run_biomee_f_bysite: R wrapper for SOFUN biomee
In stineb/rsofun: The P-Model and BiomeE Modelling Framework
View source: R/run_biomee_f_bysite.R
run_biomee_f_bysite R Documentation
R wrapper for SOFUN biomee
Description
Call to the biomee Fortran model
Usage
run_biomee_f_bysite(
sitename,
params_siml,
site_info,
forcing,
params_tile,
params_species,
params_soil,
init_cohort,
init_soil,
makecheck = TRUE
)
Arguments
sitename
Site name.
params_siml
Simulation parameters.
- spinup
A logical value indicating whether this simulation does spin-up.
- spinupyears
Number of spin-up years.
- recycle
Length of standard recycling period (days).
- firstyeartrend
First transient year.
- nyeartrend
Number of transient years.
- outputhourly
A logical value indicating whether hourly output is
produced.
- outputdaily
A logical value indicating whether daily output is produced.
- do_U_shaped_mortality
A logical value indicating whether U-shaped
mortality is used.
- update_annualLAImax
A logical value indicating whether updating
LAImax according to mineral N in soil.
- do_closedN_run
A logical value indicating whether doing N closed
runs to recover N balance.
- code_method_photosynth
String specifying the method of photosynthesis
used in the model, either "pmodel" or "gs_leuning".
- 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.
- sitename
Name of the site.
- lon
Longitud 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.
params_tile
Tile-level model parameters, into a single row data.frame
with columns:
- 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. The columns of this data.frame are:
- 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
Radious 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.
params_soil
A tibble of soil parameters (one row per soil layer).
- type
A string indicating the type of soil.
- GMD
Geometric mean particle diameter (mm).
- GSD
Geometric standard deviation of particle size.
- vwc_sat
Saturated volumetric soil water content (vol/vol).
- chb
Soil texture parameter.
- psi_sat_ref
Saturation soil water potential (m).
- k_sat_ref
Hydraulic conductivity of saturated soil (kg m^{-2}
s^{-1}).
- alphaSoil
Vertical changes of soil property, where 1 = no change.
- heat_capacity_dry
Heat capacity dry air (J m^{-3} K^{-1}).
init_cohort
A data.frame of initial cohort specifications.
- init_cohort_species
Indicates different 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.
- 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}.
makecheck
A logical specifying whether checks are performed to verify
forcings.
Value
Model output is provided as a list, with elements:
output_hourly_tileA data.frame containing hourly predictions
.
- year
Year of the simulation.
- doy
Day of the year.
- hour
Hour of the day.
- rad
Radiation, in W m^{-2}.
- Tair
Air temperature, in Kelvin.
- Prcp
Precipitation, in mm m^{-2}.
- GPP
Gross primary production (kg C m^{-2} hour^{-1}).
- Resp
Plant respiration (kg C m^{-2} hour^{-1}).
- Transp
Transpiration (mm m^{-2}).
- Evap
Evaporation (mm m^{-2}).
- Runoff
Water runoff (mm m^{-2}).
- Soilwater
Soil water content in root zone (kg m^{-2}).
- wcl
Volumetric soil water content for each layer (vol/vol).
- FLDCAP
Field capacity (vol/vol).
- WILTPT
Wilting point (vol/vol).
output_daily_tileA data.frame with daily outputs at a tile
level.
- year
Year of the simulation.
- doy
Day of the year.
- Tc
Air temperature (Kelvin).
- Prcp
Precipitation (mm m^{-2}).
- totWs
Soil water content in root zone (kg m^{-2}).
- Trsp
Transpiration (mm m^{2-}).
- Evap
Evaporation (mm m^{-2}).
- Runoff
Water runoff (mm m^{-2}).
- ws1
Volumetric soil water content for layer 1.
- ws2
Volumetric soil water content for layer 2.
- ws3
Volumetric soil water content for layer 3.
- LAI
Leaf area index (m^2/m^2).
- GPP
Gross primary production (kg C m^{-2} day^{-1}).
- Rauto
Plant autotrophic respiration (kg C m^{-2} day^{-1}).
- Rh
Heterotrophic respiration (kg C m^{-2} day^{-1}).
- NSC
Non-structural carbon (kg C m^{-2}).
- seedC
Biomass of seeds (kg C m^{-2}).
- leafC
Biomass of leaves (kg C m^{-2}).
- rootC
Biomass of fine roots (kg C m^{-2}).
- SW_C
Biomass of sapwood (kg C m^{-2}).
- HW_C
biomass of heartwood (kg C m^{-2}).
- NSN
Non-structural N pool (kg N m^{-2}).
- seedN
Nitrogen of seeds (kg N m^{-2}).
- leafN
Nitrogen of leaves (kg N m^{-2}).
- rootN
Nitrogen of roots (kg N m^{-2}).
- SW_N
Nitrogen of sapwood (kg N m^{-2}).
- HW_N
Nitrogen of heartwood (kg N m^{-2}).
- McrbC
Microbial carbon (kg C m^{-2}).
- fastSOM
Fast soil carbon pool (kg C m^{-2}).
- slowSOM
Slow soil carbon pool (kg C m^{-2}).
- McrbN
Microbial nitrogen (kg N m^{-2}).
- fastSoilN
Fast soil nitrogen pool (kg N m^{-2}).
- slowSoilN
Slow soil nitrogen pool (kg N m^{-2}).
- mineralN
Mineral nitrogen pool (kg N m^{-2}).
- N_uptk
Nitrogen uptake (kg N m^{-2}).
output_daily_cohortsA data.frame with daily predictions
for each canopy cohort.
- year
Year of the simulation.
- doy
Day of the year.
- hour
Hour of the day.
- cID
An integer indicating the cohort identity.
- PFT
An integer indicating the Plant Functional Type.
- layer
An integer indicating the crown layer, numbered from top
to bottom.
- density
Number of trees per area (trees ha^{-1}).
- f_layer
Fraction of layer area occupied by this cohort.
- LAI
Leaf area index (m^2/m^2).
- gpp
Gross primary productivity (kg C tree^{-1} day^{-1}).
- resp
Plant autotrophic respiration (kg C tree^{-1} day^{-1}).
- transp
Transpiration (mm tree^{-1} day^{-1}).
- NPPleaf
Carbon allocated to leaves (kg C tree^{-1} day^{-1}).
- NPProot
Carbon allocated to fine roots (kg C tree^{-1} day^{-1}).
- NPPwood
Carbon allocated to wood (kg C tree^{-1} day^{-1}).
- NSC
Nonstructural carbohydrates of a tree in this cohort (kg C
tree^{-1}).
- seedC
Seed biomass of a tree in this cohort (kg C tree^{-1}).
- leafC
Leaf biomass of a tree in this cohort (kg C tree^{-1}).
- rootC
Fine root biomass of a tree in this cohort (kg C tree^{-1}).
- SW_C
Sapwood biomass of a tree in this cohort (kg C tree^{-1}).
- HW_C
Heartwood biomass of a tree in this cohort (kg C tree^{-1}).
- NSN
Nonstructural nitrogen of a tree in this cohort (kg N tree^{-1}).
- seedN
Seed nitrogen of a tree in this cohort (kg N tree^{-1}).
- leafN
Leaf nitrogen of a tree in this cohort (kg N tree^{-1}).
- rootN
Fine root nitrogen of a tree in this cohort (kg N tree^{-1}).
- SW_N
Sapwood nitrogen of a tree in this cohort (kg N tree^{-1}).
- HW_N
Heartwood nitrogen of a tree in this cohort (kg N tree^{-1}).
output_annual_tileA data.frame with annual outputs at tile level.
- year
Year of the simulation.
- CAI
Crown area index (m^2/m^2).
- LAI
Leaf area index (m^2/m^2).
- Density
Number of trees per area (trees ha^{-1}).
- DBH
Diameter at tile level (cm).
- Density12
Tree density for trees with DBH > 12 cm (individuals
ha^{-1}).
- DBH12
Diameter at tile level considering trees with DBH > 12 cm
(cm).
- QMD
Quadratic mean diameter at tile level considering trees with
DBH > 12 cm (cm).
- NPP
Net primary productivity (kg C m^{-2} yr^{-1}).
- GPP
Gross primary productivity (kg C m^{-2} yr^{-1}).
- Rauto
Plant autotrophic respiration (kg C m^{-2} yr^{-1}).
- Rh
Heterotrophic respiration (kg C m^{-2} yr^{-1}).
- rain
Annual precipitation (mm m^{-2} yr^{-1}).
- SoilWater
Soil water content in root zone (kg m^{-2}).
- Transp
Transpiration (mm m^{-2} yr^{-1}).
- Evap
Evaporation (mm m^{-2} yr^{-1}).
- Runoff
Water runoff (mm m^{-2} yr^{-1}).
- plantC
Plant biomass (kg C m^{-2}).
- soilC
Soil carbon (kg C m^{-2}).
- plantN
Plant nitrogen (kg N m^{-2}).
- soilN
Soil nitrogen (kg N m^{-2}).
- totN
Total nitrogen in plant and soil (kg N m^{-2}).
- NSC
Nonstructural carbohydrates (kg C m^{-2}).
- SeedC
Seed biomass (kg C m^{-2}).
- leafC
Leaf biomass (kg C m^{-2}).
- rootC
Fine root biomass (kg C m^{-2}).
- SapwoodC
Sapwood biomass (kg C m^{-2}).
- WoodC
Heartwood biomass (kg C m^{-2}).
- NSN
Nonstructural nitrogen (kg N m^{-2}).
- SeedN
Seed nitrogen (kg N m^{-2}).
- leafN
Leaf nitrogen (kg N m^{-2}).
- rootN
Fine root nitrogen (kg N m^{-2}).
- SapwoodN
Sapwood nitrogen (kg N m^{-2}).
- WoodN
Heartwood nitrogen (kg N m^{-2}).
- McrbC
Microbial carbon (kg C m^{-2}).
- fastSOM
Fast soil carbon pool (kg C m^{-2}).
- SlowSOM
Slow soil carbon pool (kg C m^{-2}).
- McrbN
Microbial nitrogen (kg N m^{-2}).
- fastSoilN
Fast soil nitrogen pool (kg N m^{-2}).
- slowsoilN
Slow soil nitrogen pool (kg N m^{-2}).
- mineralN
Mineral nitrogen pool (kg N m^{-2}).
- N_fxed
Nitrogen fixation (kg N m^{-2}).
- N_uptk
Nitrogen uptake (kg N m^{-2}).
- N_yrMin
Annual available nitrogen (kg N m^{-2}).
- N_P25
Annual nitrogen from plants to soil (kg N m^{-2}).
- N_loss
Annual nitrogen loss (kg N m^{-2}).
- totseedC
Total seed carbon (kg C m^{-2}).
- totseedN
Total seed nitrogen (kg N m^{-2}).
- Seedling_C
Total carbon from all compartments but seeds
(kg C m^{-2}).
- Seeling_N
Total nitrogen from all compartments but seeds
(kg N m^{-2}).
- MaxAge
Age of the oldest tree in the tile (years).
- MaxVolume
Maximum volumne of a tree in the tile (m^3).
- MaxDBH
Maximum DBH of a tree in the tile (m).
- NPPL
Growth of a tree, including carbon allocated to leaves
(kg C m^{-2} year^{-1}).
- NPPW
Growth of a tree, including carbon allocated to sapwood
(kg C m^{-2} year^{-1}).
- n_deadtrees
Number of trees that died (trees m^{-2} year^{-1}).
- c_deadtrees
Carbon biomass of trees that died (kg C
m^{-2} year^{-1}).
- m_turnover
Continuous biomass turnover (kg C m^{-2} year^{-1}).
- c_turnover_time
Carbon turnover rate, calculated as the ratio
between plant biomass and NPP (year^{-1}).
output_annual_cohortsA data.frame of annual outputs at the
cohort level.
- year
Year of the simulation.
- cID
An integer indicating the cohort identity.
- PFT
An integer indicating the Plant Functional Type.
- layer
An integer indicating the crown layer, numbered from top to
bottom.
- density
Number of trees per area (trees ha^{-1}).
- f_layer
Fraction of layer area occupied by this cohort.
- dDBH
Diameter growth of a tree in this cohort (cm year^{-1}).
- dbh
Tree diameter (cm).
- height
Tree height (m).
- age
Age of the cohort (years).
- Acrow
Crown area of a tree in this cohort (m^2).
- wood
Sum of sapwood and heartwood biomass of a tree in this cohort
(kg C tree^{-1}).
- nsc
Nonstructural carbohydrates in a tree (kg C tree^{-1}).
- NSN
Nonstructural nitrogen of a tree (kg N tree^{-1}).
- NPPtr
Total growth of a tree, including carbon allocated to seeds,
leaves, fine roots, and sapwood (kg C tree^{-1} year^{-1}).
- seed
Fraction of carbon allocated to seeds to total growth.
- NPPL
Fraction of carbon allocated to leaves to total growth.
- NPPR
Fraction of carbon allocated to fine roots to total growth.
- NPPW
Fraction of carbon allocated to sapwood to total growth.
- GPP_yr
Gross primary productivity of a tree (kg C tree^{-1}
year^{-1}).
- NPP_yr
Net primary productivity of a tree (kg C tree^{-1}
year^{-1}).
- Rauto
Plant autotrophic respiration (kg C tree^{-1} yr^{-1}).
- N_uptk
Nitrogen uptake (kg N tree^{-1} yr^{-1}).
- N_fix
Nitrogen fixation (kg N tree^{-1} yr^{-1}).
- maxLAI
Maximum leaf area index for a tree (m^2 m^{-2}).
- Volume
Tree volume (m^3).
- n_deadtrees
Number of trees that died (trees yr^{-1}).
- c_deadtrees
Carbon biomass of trees that died (kg C yr^{-1}).
- deathrate
Mortality rate of this cohort (yr^{-1}).
Examples
# Example BiomeE model run
# Use example drivers data
drivers <- biomee_gs_leuning_drivers
# Run BiomeE for the first site
mod_output <- run_biomee_f_bysite(
sitename = drivers$sitename[1],
params_siml = drivers$params_siml[[1]],
site_info = drivers$site_info[[1]],
forcing = drivers$forcing[[1]],
params_tile = drivers$params_tile[[1]],
params_species = drivers$params_species[[1]],
params_soil = drivers$params_soil[[1]],
init_cohort = drivers$init_cohort[[1]],
init_soil = drivers$init_soil[[1]]
)
stineb/rsofun documentation built on April 29, 2024, 1:29 p.m.
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View source: R/run_biomee_f_bysite.R
| run_biomee_f_bysite | R Documentation |
R wrapper for SOFUN biomee
Description
Call to the biomee Fortran model
Usage
run_biomee_f_bysite(
sitename,
params_siml,
site_info,
forcing,
params_tile,
params_species,
params_soil,
init_cohort,
init_soil,
makecheck = TRUE
)
Arguments
sitename |
Site name. |
params_siml |
Simulation parameters.
|
site_info |
Site meta info in a data.frame.
|
forcing |
Forcing data.frame used as input. |
params_tile |
Tile-level model parameters, into a single row data.frame with columns:
|
params_species |
A data.frame containing species-specific model parameters, with one species per row. The columns of this data.frame are:
|
params_soil |
A tibble of soil parameters (one row per soil layer).
|
init_cohort |
A data.frame of initial cohort specifications.
|
init_soil |
A data.frame of initial soil pools.
|
makecheck |
A logical specifying whether checks are performed to verify forcings. |
Value
Model output is provided as a list, with elements:
output_hourly_tileA data.frame containing hourly predictions .
- year
Year of the simulation.
- doy
Day of the year.
- hour
Hour of the day.
- rad
Radiation, in W m
^{-2}.- Tair
Air temperature, in Kelvin.
- Prcp
Precipitation, in mm m
^{-2}.- GPP
Gross primary production (kg C m
^{-2}hour^{-1}).- Resp
Plant respiration (kg C m
^{-2}hour^{-1}).- Transp
Transpiration (mm m
^{-2}).- Evap
Evaporation (mm m
^{-2}).- Runoff
Water runoff (mm m
^{-2}).- Soilwater
Soil water content in root zone (kg m
^{-2}).- wcl
Volumetric soil water content for each layer (vol/vol).
- FLDCAP
Field capacity (vol/vol).
- WILTPT
Wilting point (vol/vol).
output_daily_tileA data.frame with daily outputs at a tile level.
- year
Year of the simulation.
- doy
Day of the year.
- Tc
Air temperature (Kelvin).
- Prcp
Precipitation (mm m
^{-2}).- totWs
Soil water content in root zone (kg m
^{-2}).- Trsp
Transpiration (mm m
^{2-}).- Evap
Evaporation (mm m
^{-2}).- Runoff
Water runoff (mm m
^{-2}).- ws1
Volumetric soil water content for layer 1.
- ws2
Volumetric soil water content for layer 2.
- ws3
Volumetric soil water content for layer 3.
- LAI
Leaf area index (m
^2/m^2).- GPP
Gross primary production (kg C m
^{-2}day^{-1}).- Rauto
Plant autotrophic respiration (kg C m
^{-2}day^{-1}).- Rh
Heterotrophic respiration (kg C m
^{-2}day^{-1}).- NSC
Non-structural carbon (kg C m
^{-2}).- seedC
Biomass of seeds (kg C m
^{-2}).- leafC
Biomass of leaves (kg C m
^{-2}).- rootC
Biomass of fine roots (kg C m
^{-2}).- SW_C
Biomass of sapwood (kg C m
^{-2}).- HW_C
biomass of heartwood (kg C m
^{-2}).- NSN
Non-structural N pool (kg N m
^{-2}).- seedN
Nitrogen of seeds (kg N m
^{-2}).- leafN
Nitrogen of leaves (kg N m
^{-2}).- rootN
Nitrogen of roots (kg N m
^{-2}).- SW_N
Nitrogen of sapwood (kg N m
^{-2}).- HW_N
Nitrogen of heartwood (kg N m
^{-2}).- McrbC
Microbial carbon (kg C m
^{-2}).- fastSOM
Fast soil carbon pool (kg C m
^{-2}).- slowSOM
Slow soil carbon pool (kg C m
^{-2}).- McrbN
Microbial nitrogen (kg N m
^{-2}).- fastSoilN
Fast soil nitrogen pool (kg N m
^{-2}).- slowSoilN
Slow soil nitrogen pool (kg N m
^{-2}).- mineralN
Mineral nitrogen pool (kg N m
^{-2}).- N_uptk
Nitrogen uptake (kg N m
^{-2}).
output_daily_cohortsA data.frame with daily predictions for each canopy cohort.
- year
Year of the simulation.
- doy
Day of the year.
- hour
Hour of the day.
- cID
An integer indicating the cohort identity.
- PFT
An integer indicating the Plant Functional Type.
- layer
An integer indicating the crown layer, numbered from top to bottom.
- density
Number of trees per area (trees ha
^{-1}).- f_layer
Fraction of layer area occupied by this cohort.
- LAI
Leaf area index (m
^2/m^2).- gpp
Gross primary productivity (kg C tree
^{-1}day^{-1}).- resp
Plant autotrophic respiration (kg C tree
^{-1}day^{-1}).- transp
Transpiration (mm tree
^{-1}day^{-1}).- NPPleaf
Carbon allocated to leaves (kg C tree
^{-1}day^{-1}).- NPProot
Carbon allocated to fine roots (kg C tree
^{-1}day^{-1}).- NPPwood
Carbon allocated to wood (kg C tree
^{-1}day^{-1}).- NSC
Nonstructural carbohydrates of a tree in this cohort (kg C tree
^{-1}).- seedC
Seed biomass of a tree in this cohort (kg C tree
^{-1}).- leafC
Leaf biomass of a tree in this cohort (kg C tree
^{-1}).- rootC
Fine root biomass of a tree in this cohort (kg C tree
^{-1}).- SW_C
Sapwood biomass of a tree in this cohort (kg C tree
^{-1}).- HW_C
Heartwood biomass of a tree in this cohort (kg C tree
^{-1}).- NSN
Nonstructural nitrogen of a tree in this cohort (kg N tree
^{-1}).- seedN
Seed nitrogen of a tree in this cohort (kg N tree
^{-1}).- leafN
Leaf nitrogen of a tree in this cohort (kg N tree
^{-1}).- rootN
Fine root nitrogen of a tree in this cohort (kg N tree
^{-1}).- SW_N
Sapwood nitrogen of a tree in this cohort (kg N tree
^{-1}).- HW_N
Heartwood nitrogen of a tree in this cohort (kg N tree
^{-1}).
output_annual_tileA data.frame with annual outputs at tile level.
- year
Year of the simulation.
- CAI
Crown area index (m
^2/m^2).- LAI
Leaf area index (m
^2/m^2).- Density
Number of trees per area (trees ha
^{-1}).- DBH
Diameter at tile level (cm).
- Density12
Tree density for trees with DBH > 12 cm (individuals ha
^{-1}).- DBH12
Diameter at tile level considering trees with DBH > 12 cm (cm).
- QMD
Quadratic mean diameter at tile level considering trees with DBH > 12 cm (cm).
- NPP
Net primary productivity (kg C m
^{-2}yr^{-1}).- GPP
Gross primary productivity (kg C m
^{-2}yr^{-1}).- Rauto
Plant autotrophic respiration (kg C m
^{-2}yr^{-1}).- Rh
Heterotrophic respiration (kg C m
^{-2}yr^{-1}).- rain
Annual precipitation (mm m
^{-2}yr^{-1}).- SoilWater
Soil water content in root zone (kg m
^{-2}).- Transp
Transpiration (mm m
^{-2}yr^{-1}).- Evap
Evaporation (mm m
^{-2}yr^{-1}).- Runoff
Water runoff (mm m
^{-2}yr^{-1}).- plantC
Plant biomass (kg C m
^{-2}).- soilC
Soil carbon (kg C m
^{-2}).- plantN
Plant nitrogen (kg N m
^{-2}).- soilN
Soil nitrogen (kg N m
^{-2}).- totN
Total nitrogen in plant and soil (kg N m
^{-2}).- NSC
Nonstructural carbohydrates (kg C m
^{-2}).- SeedC
Seed biomass (kg C m
^{-2}).- leafC
Leaf biomass (kg C m
^{-2}).- rootC
Fine root biomass (kg C m
^{-2}).- SapwoodC
Sapwood biomass (kg C m
^{-2}).- WoodC
Heartwood biomass (kg C m
^{-2}).- NSN
Nonstructural nitrogen (kg N m
^{-2}).- SeedN
Seed nitrogen (kg N m
^{-2}).- leafN
Leaf nitrogen (kg N m
^{-2}).- rootN
Fine root nitrogen (kg N m
^{-2}).- SapwoodN
Sapwood nitrogen (kg N m
^{-2}).- WoodN
Heartwood nitrogen (kg N m
^{-2}).- McrbC
Microbial carbon (kg C m
^{-2}).- fastSOM
Fast soil carbon pool (kg C m
^{-2}).- SlowSOM
Slow soil carbon pool (kg C m
^{-2}).- McrbN
Microbial nitrogen (kg N m
^{-2}).- fastSoilN
Fast soil nitrogen pool (kg N m
^{-2}).- slowsoilN
Slow soil nitrogen pool (kg N m
^{-2}).- mineralN
Mineral nitrogen pool (kg N m
^{-2}).- N_fxed
Nitrogen fixation (kg N m
^{-2}).- N_uptk
Nitrogen uptake (kg N m
^{-2}).- N_yrMin
Annual available nitrogen (kg N m
^{-2}).- N_P25
Annual nitrogen from plants to soil (kg N m
^{-2}).- N_loss
Annual nitrogen loss (kg N m
^{-2}).- totseedC
Total seed carbon (kg C m
^{-2}).- totseedN
Total seed nitrogen (kg N m
^{-2}).- Seedling_C
Total carbon from all compartments but seeds (kg C m
^{-2}).- Seeling_N
Total nitrogen from all compartments but seeds (kg N m
^{-2}).- MaxAge
Age of the oldest tree in the tile (years).
- MaxVolume
Maximum volumne of a tree in the tile (m
^3).- MaxDBH
Maximum DBH of a tree in the tile (m).
- NPPL
Growth of a tree, including carbon allocated to leaves (kg C m
^{-2}year^{-1}).- NPPW
Growth of a tree, including carbon allocated to sapwood (kg C m
^{-2}year^{-1}).- n_deadtrees
Number of trees that died (trees m
^{-2}year^{-1}).- c_deadtrees
Carbon biomass of trees that died (kg C m
^{-2}year^{-1}).- m_turnover
Continuous biomass turnover (kg C m
^{-2}year^{-1}).- c_turnover_time
Carbon turnover rate, calculated as the ratio between plant biomass and NPP (year
^{-1}).
output_annual_cohortsA data.frame of annual outputs at the cohort level.
- year
Year of the simulation.
- cID
An integer indicating the cohort identity.
- PFT
An integer indicating the Plant Functional Type.
- layer
An integer indicating the crown layer, numbered from top to bottom.
- density
Number of trees per area (trees ha
^{-1}).- f_layer
Fraction of layer area occupied by this cohort.
- dDBH
Diameter growth of a tree in this cohort (cm year
^{-1}).- dbh
Tree diameter (cm).
- height
Tree height (m).
- age
Age of the cohort (years).
- Acrow
Crown area of a tree in this cohort (m
^2).- wood
Sum of sapwood and heartwood biomass of a tree in this cohort (kg C tree
^{-1}).- nsc
Nonstructural carbohydrates in a tree (kg C tree
^{-1}).- NSN
Nonstructural nitrogen of a tree (kg N tree
^{-1}).- NPPtr
Total growth of a tree, including carbon allocated to seeds, leaves, fine roots, and sapwood (kg C tree
^{-1}year^{-1}).- seed
Fraction of carbon allocated to seeds to total growth.
- NPPL
Fraction of carbon allocated to leaves to total growth.
- NPPR
Fraction of carbon allocated to fine roots to total growth.
- NPPW
Fraction of carbon allocated to sapwood to total growth.
- GPP_yr
Gross primary productivity of a tree (kg C tree
^{-1}year^{-1}).- NPP_yr
Net primary productivity of a tree (kg C tree
^{-1}year^{-1}).- Rauto
Plant autotrophic respiration (kg C tree
^{-1}yr^{-1}).- N_uptk
Nitrogen uptake (kg N tree
^{-1}yr^{-1}).- N_fix
Nitrogen fixation (kg N tree
^{-1}yr^{-1}).- maxLAI
Maximum leaf area index for a tree (m
^2m^{-2}).- Volume
Tree volume (m
^3).- n_deadtrees
Number of trees that died (trees yr
^{-1}).- c_deadtrees
Carbon biomass of trees that died (kg C yr
^{-1}).- deathrate
Mortality rate of this cohort (yr
^{-1}).
Examples
# Example BiomeE model run
# Use example drivers data
drivers <- biomee_gs_leuning_drivers
# Run BiomeE for the first site
mod_output <- run_biomee_f_bysite(
sitename = drivers$sitename[1],
params_siml = drivers$params_siml[[1]],
site_info = drivers$site_info[[1]],
forcing = drivers$forcing[[1]],
params_tile = drivers$params_tile[[1]],
params_species = drivers$params_species[[1]],
params_soil = drivers$params_soil[[1]],
init_cohort = drivers$init_cohort[[1]],
init_soil = drivers$init_soil[[1]]
)
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