Changelog

Single-domain and dual-permeability soil water flows
Infiltration excess, saturation excess and capillarity rise reported
Lateral water flows and water table depth as inputs

Options leafCavitationEffects and stemCavitationEffects for Sperry
New taxonomic treatment (Name/AcceptedName)
Revision of Sureau sub-model
Replacement of vulnerability curve parameters by P12, P50 and P88
New parameters for Jarvis-type stomatal conductance in Sureau sub-model
XFT traits for vulnerability curves
Recording of leaf PLC for all sub-models
Richard-type soil water movement
Soil hydrology revised
New functions for spwb in agricultural lands
New function ‘extract’
New infiltration model Green-Ampt (1911)
Interception model Liu (2001) accepted as alternative to Gash (1995)
Optional “RainfallIntensity” (mm/h) as input in weather
New option “defaultRainfallIntensityPerMonth”
New functions “tree2forest”/“shrub2forest” to create forest objects with single cohorts
Van Genuchten parameters and Ksat can be specified directly when initializing soil
Saturation excess in soil flows
Evaluation of GPP, H and LE
Soil thermodynamics revised

Correction of a bug arisen in old Rcpp versions
Functions for seed production and bank dynamics (new parameter SeedLongevity)
New parameters for dispersal (SeedMass, DispersalType, DispersalDistance, DispersalShape)
Recording of leaf PLC for Sperry and Sureau sub-models

Fixing memory access errors

New option ‘months’ in simulation summaries.
Leaf area, foliar biomass and fuels of shrubs and herbs depend on the leaf area of plants above
Survival model based on basal area available as an alternative to fixed mortality baseline rates
New control thresholds ‘minimumShrubCohortCover’ and ‘minimumTreeCohortDensity’ for cohort removal
Tree bark thickness parameters added to SpParamsMED

Fire severity implemented
Crown bud percent decreases with PLC and fire, increases with SA growth and regulates primary growth rate
Forest objects can now have additional variables defined (LAI, foliar biomass, fuel loading), to override estimations from allometric models
New example forest object ‘exampleforest2’

Herbaceous information in summary.forest
Herbaceous transpiration added to the water balance
Weather input can now have dates as Date or POSIXct objects in column ‘dates’ instead of row names
Weather input can now have missing values in MinRelativeHumidity, MaxRelativeHumidity and Radiation

Leaf area limited by allometries
Functions ‘growthInput()’ and ‘spwbInput()’ no longer visible at the user level
No calculation mode forest structure (US mode removed)
Control flag options to restrict output in ‘spwb()’ ‘pwb()’ and ‘growth()’
Control flag to calculate fire hazard during ‘spwb()’ ‘pwb()’ and ‘growth()’ simulations
Integration of SurEau-Ecos v2.0 code as new transpiration mode (‘Sureau’)
Bug correction tissue moisture and water balance in granier’s model
Tree biomass allometries revised.
Tree foliar biomass corrected for high density. Shrub foliar biomass/fuel limited by tree basal area.

Bounded leaf area index
IFNcodes out of SpParams
PlantPsi lower limit set to -40 MPa
Psi_Critic no longer used in Granier submodel (Stem vulnerability curve used instead)
New parameter Exp_Extract to model transpiration decrease in Granier submodel
Update growth/recruitment parameters
Removed fordyn dependency on input PET

Allows species strings as input in forests objects
Clean code in growth.cpp

Replacing sprintf calls
Update of forest_mergeShrubs and forest_mergeTrees

Function ‘redefineSoilLayers’ moved to package ‘medfateutils’
Elements ‘ID’ and ‘patchsize’ removed from ‘forest’
Bug correction in defaultManagementFunction for ‘above-systematic’ and ‘below-systematic’
New management option ‘targetTreeSpecies’
Fire hazard estimation includes dead canopy fuels (Ruffault et al. 2023)

New meta-modelling parameters
New growth/senescence parameters

New control parameter ‘subdailyCarbonBalance’, applying to growth simulations with transpiration = “Sperry”
Hydraulic redistribution implemented for transpiration = “Granier”
Growth with “Sperry” using canopy temperature

Imputation relationship between RGRcambiummax and SRsapwood
Dynamic modification of LeafPI0 and StemPI0 removed
Non-stomatal limitations to photosynthesis removed

MeanTemperature not longer an input to medfate. It is calculated from minimum and maximum temperature.
MeanRelativeHumidity not longer an input to medfate.
PET not longer an input to medfate. It is calculated internally.
New simulation parameter ‘CO2ByYear’ to specify year by year variations in atmospheric CO2
Sensitivity of photosynthesis to VPD and CO2 concentration under Granier’s model
New species parameters ‘WUE_co2’, ‘WUE_vpd’ to regulate the effect of CO2 concentration and VPD under Granier’s model
Species parameter ‘WUE_decay’ renamed ‘WUE_par’
Control parameter ‘Catm’ renamed ‘defaultCO2’
New output data frame ‘CarbonBalance’ for growth

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 ‘cavitationRecoveryMaximumRate’
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’.

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