run_biomee_f_bysite function

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. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers
• site_info: Site meta info in a data.frame. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers
• forcing: Forcing data.frame used as input. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers
• params_tile: Tile-level model parameters, into a single row data.frame. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers
• 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. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers
• init_soil: A data.frame of initial soil pools. See examples biomee_gs_leuning_drivers or biomee_p_model_drivers
• makecheck: Flag specifying whether checks are performed to verify model inputs and parameters.

Returns

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]]
)