• Maximum stem conductance to avoid overestimation of stem conductance in small shrubs
  • Bug correction in summary.forest
  • Allows filling missing Z50/Z95 values from SpParams when creating model inputs
  • Reducing unused parameters for Sperry model
  • Reducing computational time for Sperry model
  • Function fireHazard now accepts objects spwb_day and growth_day
  • Cleaning for CRAN
  • New article to prepare model inputs
  • SpParamsMED include the results of parameter estimation exercises
  • RGRsapwoodmax and RGRcambiummax regulate sapwood formation for shrubs/trees, respectively
  • Simplified sapwood growth (no ring of cells)
  • Revision of recruitment model, with the addition of a recruitment probability (ProbRecr) within the bioclimatic limits
  • Temperature effects on sapwood conversion to heartwood
  • Correction of estimation of Psi_Extract from turgor loss point
  • Estimation of RSSG from shade tolerance
  • Minimum DBH parameter in stand metrics
  • Basic water balance model with relative water content
  • ‘pRootDisc’ eliminated from species parameters
  • Plant water balance and cuticular transpiration added to the basic water balance model
  • Water pools revised for the basic and water balance models
  • Shared water pools is now controlled via parameter ‘rhizosphereOverlap’
  • New species-specific parameter ‘MortalityBaselineRate’
  • Live fuel moisture content now included in simulation results
  • New species-specific parameter ‘RSSG’ (minimum relative starch for sapwood growth)
  • Control parameter ‘modifyInput’ is no longer available. Functions ‘spwb’, ‘pwb’ and ‘growth’ do not modify input objects and return an element ‘spwbOutput’ or ‘growthOutput’ with a copy of the final state.
  • Tree cover (open grown assumption)
  • Parameters ‘ShrubCover’ and ‘CanopyCover’ no longer required in function fuel_FCCS
  • Input weather stored in output from functions ‘spwb’, ‘pwb’ and ‘growth’
  • New function ‘fireHazard’.
  • Relative bias and relative MAE as evaluation metrics
  • Drought-related leaf senescence only occurring if ‘StemPLC’ increases
  • Embolized sapwood proportion discounted from sapwood maintenance respiration
  • Evaluation of diameter increment (DI), DBH and Height series
  • Output growth rates not relative to sapwood area
  • Nitrogen content for leaves, sapwood and fine roots added. ‘Nleaf’ replaces ‘Narea’ as the latter can be calculated from ‘Nleaf’ using ‘SLA’.
  • Maintenance respiration rates based on N concentration of tissues
  • spwb model with Granier transpiration now extracts water from soil layer according to unsaturated conductivity.
  • shinyplot generic function.
  • Update parameters fHDmin and fHDmax.
  • New vignette ‘IFNEvaluation’
  • New parameter ‘WUE_decay’ for reduction of relative WUE in Granier’s model
  • Tissue construction costs are now species-specific parameters.
  • Fine root growth and senescence made equal between Granier and Sperry models, inducing a new parameter ‘Ar2Al’ for Granier’s model.
  • Functions ‘spwb_stress’, ‘spwb_resistances’ and ‘spwb_waterUseEfficiency’ renamed to ‘droughtStress’, ‘resistances’ and ‘waterUseEfficiency’, respectively, since they can now be applied to the output of several simulation function.
  • Plant biomass balance in growth. Structural changes are now daily in growth simulations.
  • Bug correction in shrub structural update. Shrub dynamics default set to TRUE.
  • DBH/Height plots from growth output.
  • IMPORTANT: New species parameter table.
  • Summary functions revised, including new function ‘summary.fordyn’
  • Collating intra-annual ‘fordyn’ results for plotting.
  • Forest management enabled in function ‘fordyn’ and default management actions defined in ‘defaultManagementFunction’ and ‘defaultManagementArguments’
  • DOY, Photoperiod and JulianDay can be taken from weather input in functions ‘spwb’, ‘pwb’ and ‘growth’.
  • CO2 made an daily input weather variable, in addition to the default control parameter ‘Catm’
  • New function ‘shinyplot’ to create interactive graphics
  • New function ‘plot.fordyn’ to display annual (step) summaries of forest dynamics
  • New example vignette ‘FontBlanche’
  • Modification of evaluation functions to separate the evaluation of total evapotranspiration (‘ETR’) from the evaluation of soil evaporation + plant transpiration (‘SE+TR’)
  • Bug correction: sub-daily stomatal conductance plots
  • Maximum relative sapwood growth rates effective
  • New option ‘summary.freq’ in plot.spwb and plot.growth
  • New species parameters (sapwood and fine root senescence rates)
  • Defaults for ‘conduit2sapwood’ from taxonomical family
  • IMPORTANT: New species parameter tables (including estimates for conduit2sapwood)
  • Parameter ‘ParticleDensity’ eliminated, as it is now calculated from ‘LeafDensity’, ‘WoodDensity’ and ‘r635’
  • IMPORTANT: New species parameter tables
  • New control parameter ‘fillMissingSpParams’
  • Defaults for ‘LeafDensity’, ‘WoodDensity’, ‘LeafPI0’, ‘LeafEPS’ and ‘LeafAF’ from taxonomical family.
  • New species categorical params (for inbuilt imputation) ‘LeafShape’ and ‘LeafSize’
  • Parameter ‘Flammability’ index eliminated (non-meansurable property of flammability).
  • Parameter ‘LeafLitterFuelType’ eliminated because it is derived from ‘LeafShape’ and ‘LeafSize’.
  • Defaults added for ‘r635’, ‘heatContent’, ‘LigninPercent’ and ‘SAV’ according to ‘LeafShape’ and ‘LeafSize’
  • New function ‘getSpParamsDefinition()’ returns definition of species parameters.
  • Inbuilt defaults added for shrub allometries, depending on ‘LifeForm’ and ‘Hmax’, and for tree allometries, depending on ‘Group’.
  • Default value added for ‘pDead’.
  • Functions soilgridsParams() and forest_map*Tables() moved to package ‘medfateutils’ available at GitHub (emf-creaf/medfateutils).
  • Dependency ‘spdep’ removed
  • Bug correction ‘windKatul.cpp’
  • Calibrated minimum bioclimatic parameters for recruitment (SpParamsMED)
  • Explicit species input parameters for phenology
  • New simulation function ‘fordyn()’, including recruitment process
  • New function ‘mergeShrubs’
  • New functions ‘species_parameter’ and ‘species_characterParameter’
  • Dessication/defoliation homogenized across transpiration modes in growth function
  • Revision of mortality (stochastic/deterministic, whole-cohort/density)
  • Update Psi_Extract according to Psi_TLP (Hydratry)
  • New control flags for defoliation/starvation/dessication in growth simulations
  • New control flag for sink limitation in growth simulations
  • Revision of phenology submodel
  • Respiration rate for leaves made optionally species-specific.
  • Update shrub allometries from De Caceres et al. (2019).
  • LAI_live and LAI_expanded in growth.
  • Update SpParamsUS (missing values for new parameters).
  • Parameters of Granier’s equation made species-specific if available
  • Parameter modification dependencies revised
  • Modification of input objects is now optional
  • Update of function transp_maximumTranspirationModel
  • Photosynthesis in Granier’s model corresponds to gross photosynthesis and is proportional to transpiration
  • Cloning initial object for optimization
  • Leaf growth costs always drawn from sugar sapwood
  • Bug correction: LWRnet calculation
  • Bug correction: Sperry model does not crash when LAIstand = 0
  • IMPORTANT: Soil input merged with model input. Now the calls to simulation functions (e.g., spwb, growth) do not need to include soil as input parameter.
  • Bug correction: NaN values for theta > theta_sat in van Genuchten psi computation
  • Function modifyInputParams now accepts modification of soil layer properties
  • Sensitivity/Calibration vignette updated
  • New canopy turbulence models by Katul et al (2004).
  • Long-wave net radiation balance for layered canopies following Flerchinger et al. (2009).
  • Multi-layer canopy energy balance as in Bonan et al. (2014)
  • New option ‘depthMode’ to calculate fuel depth in ‘fuel_FCCS’.
  • Modification of ‘vprofile_windExtinction’ to draw turbulence models.
  • Stomatal conductance now denoted as Gsw or GSW
  • Boundary layer conductance considered
  • Leaf water potential influencing leaf vapour pressure
  • Flexible temporal resolution of model evaluation
  • Basal area index evaluation
  • New model evaluation functions
  • New optimization function factories
  • New function ‘modifyInputParams’
  • Control parameters set to a nested list
  • New vignette for calibration and sensitivity analysis
  • GW sunlit/shade minimum/maximum daily output
  • FMC calculations with basic water balance output
  • New output in growth simulation (biomass values)
  • New function ‘moisture_cohortFMCDay’
  • Modification of Z50/Z95
  • Root exudation added to carbon balance
  • Revision sapwood growth
  • Growth cost for fine roots in basic model
  • Translocation for carbon during senescence
  • Bug correction in fuel calculations with US mode
  • Control option ‘rockyLayerDrainage’ instead of ‘drainage’ to disable macropore vertical outflow in layers with > 95% of rocks
  • Soil parameter Kdrain for saturated vertical hydraulic conductivity towards groundwaters (deep drainage)
  • Improved validation plots with confidence intervals
  • Nash-Sutcliffe efficiency (NSE) implemented in spwb_validation
  • Bug correction on the use of organic matter in Saxton (2006) equations (thanks to Milan Fischer).
  • Recodification of soilgridParams due to new SoilGrids REST API (removed dependency from GSIF).
  • New function ‘redefineSoilLayers’
  • New root functions
  • Bulk density stored in soil object initialization
  • Advanced plant water pools
  • Belowground inputs restructured
  • Reorganization of growth function
  • Clarification of gross and net photosynthesis
  • ‘spwb_resetInputs’ to ‘resetInputs’
  • Dependence of kmax on temperature (due to sap dynamic viscosity) incorporated
  • Functions plot.spwb and plot.pwb modified to draw subdaily dynamics for a subset of dates
  • Small bug fixes
  • update ‘spwb_resetInputs’
  • Update of plant water pools
  • New output (annual stand summaries and aboveground structure) for function ‘growth’
  • New parametrization data set ‘SpParamsUS’
  • Function ‘hydrology_verticalInputs’ replaced by ‘hydrology_soilWaterInputs’ and ‘hydrology_soilInfiltrationPercolation’.
  • New simulation control option: ‘plantWaterPools’.
  • Hard (Imports) dependency from GSIF changed to soft (Suggests) one.
  • Update supply function plot.
  • New function ‘soil_rockWeight2Volume’
  • Corrections to energy balance for zero LAI (deciduous species)
  • SFI functions moved to medfateland
  • soilgridParams modified to accept a SpatialPoints object as input
  • New function ‘spwb_sensitivity’ for sensitivity analyses
  • New control parameter ‘unlimitedSoilWater’
  • Bug correction in canopy height with LAI = 0
  • Modifications of spwb_ldrOptimization to work with transpirationMode = “Sperry”
  • New function spwb_ldrExploration
  • New control parameter ‘fracLeafResistance’
  • Different control options for parameter ‘cavitationRefill’
  • New control parameter ‘refillMaximumRate’
  • Control parameter ‘hydraulicCostFunction’ replaced by ‘costModifier’ and ‘gainModifier’
  • New control parameter ‘cuticularTranspiration’
  • Numerical controls to avoid NaN in functions ‘soil_theta2psiSX’ and ‘soil_psi2thetaSX’
  • Bug correction in estimation of root conductance proportions
  • Water balance console output modified in spwb
  • New approach to plant water compartments ‘capacitance = TRUE’
  • Output of plant water balance
  • New option in control
  • Stem segments fixed to two
  • functional parameter pRootDisc removed from Sperry’s advanced model
  • Bug correction in fuel_cohortFineFMC
  • Remove ksympver and add klatleaf/klatstem to control parameters
  • Reference book (medfatebook) launched
  • Fraction of absorbed SWR output in Granier’s transpiration
  • ‘Stand’ data frame output in spwb(), separated from ‘WaterBalance’
  • New function ‘forest_mapTreeTable’, ‘forest_mapShrubTable’ and ‘forest_mapWoodyTables’
  • ’stand_*’ functions for stand-level properties
  • No SWR soil absorption when snow pack is present in Sperry’s model
  • verticalLayerSize made a control parameter for Granier’s model
  • Changes in light parameters: New parameter ‘alphaSWR’. ‘albedo’ renamed to ‘gammaSWR’. ‘k’ renamed to ‘kPAR’
  • Modification of meteoland to better calculate direct/diffuse light on slopes
  • Added Narea parameter to facilitate estimation of Vmax298
  • New function ‘spwb_validation’.
  • Plot functions using ggplot.
  • Improvement of infiltration repartition for varying macroporosity.
  • Input values for latitude and topography stored in the result of simulations.
  • Wind for each cohort stored in the result of transp_transpirationSperry and spwb_day.
  • Export Ci from spwb_day.
  • New function ‘maximumTranspirationRatioPlot’
  • Output of min/max water potential for sunlit and shade leaves.
  • New function ‘soil_waterRetentionPlot’
  • New function ‘waterUseEfficiency’
  • Default Van Genuchten PTF set to ‘Toth’
  • New functions ‘modifySpParams’ and ‘modifyCohortParams’.
  • New function ‘hydrology_interceptionPlot’
  • Move spatial classes and methods to package ‘medfateland’
  • Implement underscores instead of dots to separate function groups and function names
  • New function transp_Granier.
  • Bug corrected in spwb.plot for snow plotting.
  • New function ‘pwb’.
  • New function ‘snowMelt’.
  • Transpiration model changed to Granier and Sperry.
  • PLC set to zero when DOY = 1
  • New functions for leaf phenology
  • Fixing bugs for installation in all platforms
  • Update docs
  • Shrub root system using LDR (Z50 and Z95)
  • Percolation of infiltrated water consistent with layer subdivision
  • New function soil.infiltrationRepartition()
  • Adding interception to evapotranspiration
  • Checked for CRAN
  • Accounting of hydraulic redistribution
  • Update plotting functions
  • New function vprofile.RootDistribution.
  • New functions for water at wilting point (-1.5 MPa)
  • Print extractable water of soil
  • Bug correction in photosynthesis (now done per leaf area basis)
  • Leaf area distribution (and crown fine biomass distribution) following truncated normal [-1.5,1.5]
  • Interception corrected in the complex model
  • Etol set to 0.0000001
  • spwb export of dEdP (equivalent to soil-plant conductance)
  • Subdaily results can be stored for spwb
  • New function spwb.resistances to calculate and draw segment resistances for spwb simulation results.
  • Cohort parameter search by SpIndex
  • Gwmin set to zero when capacitance = FALSE
  • New function spwb.stress to calculate drought stress indices
  • PlantStress in complex mode now is calculated as relative soil-plant conductance, for compatibility with the simple mode.
  • Function name changes for interception and soil hydrology
  • Leaf and stem water compartments added
  • Update of functions ‘spwb.day’ and ‘plot.spwb.day’
  • Analytical integral of the van Genuchten function
  • Analytical inverse of the incomplete gamma function
  • Adapt to Rcpp changes
  • Stem water compartments
  • Saturated theta in Saxton model
  • Water table depth added
  • Boolean option ‘drainage’ added to soil water balance
  • Added subsurface flow processes to spwbgrid
  • Function name ‘swb’ (and all related functions) changed to ‘spwb’
  • Added snow pack to soil state variables.
  • Added new control option ‘snowpack’ for snowpack dynamics simulation (only when transpirationMode=‘Simple’)
  • Changed names of spatial classes from ‘Forest’ to ‘Landscape’
  • Changed name of ‘exampleSPF’ to ‘exampleSPL’.
  • Function ‘spwbgrid’ functional again.
  • Improved documentation of function ‘spwb.day’
  • ‘DOY’ no longer needed as column in meteorological input.
  • Growth degree days added as output of ‘swb()’
  • New function ‘swb.resetInputs()’
  • New function ‘hydraulics.vulnerabilityCurvePlot()’
  • Reorganization of help for hydraulics.
  • Documentation of tissue moisture functions.
  • Update function ‘plot.growth()’
  • New functions for tissue moisture
  • New function ‘fuel.cohortFineFMC’
  • New option ‘bySpecies’ to aggregate results by species in functions ‘summary.swb’ and ‘summary.growth’
  • New option ‘bySpecies’ to aggregate results by species in functions ‘plot.swb’ and ‘plot.swb.day’
  • Bulk density added to soil parameters
  • New set of pedotransfer functions to calculate VG parameters from texture, bulk density and organic content
  • New functions for pressure-volume curves
  • Rmarkdown vignettes
  • Added Van Genuchten pedotransfer functions
  • New control parameter added (for soil functions)
  • New function ‘forest2belowground’
  • Update ‘summary.swb’ function
  • Network representation of the continuum now includes a leaf segment
  • Stem fraction of total resistance removed as estimation of root xylem conductance
  • Default kleaf_max (8 for temperate angiosperms and 5 for gymnosperms)
  • New parameter rootxylem_kmax (hydraulic conductivity of roots)
  • Modification of default for ntrial
  • Three element supply function added
  • Parameters of the leaf maximum conductance and leaf vulnerability curve added
  • Structure of swb.day output
  • Increased output (leaf temperature, stomatal conductance and leaf VPD) in swb.day
  • Taper modifications
  • New function plot.swb.day
  • Atmospheric CO2 is an input control parameter
  • Added Hmed as species parameter (to correct reference conductivity values)
  • Modified documentation
  • Alternative way of calculating maximum root conductance
  • Default value for averageFracRhizosphereResistance changed to 0.15
  • Root vulnerability curve parameters taken from stem vulnerability curve when missing (d_root = d_stem/2)
  • Leaf radiation balance with LWR from soil
  • New output for swb
  • Bug fix in plot.swb (match according to transpiration model)
  • Profit maximization for sunlit and shade leaves separately
  • Bug correction in swb
  • Check on stomatal conductances in profit maximization
  • Radiation absorbed by trunks
  • Separation of energy balance components
  • New control parameter: Canopy thermal capacity per LAI
  • Update of calls to meteoland (diffuse radiation)
  • Wind value when missing data added to control
  • Minimum windspeed (1.0 m/s)
  • Progressive leaf fall
  • Bug correction (swb.plot)
  • Energy balance output/plot
  • Modified conductance scaling
  • Added new parameter ‘LeafWidth’
  • Design changes for radiation balance (soil/canopy/atmosphere)
  • Added temperature balance in summary.swb and plot.swb
  • Added new parameter ‘albedo’
  • Documentation of soil thermodynamics
  • Energy balance output in swb.day
  • Added soil temperature state variables (for ‘complex’ mode)
  • Added canopy temperature state variable (for ‘complex’ mode)
  • ‘gdd’ in swbInput used as initial growth degree days
  • Soil thermodynamics.
  • Added vertical layer size as option in control.
  • New function ‘soilgridsParams’ (calls functions in package ‘GSIF’)
  • Added longwave radiation to leaf energy balance.
  • Added new pedotransfer functions with organic matter.
  • New function added ‘soil.waterFC’.
  • Xylem taper added as option in control.
  • Hydraulic cost function added as option in control.
  • New function ‘light.instantaneousLightExtinctionAbsortion’.
  • New functions ‘transp.dayCanopyTranspiration’ and ‘transp.dayCanopyTranspirationPlot’.
  • Control of numerical methods for supply function added to ‘defaulControlParams’.
  • Added new function ‘swb.ldrCalibration’ to calibrate root distribution for swb simulations (by Victor Granda)
  • Added documentation for light extinction functions ‘light.layerIrradianceFraction’, ‘light.layerSunlitFraction’ and ‘light.cohortSunlitShadeAbsorbedRadiation’.