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 ‘exampleforestMED2’
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 (‘Cochard’)
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’)