_K2Psi hydraulics_maximumSoilPlantConductance hydraulics_maximumStemHydraulicConductance hydraulics_proportionDefoliationSigmoid hydraulics_proportionDefoliationWeibull hydraulics_psi2K hydraulics_psi2Weibull hydraulics_psiCrit hydraulics_referenceConductivityHeightFactor hydraulics_regulatedPsiTwoElements hydraulics_regulatedPsiXylem hydraulics_rootxylemConductanceProportions hydraulics_soilPlantResistancesSigmoid hydraulics_soilPlantResistancesWeibull hydraulics_supplyFunctionAboveground hydraulics_supplyFunctionBelowground hydraulics_supplyFunctionNetwork hydraulics_supplyFunctionOneXylem hydraulics_supplyFunctionPlot hydraulics_supplyFunctionThreeElements hydraulics_supplyFunctionTwoElements hydraulics_taperFactorSavage hydraulics_terminalConduitRadius hydraulics_vanGenuchtenConductance hydraulics_vulnerabilityCurvePlot hydraulics_xylemConductance hydraulics_xylemConductanceSigmoid hydraulics_xylemPsi hydrology_herbaceousTranspiration hydrology_infiltrationAmount hydrology_infiltrationBoughton hydrology_infiltrationGreenAmpt hydrology_infiltrationRepartition hydrology_interceptionPlot hydrology_rainfallIntensity hydrology_rainInterception hydrology_snowMelt hydrology_soilEvaporation hydrology_soilEvaporationAmount hydrology_soilWaterBalance hydrology_waterInputs initSureauNetworks instance_communication_structures light_cohortAbsorbedSWRFraction light_cohortSunlitShadeAbsorbedRadiation light_directionalExtinctionCoefficient light_instantaneousLightExtinctionAbsortion light_layerDiffuseIrradianceFraction light_layerDirectIrradianceFraction light_layerSunlitFraction light_leafAngleBetaParameters light_leafAngleCDF light_longwaveRadiationSHAW light_PARcohort light_PARground light_SWRground modifyCohortParams modifyInputParams modifySpParams moisture_apoplasticPsi moisture_apoplasticRWC moisture_leafWaterCapacity moisture_pressureVolumeCurvePlot moisture_sapwoodWaterCapacity moisture_symplasticPsi moisture_symplasticRWC moisture_tissueRWC moisture_turgorLossPoint mortality_dailyProbability multiple_runs optimization_evaluation_function optimization_evaluation_multicohort_function optimization_function optimization_multicohort_function pheno_leafDevelopmentStatus pheno_leafSenescenceStatus pheno_updateLeaves pheno_updatePhenology photo_electronLimitedPhotosynthesis photo_GammaTemp photo_JmaxTemp photo_KmTemp photo_leafPhotosynthesisFunction photo_leafPhotosynthesisFunction2 photo_multilayerPhotosynthesisFunction photo_photosynthesis photo_photosynthesisBaldocchi photo_rubiscoLimitedPhotosynthesis photo_sunshadePhotosynthesisFunction photo_VmaxTemp plant_basalArea plant_characterParameter plant_cover plant_crownBaseHeight plant_crownLength plant_crownRatio plant_density plant_equilibriumLeafLitter plant_equilibriumSmallBranchLitter plant_foliarBiomass plant_fuelLoading plant_height plant_ID plant_individualArea plant_LAI plant_largerTreeBasalArea plant_parameter plant_phytovolume plant_species plant_speciesName plant_water plot.fordyn plot.forest plot.growth plot.growth_day plot.pwb plot.pwb_day plot.spwb plot.spwb_day print.summary.forest pwb regeneration_recruitment regeneration_resprouting regeneration_seedmortality regeneration_seedproduction regeneration_seedrefill resetInputs resistances root_coarseRootLengths root_coarseRootLengthsFromVolume root_coarseRootSoilVolume root_coarseRootSoilVolumeFromConductance root_conicDistribution root_fineRootAreaIndex root_fineRootBiomass root_fineRootHalfDistance root_fineRootRadius root_fineRootSoilVolume root_horizontalProportions root_individualRootedGroundArea root_ldrDistribution root_rhizosphereMaximumConductance root_specificRootSurfaceArea semi_implicit_integration shinyplot shinyplot.fordyn shinyplot.forest shinyplot.growth shinyplot.growth_day shinyplot.pwb shinyplot.pwb_day shinyplot.spwb shinyplot.spwb_day shrub2forest soil soil_campbellParamsClappHornberger soil_capacitance soil_conductivity soil_psi soil_psi2cVG soil_psi2kVG soil_psi2thetaSX soil_psi2thetaVG soil_redefineLayers soil_retentionCurvePlot soil_rockWeight2Volume soil_saturatedConductivitySX soil_saturatedWaterDepth soil_temperatureChange soil_temperatureGradient soil_thermalCapacity soil_thermalConductivity soil_theta soil_theta2psiSX soil_theta2psiVG soil_thetaFC soil_thetaSAT soil_thetaSATSX soil_thetaWP soil_unsaturatedConductivitySX soil_USDAType soil_vanGenuchtenParamsCarsel soil_vanGenuchtenParamsToth soil_water soil_waterExtractable soil_waterFC soil_waterPsi soil_waterSAT soil_waterWP species_basalArea species_characterParameter species_cover species_density species_foliarBiomass species_fuelLoading species_LAI species_parameter spwb spwb_day spwb_day_inner spwbInput stand_basalArea stand_dominantTreeDiameter stand_dominantTreeHeight stand_dominantTreeSpecies stand_foliarBiomass stand_fuelLoading stand_hartBeckingIndex stand_LAI stand_meanTreeHeight stand_quadraticMeanTreeDiameter stand_shrubVolume stand_treeDensity summary.fordyn summary.forest summary.growth summary.pwb summary.soil summary.spwb trait_family_means transp_maximumTranspirationModel transp_profitMaximization transp_stomatalRegulationPlot transp_transpirationGranier transp_transpirationSperry transp_transpirationSureau tree2forest vprofile_fuelBulkDensity vprofile_leafAreaDensity vprofile_PARExtinction vprofile_rootDistribution vprofile_SWRExtinction vprofile_windExtinction waterUseEfficiency wind_canopyTurbulence wind_canopyTurbulenceModel woodformation_growRing woodformation_initRing woodformation_relativeExpansionRate woodformation_relativeGrowthRate woodformation_temperatureEffect

Dependencies:abind areal assertthat base64enc bslib cachem CFtime class classInt cli colorspace commonmark cpp11 crayon cubelyr DBI digest dplyr e1071 fansi farver fastmap fontawesome fs generics ggplot2 glue gtable htmltools httpuv isoband jquerylib jsonlite KernSmooth labeling later lattice lifecycle lubridate magrittr MASS Matrix memoise meteoland mgcv mime munsell ncdfgeom ncmeta nlme pillar pkgconfig promises proxy purrr R6 rappdirs RColorBrewer Rcpp rlang RNetCDF s2 sass scales sf shiny sourcetools stars stringi stringr tibble tidyr tidyselect timechange units utf8 vctrs viridisLite withr wk xtable

Citation

Development and contributors

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