model: Model

In fischer-fjd/RconTroll: Package for individual-based forest growth simulator TROLL (wip)

Description

Create and open a TROLL model

Usage

model(name = getOption("RconTroll.name"),
  path = getOption("RconTroll.path"), src = getOption("RconTroll.src"),
  optimisation = NULL, app = getOption("RconTroll.app"),
  input = getOption("RconTroll.init"),
  output = getOption("RconTroll.output"), build = TRUE, overwrite = TRUE,
  verbose = TRUE, nbcol = 400, nbrows = 400, nbiter = 12, iter = 12,
  NV = 1, NH = 1, nbout = 4, numesp = 163, p = 0.05,
  disturb_iter = 4, disturb_intensity = 0.4, daylight = c(0.03, 0.108,
  0.208, 0.304, 0.473, 0.617, 0.723, 0.823, 0.925, 0.965, 0.995, 0.988, 1,
  0.942, 0.854, 0.766, 0.646, 0.493, 0.36, 0.277, 0.183, 0.102, 0.058, 0.022),
  dayT = c(0.012, 0.018, 0.042, 0.087, 0.175, 0.304, 0.445, 0.569, 0.672,
  0.767, 0.856, 0.915, 0.961, 0.986, 1, 0.985, 0.952, 0.908, 0.863, 0.82, 0.767,
  0.699, 0.611, 0.498), dayVPD = c(0.768, 0.776, 0.795, 0.82, 0.851, 0.884,
  0.912, 0.934, 0.95, 0.966, 0.98, 0.989, 0.997, 0.999, 1, 0.9996, 0.99, 0.982,
  0.974, 0.966, 0.957, 0.945, 0.929, 0.906), klight = 0.9, phi = 0.06,
  vC = 0.1, DBH0 = 0.01, H0 = 1, ra0 = 0.5, ra1 = 10, de0 = 0.3,
  de1 = 0.12, dens = 0.8, fbranchstem = 0.35, fcanopy = 0.3,
  seedrain = 200, nbseeds = 10, mindeathrate = 0.035, m1 = 0.035,
  CO2 = 360, species = read.table(getOption("RconTroll.species"), header =
  TRUE, dec = ".", sep = ""), Tyear = c(24.64982014, 24.60624211, 24.49933474,
  24.96279395, 24.88365139, 24.87594184, 24.98313802, 25.68910135, 26.58033805,
  26.98619405, 25.87259696, 25.16530008), maxT = c(29.08402, 28.86072,
  28.51707, 29.56514, 29.0068, 29.83177, 30.19183, 31.34605, 32.93941, 33.14729,
  31.72165, 30.32959), nightmeanT = c(23.22247, 23.15235, 23.21073, 23.35492,
  23.58619, 23.29334, 23.3578, 23.6699, 24.09092, 24.55815, 23.71159, 23.34976),
  rainfall = c(296.726, 253.528, 454.302, 320.562, 425.2, 277.966, 163.426,
  102.012, 43.834, 26.466, 76, 157.1), wind = c(0.901671724, 0.864544643,
  0.836516801, 0.851327994, 0.787419637, 0.774398649, 0.831167015, 0.91152957,
  1.021909722, 1.053285523, 1.041843217, 0.921361559),
  maxIrradiance = c(719.7763, 765.6474679, 769.9658806, 794.82337,
  717.8013194, 795.2024929, 791.62932, 797.9236677, 874.5701367, 857.4397219,
  858.60655323, 779.2854645), irradiance = c(133.0579717, 158.3033498,
  148.2984963, 164.1783546, 143.7356799, 167.5139082, 172.4494762, 190.3358903,
  229.3920961, 225.1016445, 196.6685388, 170.289151), e_s = c(3.126835644,
  3.122050934, 3.097285304, 3.194593888, 3.167241554, 3.173096221, 3.197669097,
  3.351896181, 3.552115706, 3.634188446, 3.388384875, 3.239834054),
  e_a = c(2.820456547, 2.781722195, 2.794117369, 2.81884079, 2.918981525,
  2.889089767, 2.862294539, 2.823627394, 2.730098975, 2.774015541, 2.794606935,
  2.801060958), VPD = c(0.306379098, 0.340328739, 0.303167936, 0.375753098,
  0.24826003, 0.284006455, 0.335374559, 0.528268788, 0.822016731, 0.860172905,
  0.59377794, 0.438773096), dailymeanVPD = c(0.5873121, 0.6411128, 0.5661197,
  0.72542, 0.4913662, 0.583989, 0.7444557, 1.0074374, 1.4987548, 1.5640231,
  1.1442166, 0.8511218), dailymaxVPD = c(1.183852, 1.178975, 1.074576,
  1.305361, 1.034367, 1.280059, 1.439207, 1.787562, 2.418552, 2.471909,
  2.020966, 1.567758))

Arguments

name	char. name of the model
path	char. working directory
src	char. path to src file
optimisation	char. optimisation level to build cpp with g++ (default NULL)
app	char. path to troll app (e.g. TROLL.out)
input	char. input file to create
output	char. output folder name
build	logical. do you want to (re)-build the model
overwrite	logical. allow to overwrite existing input and outputs files
verbose	logical. allow output in console
nbcol	int. number of columns
nbrows	int. number of rows
nbiter	int. total number of time step
iter	int. number of iteration per year
NV	int. vertical number of cells (nb per m)
NH	int. horizontal number of cells (nb per m)
nbout	int. number of outputs
numesp	int. number of species
p	num. light incidence parameter (diff through turbid medium)
disturb_iter	num. iteration step where the disturbation occure
disturb_intensity	num. intensity of disturbance in percent of BA
daylight	num. normalized daily light course (from 7am to 7 pm, with a half-hour time step)
dayT	num. normalized daily VPD course (from 7am to 7 pm, with a half-hour time step)
dayVPD	num. normalized daily T course (from 7am to 7 pm, with a half-hour time step)
klight	num. light attenuation in the canopy Beer-Lambert
phi	quantum yield (in micromol C/micromol photon)
vC	num. variance of the flexion moment
DBH0	num. initial dbh (m)
H0	num. initial height (m)
ra0	num. intial crown radius (m)
ra1	num. crown radius - dbh slope (m/m)
de0	num. initial crown depth (m)
de1	num Crown_Depth/height slope (m/m)
dens	num. leaf density (m^2/m^2)
fbranchstem	num. fraction of biomass allocated to above ground wood (branches+stem)
fcanopy	num. fraction of biomass allocated to canopy (leaves + reproductive organs + twigs)
seedrain	int. constant used to scale total seed rain per hectare across species (in next computation)
nbseeds	int. nb of seeds produced and dispersed by each mature tree when SEEDTRADEOFF is not defined
mindeathrate	num. inimal death rate
m1	num. slope of death rate
CO2	num. atmospheric CO2 concentration in micromol/mol
species	df. species trait values (can be open from external file)
Tyear	num. Temperature in degree C
maxT	num. mean daily max temperature in degree C
nightmeanT	num. Night mean temperature in degree C
rainfall	num. Rainfall in mm
wind	num. Wind speed in m.s-1
maxIrradiance	num. Daily max irradiance mean in W.m-2
irradiance	num. Irradiance mean in W.m-2
e_s	num. e_s in kPa
e_a	num. e_a in kPa
VPD	num. VPD in kPa
dailymeanVPD	num. Daily mean VPD
dailymaxVPD	num. daily max VPD in kPa

Value

an S4 TROLLsim class object

Examples

NA

fischer-fjd/RconTroll documentation built on May 16, 2019, 12:57 p.m.