run_biomee_f_bysite {rsofun} | R Documentation |
Run BiomeE (R wrapper)
Description
Run BiomeE Fortran model on single site.
Usage
run_biomee_f_bysite(
sitename,
params_siml,
site_info,
forcing,
params_tile,
params_species,
init_cohort,
init_soil,
makecheck = TRUE
)
Arguments
sitename |
Site name. |
params_siml |
Simulation parameters.
See examples |
site_info |
Site meta info in a data.frame.
See examples |
forcing |
Forcing data.frame used as input.
See examples |
params_tile |
Tile-level model parameters, into a single row data.frame.
See examples |
params_species |
A data.frame containing species-specific model parameters,
with one species per row. See examples |
init_cohort |
A data.frame of initial cohort specifications.
See examples |
init_soil |
A data.frame of initial soil pools.
See examples |
makecheck |
Flag specifying whether checks are performed to verify model inputs and parameters. |
Value
Model output is provided as a list, with elements:
output_hourly_tile
A 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_tile
A 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_cohorts
A 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_tile
A 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).
- QMD12
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_cohorts
A 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]],
init_cohort = drivers$init_cohort[[1]],
init_soil = drivers$init_soil[[1]]
)