R/model.R
In fischer-fjd/RconTroll: Package for individual-based forest growth simulator TROLL (wip)
#' @include build.R
#' @include run.R
#' @include loadOutput.R
NULL
#' Model
#'
#' Create and open a TROLL model
#'
#' @param name char. name of the model
#' @param path char. working directory
#' @param src char. path to src file
#' @param optimisation char. optimisation level to build cpp with g++ (default NULL)
#' @param app char. path to troll app (e.g. TROLL.out)
#' @param input char. input file to create
#' @param output char. output folder name
#' @param build logical. do you want to (re)-build the model
#' @param overwrite logical. allow to overwrite existing input and outputs files
#' @param verbose logical. allow output in console
#' @param nbcol int. number of columns
#' @param nbrows int. number of rows
#' @param nbiter int. total number of time step
#' @param iter int. number of iteration per year
#' @param NV int. vertical number of cells (nb per m)
#' @param NH int. horizontal number of cells (nb per m)
#' @param nbout int. number of outputs
#' @param numesp int. number of species
#' @param p num. light incidence parameter (diff through turbid medium)
#' @param disturb_iter num. iteration step where the disturbation occure
#' @param disturb_intensity num. intensity of disturbance in percent of BA
#' @param daylight num. normalized daily light course (from 7am to 7 pm, with a half-hour time step)
#' @param dayT num. normalized daily VPD course (from 7am to 7 pm, with a half-hour time step)
#' @param dayVPD num. normalized daily T course (from 7am to 7 pm, with a half-hour time step)
#' @param klight num. light attenuation in the canopy Beer-Lambert
#' @param phi quantum yield (in micromol C/micromol photon)
#' @param vC num. variance of the flexion moment
#' @param DBH0 num. initial dbh (m)
#' @param H0 num. initial height (m)
#' @param ra0 num. intial crown radius (m)
#' @param ra1 num. crown radius - dbh slope (m/m)
#' @param de0 num. initial crown depth (m)
#' @param de1 num Crown_Depth/height slope (m/m)
#' @param dens num. leaf density (m^2/m^2)
#' @param fbranchstem num. fraction of biomass allocated to above ground wood (branches+stem)
#' @param fcanopy num. fraction of biomass allocated to canopy (leaves + reproductive organs + twigs)
#' @param seedrain int. constant used to scale total seed rain per hectare across species (in next computation)
#' @param nbseeds int. nb of seeds produced and dispersed by each mature tree when SEEDTRADEOFF is not defined
#' @param mindeathrate num. inimal death rate
#' @param m1 num. slope of death rate
#' @param CO2 num. atmospheric CO2 concentration in micromol/mol
#' @param species df. species trait values (can be open from external file)
#' @param Tyear num. Temperature in degree C
#' @param maxT num. mean daily max temperature in degree C
#' @param nightmeanT num. Night mean temperature in degree C
#' @param rainfall num. Rainfall in mm
#' @param wind num. Wind speed in m.s-1
#' @param maxIrradiance num. Daily max irradiance mean in W.m-2
#' @param irradiance num. Irradiance mean in W.m-2
#' @param e_s num. e_s in kPa
#' @param e_a num. e_a in kPa
#' @param VPD num. VPD in kPa
#' @param dailymeanVPD num. Daily mean VPD
#' @param dailymaxVPD num. daily max VPD in kPa
#'
#' @return an S4 \linkS4class{TROLLsim} class object
#'
#' @export
#'
#' @examples
#' NA
#'
model <- function(
# function options
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,
# general parameters
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(0.030, 0.108, 0.208, 0.304, 0.473, 0.617, 0.723, 0.823, 0.925,
0.965, 0.995, 0.988, 1.000, 0.942, 0.854, 0.766, 0.646, 0.493,
0.360, 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, 1.000, 0.985, 0.952, 0.908,
0.863, 0.820, 0.767, 0.699, 0.611, 0.498),
dayVPD = c(0.768, 0.776, 0.795, 0.820, 0.851, 0.884, 0.912, 0.934, 0.950,
0.966, 0.980, 0.989, 0.997, 0.999, 1.000, 0.9996, 0.990, 0.982,
0.974, 0.966, 0.957, 0.945, 0.929, 0.906),
# species parameters
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 = 0.30,
seedrain = 200,
nbseeds = 10,
mindeathrate = 0.035,
m1 = 0.035,
CO2 = 360,
# species data
species = read.table(getOption("RconTroll.species"),
header=TRUE, dec=".", sep=""),
# climate data
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, 29.00680, 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,
23.35780, 23.66990, 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, 0.7254200, 0.4913662,
0.5839890, 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)
){
init(path = path,
input = input,
overwrite = overwrite,
nbcol = nbcol,
nbrows = nbrows,
nbiter = nbiter,
iter = iter,
NV = NV,
NH = NH,
nbout = nbout,
numesp = numesp,
p = p,
disturb_iter = disturb_iter,
disturb_intensity = disturb_intensity,
daylight = daylight,
dayT = dayT,
dayVPD = dayVPD,
klight = klight,
phi = phi,
vC = vC,
DBH0 = DBH0,
H0 = H0,
ra0 = ra0,
ra1 = ra1,
de0 = de0,
de1 = de1,
dens = dens,
fbranchstem = fbranchstem,
fcanopy = fcanopy,
seedrain = seedrain,
nbseeds = nbseeds,
mindeathrate = mindeathrate,
m1 = m1,
CO2 = CO2,
species = species,
Tyear = Tyear,
maxT = maxT,
nightmeanT = nightmeanT,
rainfall = rainfall,
wind = wind,
maxIrradiance = maxIrradiance,
irradiance = irradiance,
e_s = e_s,
e_a = e_a,
VPD = VPD,
dailymeanVPD = dailymeanVPD,
dailymaxVPD = dailymaxVPD)
if(build)
build(src = src,
app = app,
path = path,
optimisation = optimisation,
verbose = verbose)
run(name = name,
path = path,
app = app,
input = input,
overwrite = overwrite,
verbose = verbose)
path <- file.path(path, name)
model <- loadOutput(name = name, path = path)
return(model)
}
fischer-fjd/RconTroll documentation built on May 16, 2019, 12:57 p.m.
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#' @include build.R
#' @include run.R
#' @include loadOutput.R
NULL
#' Model
#'
#' Create and open a TROLL model
#'
#' @param name char. name of the model
#' @param path char. working directory
#' @param src char. path to src file
#' @param optimisation char. optimisation level to build cpp with g++ (default NULL)
#' @param app char. path to troll app (e.g. TROLL.out)
#' @param input char. input file to create
#' @param output char. output folder name
#' @param build logical. do you want to (re)-build the model
#' @param overwrite logical. allow to overwrite existing input and outputs files
#' @param verbose logical. allow output in console
#' @param nbcol int. number of columns
#' @param nbrows int. number of rows
#' @param nbiter int. total number of time step
#' @param iter int. number of iteration per year
#' @param NV int. vertical number of cells (nb per m)
#' @param NH int. horizontal number of cells (nb per m)
#' @param nbout int. number of outputs
#' @param numesp int. number of species
#' @param p num. light incidence parameter (diff through turbid medium)
#' @param disturb_iter num. iteration step where the disturbation occure
#' @param disturb_intensity num. intensity of disturbance in percent of BA
#' @param daylight num. normalized daily light course (from 7am to 7 pm, with a half-hour time step)
#' @param dayT num. normalized daily VPD course (from 7am to 7 pm, with a half-hour time step)
#' @param dayVPD num. normalized daily T course (from 7am to 7 pm, with a half-hour time step)
#' @param klight num. light attenuation in the canopy Beer-Lambert
#' @param phi quantum yield (in micromol C/micromol photon)
#' @param vC num. variance of the flexion moment
#' @param DBH0 num. initial dbh (m)
#' @param H0 num. initial height (m)
#' @param ra0 num. intial crown radius (m)
#' @param ra1 num. crown radius - dbh slope (m/m)
#' @param de0 num. initial crown depth (m)
#' @param de1 num Crown_Depth/height slope (m/m)
#' @param dens num. leaf density (m^2/m^2)
#' @param fbranchstem num. fraction of biomass allocated to above ground wood (branches+stem)
#' @param fcanopy num. fraction of biomass allocated to canopy (leaves + reproductive organs + twigs)
#' @param seedrain int. constant used to scale total seed rain per hectare across species (in next computation)
#' @param nbseeds int. nb of seeds produced and dispersed by each mature tree when SEEDTRADEOFF is not defined
#' @param mindeathrate num. inimal death rate
#' @param m1 num. slope of death rate
#' @param CO2 num. atmospheric CO2 concentration in micromol/mol
#' @param species df. species trait values (can be open from external file)
#' @param Tyear num. Temperature in degree C
#' @param maxT num. mean daily max temperature in degree C
#' @param nightmeanT num. Night mean temperature in degree C
#' @param rainfall num. Rainfall in mm
#' @param wind num. Wind speed in m.s-1
#' @param maxIrradiance num. Daily max irradiance mean in W.m-2
#' @param irradiance num. Irradiance mean in W.m-2
#' @param e_s num. e_s in kPa
#' @param e_a num. e_a in kPa
#' @param VPD num. VPD in kPa
#' @param dailymeanVPD num. Daily mean VPD
#' @param dailymaxVPD num. daily max VPD in kPa
#'
#' @return an S4 \linkS4class{TROLLsim} class object
#'
#' @export
#'
#' @examples
#' NA
#'
model <- function(
# function options
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,
# general parameters
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(0.030, 0.108, 0.208, 0.304, 0.473, 0.617, 0.723, 0.823, 0.925,
0.965, 0.995, 0.988, 1.000, 0.942, 0.854, 0.766, 0.646, 0.493,
0.360, 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, 1.000, 0.985, 0.952, 0.908,
0.863, 0.820, 0.767, 0.699, 0.611, 0.498),
dayVPD = c(0.768, 0.776, 0.795, 0.820, 0.851, 0.884, 0.912, 0.934, 0.950,
0.966, 0.980, 0.989, 0.997, 0.999, 1.000, 0.9996, 0.990, 0.982,
0.974, 0.966, 0.957, 0.945, 0.929, 0.906),
# species parameters
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 = 0.30,
seedrain = 200,
nbseeds = 10,
mindeathrate = 0.035,
m1 = 0.035,
CO2 = 360,
# species data
species = read.table(getOption("RconTroll.species"),
header=TRUE, dec=".", sep=""),
# climate data
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, 29.00680, 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,
23.35780, 23.66990, 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, 0.7254200, 0.4913662,
0.5839890, 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)
){
init(path = path,
input = input,
overwrite = overwrite,
nbcol = nbcol,
nbrows = nbrows,
nbiter = nbiter,
iter = iter,
NV = NV,
NH = NH,
nbout = nbout,
numesp = numesp,
p = p,
disturb_iter = disturb_iter,
disturb_intensity = disturb_intensity,
daylight = daylight,
dayT = dayT,
dayVPD = dayVPD,
klight = klight,
phi = phi,
vC = vC,
DBH0 = DBH0,
H0 = H0,
ra0 = ra0,
ra1 = ra1,
de0 = de0,
de1 = de1,
dens = dens,
fbranchstem = fbranchstem,
fcanopy = fcanopy,
seedrain = seedrain,
nbseeds = nbseeds,
mindeathrate = mindeathrate,
m1 = m1,
CO2 = CO2,
species = species,
Tyear = Tyear,
maxT = maxT,
nightmeanT = nightmeanT,
rainfall = rainfall,
wind = wind,
maxIrradiance = maxIrradiance,
irradiance = irradiance,
e_s = e_s,
e_a = e_a,
VPD = VPD,
dailymeanVPD = dailymeanVPD,
dailymaxVPD = dailymaxVPD)
if(build)
build(src = src,
app = app,
path = path,
optimisation = optimisation,
verbose = verbose)
run(name = name,
path = path,
app = app,
input = input,
overwrite = overwrite,
verbose = verbose)
path <- file.path(path, name)
model <- loadOutput(name = name, path = path)
return(model)
}
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