generate_parameters() generate the global parameters used in the TROLL
simulation. All parameters have a default value used in French Guiana
simulations.
generate_parameters(
cols = 200,
rows = 200,
HEIGHT = 70,
length_dcell = 25,
nbiter,
iterperyear = 12,
NV = 1,
NH = 1,
nbout = 4,
nbspp = 45,
SWtoPPFD = 2.27,
p_nonvert = 0.05,
klight = 0.63,
phi = 0.093,
absorptance_leaves = 0.9,
theta = 0.7,
g1 = 3.77,
vC = 0.021,
DBH0 = 0.005,
H0 = 0.95,
CR_min = 0.3,
CR_a = 2.13,
CR_b = 0.63,
CD_a = 0,
CD_b = 0.2,
CD0 = 0.3,
shape_crown = 0.72,
dens = 1,
fallocwood = 0.35,
falloccanopy = 0.25,
Cseedrain = 50000,
nbs0 = 10,
sigma_height = 0,
sigma_CR = 0,
sigma_CD = 0,
sigma_P = 0,
sigma_N = 0,
sigma_LMA = 0,
sigma_wsg = 0,
sigma_dbhmax = 0,
corr_CR_height = 0,
corr_N_P = 0,
corr_N_LMA = 0,
corr_P_LMA = 0,
leafdem_resolution = 30,
p_tfsecondary = 1,
hurt_decay = 0,
crown_gap_fraction = 0.15,
m = 0.013,
m1 = 0.013,
Cair = 400,
LL_parameterization = 1,
LA_regulation = 2,
sapwood = 1,
seedsadditional = 0,
NONRANDOM = 1,
GPPcrown = 0,
BASICTREEFALL = 1,
SEEDTRADEOFF = 0,
CROWN_MM = 0,
OUTPUT_extended = 1,
extent_visual = 0
)num. Number of columns.
num. Number of rows.
num. Vertical extent of simulation.
num. Linear size of a dcell.
num. Total number of timesteps.
num. Number of iterations per year.
num. Vertical number of cells (per m).
num. Horizontal number of cells (per m).
num. Number of outputs.
num. Number of species
num. Convert shortwave irradiance to PAR photons.
num. Light incidence parameter (difference through turbid medium).
num. Light attenuation in the canopy following a Beer-Lambert law.
num. Quantum yield (in micromol C/micromol photon).
num. Absorptance of individual leaves.
num. Parameter of the Farquhar model.
num. Parameter g1 of Medlyn et al stomatal conductance model.
num. Variance of the flexion moment.
num. Initial diameter at breast height (m).
num. Initial height (m).
num. Minimum crown radius (in m).
num. Crown radius log intercept or Michaelis Menten initial growth.
num. Crown radius log slope or Michaelis Menten asymptotic CR.
num. Crown depth intercept (absolute value).
num. Crown depth slope (as fraction of tree height).
num. Initial crown depth (in m).
num. Crown shape parameter.
num. Initial leaf density (m^2/m^2).
num. Fraction of biomass allocated to above ground wood (branch turnover+stem).
num. Fraction of biomass allocated to canopy (leaves + reproductive organs + twigs).
num. Constant used to scale total seed rain per hectare across species.
num. Number of seeds produced and dispersed by each mature tree when SEEDTRADEOFF is not defined.
num. Intraspecific variation in tree height (lognormal).
num. Intraspecific variation in crown radius (lognormal).
num. Intraspecific variation in crown depth (lognormal).
num. Intraspecific variation in leaf phosphorus (lognormal).
num. Intraspecific variation in leaf nitrogen (lognormal).
num. Intraspecific variation in leaf mass per area (lognormal).
num. Intraspecific variation in wood specific gravity.
num. Intraspecific variation in maximum diameter.
num. Correlation coefficient between crown radius and tree height.
num. Correlation coefficient between leaf nitrogen and leaf phosphorus.
num. Correlation coefficient between leaf nitrogen and leaf mass per area
num. Correlation coefficient between leaf phosphorus and leaf mass per area
num. Resolution of leaf demography model.
num. Probability of secondary treefall.
num. Parameter determining how tree damages are repaired.
num. Fraction of gaps in the crown.
num. Minimal death rate.
num. Slope of death rate m1.
num. Atmospheric CO2 concentration in micromol/mol.
num. Leaf lifespan parameterizations: Reich empirical, Kikuzawa model, and Kikuzawa model with leaf plasticity (0,1,2).
num. Dynamic LA regulation: off, 1.0, 0.75, or 0.5 (0,1,2,3).
num. Sapwood parameterizations: constant thickness (0.04), Fyllas percentage, Fyllas lower limit (0,1,2).
num. Excess biomass into seeds after maturation (0,1).
num. If _NONRANDOM >= 1, the seeds for the random number generators will be set using fixed seed in R, default for bug fixing (0,1).
num. This defines an option to compute only GPP from the topmost value of PPFD and GPP, instead of looping within the crown (0,1).
num. If defined: treefall is a source of tree death (0,1).
num. if defined: the number of seeds produced is determined by NPP allocated to reproduction and seed mass, otherwise the number of seeds is fixed (0,1).
num. Michaelis Menten allometry for crowns instead of power law, parameters have to be changed in other input sheets accordingly (0,1).
num. extended set of ouput files (0,1).
num. extent for visualization output. Unactivated when equal 0.
A data frame of global parameters.
generate_parameters(nbiter = 12)
#> param value
#> 1 cols 2.00e+02
#> 2 rows 2.00e+02
#> 3 HEIGHT 7.00e+01
#> 4 length_dcell 2.50e+01
#> 5 nbiter 1.20e+01
#> 6 iterperyear 1.20e+01
#> 7 NV 1.00e+00
#> 8 NH 1.00e+00
#> 9 nbout 4.00e+00
#> 10 nbspp 4.50e+01
#> 11 SWtoPPFD 2.27e+00
#> 12 p_nonvert 5.00e-02
#> 13 klight 6.30e-01
#> 14 phi 9.30e-02
#> 15 absorptance_leaves 9.00e-01
#> 16 theta 7.00e-01
#> 17 g1 3.77e+00
#> 18 vC 2.10e-02
#> 19 DBH0 5.00e-03
#> 20 H0 9.50e-01
#> 21 CR_min 3.00e-01
#> 22 CR_a 2.13e+00
#> 23 CR_b 6.30e-01
#> 24 CD_a 0.00e+00
#> 25 CD_b 2.00e-01
#> 26 CD0 3.00e-01
#> 27 shape_crown 7.20e-01
#> 28 dens 1.00e+00
#> 29 fallocwood 3.50e-01
#> 30 falloccanopy 2.50e-01
#> 31 Cseedrain 5.00e+04
#> 32 nbs0 1.00e+01
#> 33 sigma_height 0.00e+00
#> 34 sigma_CR 0.00e+00
#> 35 sigma_CD 0.00e+00
#> 36 sigma_P 0.00e+00
#> 37 sigma_N 0.00e+00
#> 38 sigma_LMA 0.00e+00
#> 39 sigma_wsg 0.00e+00
#> 40 sigma_dbhmax 0.00e+00
#> 41 corr_CR_height 0.00e+00
#> 42 corr_N_P 0.00e+00
#> 43 corr_N_LMA 0.00e+00
#> 44 corr_P_LMA 0.00e+00
#> 45 leafdem_resolution 3.00e+01
#> 46 p_tfsecondary 1.00e+00
#> 47 hurt_decay 0.00e+00
#> 48 crown_gap_fraction 1.50e-01
#> 49 m 1.30e-02
#> 50 m1 1.30e-02
#> 51 Cair 4.00e+02
#> 52 _LL_parameterization 1.00e+00
#> 53 _LA_regulation 2.00e+00
#> 54 _sapwood 1.00e+00
#> 55 _seedsadditional 0.00e+00
#> 56 _NONRANDOM 1.00e+00
#> 57 Rseed 1.00e+00
#> 58 _GPPcrown 0.00e+00
#> 59 _BASICTREEFALL 1.00e+00
#> 60 _SEEDTRADEOFF 0.00e+00
#> 61 _CROWN_MM 0.00e+00
#> 62 _OUTPUT_extended 1.00e+00
#> 63 extent_visual 0.00e+00
#> description
#> 1 /* nb of columns */
#> 2 /* nb of rows */
#> 3 /* vertical extent of simulation */
#> 4 /* linear size of a dcell */
#> 5 /* total nb of timesteps */
#> 6 /* number of iteration per year */
#> 7 /* vertical nb of cells (nb per m) */
#> 8 /* horizontal nb of cells (nb per m) */
#> 9 /* Number of outputs */
#> 10 /* Number of species */
#> 11 /* convert short wave irradiance to PAR photons (cf. code) */
#> 12 /* light incidence param (diff through turbid medium) */
#> 13 /* light attenuation in the canopy Beer-Lambert */
#> 14 /* quantum yield (in micromol C/micromol photon) */
#> 15 /* absorptance of individual leaves */
#> 16 /* parameter of the Farquhar model */
#> 17 /* parameter g1 of Medlyn et al s stomatal conductance model */
#> 18 /* variance of the flexion moment */
#> 19 /* initial dbh (m) */
#> 20 /* initial height (m) */
#> 21 /* minimum crown radius (in m) */
#> 22 /* CR log intercept or Michaelis Menten initial growth */
#> 23 /* CR log slope or Michaelis Menten asymptotic CR */
#> 24 /* CD intercept (absolute value) */
#> 25 /* CD slope (as fraction of tree height) */
#> 26 /* initial crown depth(in m) */
#> 27 /* crown shape parameter */
#> 28 /* initial leaf density (m^2/m^2) */
#> 29 /* fraction of biomass allocated to above ground wood (branch turnover+stem) */
#> 30 /* fraction of biomass allocated to canopy (leaves + reproductive organs + twigs) */
#> 31 /* constant used to scale total seed rain per hectare across species (in next computation) */
#> 32 /* nb of seeds produced and dispersed by each mature tree when SEEDTRADEOFF is not defined */
#> 33 /* intraspecific variation in tree height (lognormal) */
#> 34 /* intraspecific variation in crown radius (lognormal) */
#> 35 /* intraspecific variation in crown depth (lognormal) */
#> 36 /* intraspecific variation in leaf phosphorus (lognormal) */
#> 37 /* intraspecific variation in leaf nitrogen (lognormal) */
#> 38 /* intraspecific variation in LMA (lognormal) */
#> 39 /* intraspecific variation in wood specific gravity */
#> 40 /* intraspecific variation in maximum diameter */
#> 41 /* correlation coefficient between crown radius and tree height */
#> 42 /* correlation coefficient between leaf nitrogen and leaf phosphorus */
#> 43 /* correlation coefficient between leaf nitrogen and LMA */
#> 44 /* correlation coefficient between leaf phosphorus and LMA */
#> 45 /* resolution of leaf demography model */
#> 46 /* probability of secondary treefall */
#> 47 /* parameter determining how tree damages are repaired */
#> 48 /* fraction of gaps in the crown */
#> 49 /* minimal death rate */
#> 50 /* m1 (slope of death rate) */
#> 51 /* atmospheric CO2 concentration in micromol/mol */
#> 52 /* LL parameterizations: Reich empirical, Kikuzawa model, and Kikuzawa model with leaf plasticity (0,1,2) */
#> 53 /* dynamic LA regulation: off, 1.0, 0.75, or 0.5 (0,1,2,3) */
#> 54 /* sapwood parameterizations: constant thickness (0.04), Fyllas percentage, Fyllas lower limit (0,1,2) */
#> 55 /* excess biomass into seeds after maturation (0,1) */
#> 56 /* If _NONRANDOM == 1, the seeds for the random number generators will be kept fixed at 1, default for bug fixing */
#> 57 /* selected seed according to _NONRANDOM and R fixed seed */
#> 58 /* This defines an option to compute only GPP from the topmost value of PPFD and GPP, instead of looping within the crown. */
#> 59 /* if defined: treefall is a source of tree death */
#> 60 /* if defined: the number of seeds produced is determined by NPP allocated to reproduction and seed mass, otherwise the number of seeds is fixed */
#> 61 /* Michaelis Menten allometry for crowns instead of power law, parameters have to be changed in other input sheets accordingly */
#> 62 /* extended set of ouput files */
#> 63 /* extent for visualization output *