biomee_gs_leuning_drivers {rsofun} | R Documentation |
rsofun BiomeE driver data (Leuning photosynthesis model)
Description
Small dataset representing the driver to run the BiomeE-model at the CH-LAE site
using the Leuning photosynthesis specification (and half-hourly time step)
It can also be used together with leaf trait data from CH-LAE (biomee_validation
)
to optimize model parameters.
Usage
biomee_gs_leuning_drivers
Format
A tibble of driver data.
- sitename
Site name
- params_siml
Simulation parameters as a data.frame, including the following data:
- spinup
Flag indicating whether this simulation does spin-up.
- spinupyears
Number of spin-up years.
- recycle
Length of standard recycling period (years).
- firstyeartrend
First transient year.
- nyeartrend
Number of transient years.
- steps_per_day
Time resolution (day-1).
- do_U_shaped_mortality
Flag indicating whether U-shaped mortality is used.
- update_annualLAImax
Flag indicating whether updating LAImax according to mineral N in soil.
- do_closedN_run
Flag indicating whether doing N closed runs to recover N balance enforcing 0.2 kg N m-2 in the inorganic N pool.
- code_method_photosynth
String specifying the method of photosynthesis used in the model, either "pmodel" or "gs_leuning".document()
- code_method_mortality
String indicating the type of mortality in the model. One of the following: "dbh" is size-dependent mortality, "const_selfthin" is constant self thinning (in development), "cstarvation" is carbon starvation, and "growthrate" is growth rate dependent mortality.
- site_info
Site meta info in a data.frame. This data structure can be freely used for documenting the dataset, but must include at least the following data:
- lon
Longitude of the site location.
- lat
Latitude of the site location.
- elv
Elevation of the site location, in meters.
- forcing
Forcing data.frame used as input
- ppfd
Photosynthetic photon flux density (mol s-1 m-2)
- tair
Air temperature (deg C)
- vpd
Vapor pressure deficit (Pa)
- rain
Precipitation (kgH2O m-2 s-1 == mm s-1)
- wind
Wind velocity (m s-1)
- pair
Atmospheric pressure (pa)
- co2
CO2 atmospheric concentration (ppm)
- params_tile
Tile-level model parameters, into a single row data.frame, including the following data:
- soiltype
Integer indicating the type of soil: Sand = 1, LoamySand = 2, SandyLoam = 3, SiltLoam = 4, FrittedClay = 5, Loam = 6, Clay = 7.
- FLDCAP
Field capacity (vol/vol). Water remaining in a soil after it has been thoroughly saturated and allowed to drain freely.
- WILTPT
Wilting point (vol/vol). Water content of a soil at which plants wilt and fail to recover.
- K1
Fast soil C decomposition rate (year
^{-1}
).- K2
Slow soil C decomposition rate (year
^{-1}
).- K_nitrogen
Mineral Nitrogen turnover rate (year
^{-1}
).- MLmixRatio
Ratio of C and N returned to litters from microbes.
- etaN
N loss rate through runoff (organic and mineral) (year
^{-1}
).- LMAmin
Minimum LMA, leaf mass per unit area, kg C m
^{-2}
.- fsc_fine
Fraction of fast turnover carbon in fine biomass.
- fsc_wood
Fraction of fast turnover carbon in wood biomass.
- GR_factor
Growth respiration factor.
- l_fract
Fraction of the carbon retained after leaf drop.
- retransN
Retranslocation coefficient of nitrogen.
- f_initialBSW
Coefficient for setting up initial sapwood.
- f_N_add
Re-fill of N for sapwood.
- tf_base
Calibratable scalar for respiration, used to increase LUE levels.
- par_mort
Canopy mortality parameter.
- par_mort_under
Parameter for understory mortality.
- params_species
A data.frame containing species-specific model parameters, with one species per row, including the following data:
- lifeform
Integer set to 0 for grasses and 1 for trees.
- phenotype
Integer set to 0 for deciduous and 1 for evergreen.
- pt
Integer indicating the type of plant according to photosynthesis: 0 for C3; 1 for C4
- alpha_FR
Fine root turnonver rate (year
^{-1}
).- rho_FR
Material density of fine roots (kg C m
^{-3}
).- root_r
Radius of the fine roots, in m.
- root_zeta
e-folding parameter of root vertical distribution, in m.
- Kw_root
Fine root water conductivity (mol m
^{-2}
s^{-1}
MPa^{-1}
).- leaf_size
Characteristic leaf size.
- Vmax
Max RuBisCo rate, in mol m
^{-2}
s^{-1}
.- Vannual
Annual productivity per unit area at full sun (kg C m
^{-2}
year^{-2}
).- wet_leaf_dreg
Wet leaf photosynthesis down-regulation.
- m_cond
Factor of stomatal conductance.
- alpha_phot
Photosynthesis efficiency.
- gamma_L
Leaf respiration coefficient, in year
^{-1}
.- gamma_LN
Leaf respiration coefficient per unit N.
- gamma_SW
Sapwood respiration rate, in kg C m
^{-2}
year^{-1}
.- gamma_FR
Fine root respiration rate, kg C kg C
^{-1}
year^{-1}
.- tc_crit
Critical temperature triggerng offset of phenology, in Kelvin.
- tc_crit_on
Critical temperature triggerng onset of phenology, in Kelvin.
- gdd_crit
Critical value of GDD5 for turning ON growth season.
- betaON
Critical soil moisture for phenology onset.
- betaOFF
Critical soil moisture for phenology offset.
- seedlingsize
Initial size of seedlings, in kg C per individual.
- LNbase
Basal leaf N per unit area, in kg N m
^{-2}
.- lAImax
Maximum crown LAI (leaf area index).
- Nfixrate0
Reference N fixation rate (kg N kg C
^{-1}
root).- NfixCost0
Carbon cost of N fixation (kg C kg N
^{-1}
).- phiCSA
Ratio of sapwood area to leaf area.
- mortrate_d_c
Canopy tree mortality rate (year
^{-1}
).- mortrate_d_u
Understory tree mortality rate (year
^{-1}
).- maturalage
Age at which trees can reproduce (years).
- v_seed
Fraction of G_SF to G_F.
- fNSmax
Multiplier for NSNmax as sum of potential bl and br.
- LMA
Leaf mass per unit area (kg C m
^{-2}
).- rho_wood
Wood density (kg C m
^{-3}
).- alphaBM
Coefficient for allometry (biomass = alphaBM * DBH ** thetaBM).
- thetaBM
Coefficient for allometry (biomass = alphaBM * DBH ** thetaBM).
- kphio
Quantum yield efficiency
\varphi_0
, in mol mol^{-1}
.- phiRL
Ratio of fine root to leaf area.
- LAI_light
Maximum LAI limited by light.
- init_cohort
A data.frame of initial cohort specifications, including the following data:
- init_cohort_species
Index of a species described in param_species.
- init_cohort_nindivs
Initial individual density, in individuals per m
^{2}
.- init_cohort_bsw
Initial biomass of sapwood, in kg C per individual.
- init_cohort_bHW
Initial biomass of heartwood, in kg C per tree.
- init_cohort_nsc
Initial non-structural biomass.
- init_soil
A data.frame of initial soil pools, including the following data:
- init_fast_soil_C
Initial fast soil carbon, in kg C m
^{-2}
.- init_slow_soil_C
Initial slow soil carbon, in kg C m
^{-2}
.- init_Nmineral
Mineral nitrogen pool, in kg N m
^{-2}
.- N_input
Annual nitrogen input to soil N pool, in kg N m
^{-2}
year^{-1}
.