Run BiomeE (R wrapper)

Run BiomeE Fortran model on single site.

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.

site_info

Site meta info in a data.frame.

forcing

A data frame of forcing climate data, used as input.

params_tile

Tile-level model parameters, into a single row data.frame.

params_species

A data.frame containing species-specific model parameters, with one species per row. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers

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 and model parameters. TRUE by default.

For further specifications of above inputs and examples see biomee_gs_leuning_drivers or biomee_p_model_drivers

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

# \donttest{
# 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]]
)
# }

Arguments

Value

Examples

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