R/0-Tree.R

In VEZY/DynACof: A Process-Based Model to Study Growth, Yield and Ecosystem Services of Coffee Agroforestry Systems

#' @rdname site
#' @export
Tree= function(){
  list(
    Tree_Species         = "Erythrina poeppigiana",   # Names of the shade Tree species
    Species_ID           = "Erythrina_Aquiares",      # Optional species ID
    StockingTree_treeha1 = 250,                       # density at planting (trees ha-1). Source: Taugourdeau et al. (2014)
    SLA_Tree             = 17.4,                      # Specific leaf area (m2 kg-1). Source: Van Oijen et al. (2010, I)
    wleaf_Tree           = 0.068,                     # Leaf width (m)
    DELM_Tree            = 778.5,                     # Max Leaf carbon demand (gC tree d-1).
    LAI_max_Tree         = 1,                         # Max measured LAI to compute leaf demand. Should be ~1.5*higher than measured.
    Leaf_fall_rate_Tree  = list(0.07,0.02,            # Mortality during leaf fall (fraction of the leaf mass).
                                0.015,0.04),
    Fall_Period_Tree     = list(1:55,175:240,         # Time period were leaves fall at high rate (DOY). List of length= Leaf_fall_rate_Tree
                                300:354,355:365),
    Thin_Age_Tree        = 22,                        # Ages at which thinning is made (age). Set to NULL if no thinning
    ThinThresh           = 0,                         # (option) Lowest transmittance threshold under wich thinning is triggered (0-1)
    RateThinning_Tree    = 0.97072,                   # How many trees are thinned per thinning event, in percentage.
    date_Thin_Tree       = 100,                       # Date(s) of thinning (DOY)
    D_pruning_Tree       = 213,                       # Date(s) of pruning each year (DOY)
    pruningIntensity_Tree= 0.7,                       # Pruning intensity (% dry mass)
    m_FRoot_Tree         = 0.005,                     # Fine root percentage that die at pruning
    Pruning_Age_Tree     = 1:21,                      # Ages at which pruning is made (age). Set to NULL if no pruning.
    # k_Dif_Tree           = 0.305,                   # Light extinction coefficient for diffuse light. Now computed by metamodels
    # k_Dir_Tree           = 0.304,                   # Light extinction coefficient for direct light. Now computed by metamodels
    # lue_Tree             = 1.1375,                  # Light-use efficiency (gc MJ-1). Now computed by metamodels
    lambda_Stem_Tree     = 0.19,                      # Allocation coefficient to the stem. Source: Litton (2007)
    lambda_Branch_Tree   = 0.25,                      # Allocation coefficient to the branches wood. Source: Litton (2007)
    lambda_CR_Tree       = 0.10,                      # Allocation coefficient to the coarse roots. Source: Litton (2007)
    lambda_Leaf_Tree     = 0.26,                      # Allocation coefficient to the Leaves. Source: Litton (2007)
    lambda_FRoot_Tree    = 0.05,                      # Allocation coefficient to the fine roots. Source: Litton (2007)
    kres_max_Tree        = 1.2,                       # Maximum carbon extracted from reserves compared to maintenance respiration
    Res_max_Tree         = 500,                       # Maximum reserve until Tree always use it for growth
    CC_Leaf_Tree         = 0.47,                      # Leaf carbon content in gC gDM-1. Source: Van Oijen et al. (2010)
    CC_wood_Tree         = 0.47,                      # Wood carbon content in gC gDM-1. Source: Van Oijen et al. (2010)
    epsilon_Branch_Tree  = 1.2,                       # Branch growth cost coefficient (gC.gC-1). Source: This study
    epsilon_Stem_Tree    = 1.2,                       # Stem growth cost coefficient (gC.gC-1). Source: This study
    epsilon_CR_Tree      = 1.33,                      # Coarse root growth cost coefficient (gC.gC-1). Source: Litton et al. (2007)
    epsilon_Leaf_Tree    = 1.392,                     # Leaf growth cost coefficient (gC.gC-1). Source: Erythrina excelsa Villar and Merino (2001),
    epsilon_FRoot_Tree   = 1.392,                     # Leaf growth cost coefficient (gC.gC-1). Considered = to leaves
    epsilon_RE_Tree      = 1.000001,                  # Reserves growth cost coefficient (gC.gC-1). No cost, unknown.
    lifespan_Branch_Tree = 7300,                      # Branch lifespan, natural mortality (d)
    lifespan_Leaf_Tree   = 10^5,                      # Leaf lifespan (d). Taken infinite because regulated by leaf fall phenology.
    lifespan_FRoot_Tree  = 90,                        # Fine roots lifespan (d).
    lifespan_CR_Tree     = 7300,                      # Coarse roots lifespan (d). Source: Van Oijen et al. (2010,I)
    Kh                   = 0.46,                      # Allometries, source: CAF2007, Van Oijen et al. (2010). Adjusted to fit our observations.
    KhExp                = 0.5,                       # Allometries, source: CAF2007, Van Oijen et al. (2010). Adjusted to fit our observations.
    Kc                   = 8,                         # Allometries, source: CAF2007, Van Oijen et al. (2010). Adjusted to fit our observations.
    KcExp                = 0.45,                      # Allometries, source: CAF2007, Van Oijen et al. (2010). Adjusted to fit our observations.
    MRN_Tree             = 0.20,                      # Base maintenance respiration (gC.gN.day-1)
    NC_Branch_Tree       = 0.005,                     # Branch nitrogen content (gN.gDM-1).
    NC_Stem_Tree         = 0.005,                     # Stem nitrogen content (gN.gDM-1).
    NC_CR_Tree           = 0.0084,                    # Coarse roots nitrogen content (gN.gDM-1). Source: Van Oijen et al. (2010,I)
    NC_Leaf_Tree         = 0.0359,                    # Leaf nitrogen content (gN.gDM-1). Source: average 3.35 to 3.82%, Van Oijen et al. (2010,I)
    NC_FRoot_Tree        = 0.0084,                    # Fine root nitrogen content (gN.gDM-1). Taken = to leaves
    Q10Branch_Tree       = 2.1,                       # Branch Q10 (-)
    Q10Stem_Tree         = 1.7,                       # Stem Q10 (-)
    Q10CR_Tree           = 2.1,                       # Coarse root Q10 (-)
    Q10Leaf_Tree         = 1.896,                     # Leaf Q10 (-), see 1-DATA/Erythrina/Respiration.docx
    Q10FRoot_Tree        = 1.4,                       # Fine root Q10 (-). Source: Van Oijen et al (2010,I)
    pa_Branch_Tree       = Paliv_dis(41,0.4,0.03,5),  # Branch living tissue (fraction). Not used (replaced by pa_Stem_Tree).
    pa_Stem_Tree         = Paliv_dis(41,0.3,0.03,5),  # Computation of living tissue at each age (do not modify)
    pa_CR_Tree           = 0.21,                      # Coarse roots living tissue (fraction)
    pa_Leaf_Tree         = 1,                         # Leaf living tissue (fraction)
    pa_FRoot_Tree        = 1,                         # Fine root living tissue (fraction)
    k                    = Light_extinction_K,        # Light extinction coefficient (call external function)
    KTOT_Tree            = 80.0,                      # soil to leaf hydrolic conducance (mol m-2 s-1 MPa-1)
    T_Tree               = function(S,i){             # Metamodel for tree transpiration
      Transp=
        -0.54141773 + 0.01775386 * S$Met_c$Tair[i] + 0.01619095 * S$Met_c$VPD[i] +
        0.16202098 * S$Sim$LAI_Tree[i] + 0.50673098 * S$Sim$APAR_Tree[i]
      Transp[Transp<0]= 0 #to discard negative values
      Transp
    },
    H_Tree               = function(S,i){             # Metamodel for tree sensible heat
      0.15311742  +  0.74344303 * S$Sim$APAR_Tree[i] -  0.73439407 * S$Sim$LAI_Tree[i] -  0.71071620 * S$Sim$T_Tree[i] -  0.03509675 * S$Met_c$VPD[i] +
        0.09494137 * S$Met_c$WindSpeed[i]
    },
    lue_Tree             = function(S,i){             # Metamodel for tree lue
      2.83661957 + 0.07542358 * S$Met_c$Tair[i] - 0.03009240 * S$Met_c$VPD[i] - 0.24074124 * S$Met_c$PAR[i]
    },
    Allometries          = Allometries                # Idem for allometric equations (optional, any kind of variable can be added here).
  )
}