FATE simulationR/PRE_FATE.params_globalParameters.R
PRE_FATE.params_globalParameters.RdThis script is designed to create parameter file(s)
containing GLOBAL PARAMETERS used in FATE model.
PRE_FATE.params_globalParameters(
name.simulation,
opt.global.name = NULL,
opt.no_CPU = 1,
opt.replacePrevious = FALSE,
opt.saving_abund_PFG_stratum = TRUE,
opt.saving_abund_PFG = TRUE,
opt.saving_abund_stratum = FALSE,
required.no_PFG,
required.no_strata,
required.simul_duration = 1000,
required.seeding_duration = 300,
required.seeding_timestep = 1,
required.seeding_input = 100,
required.potential_fecundity = 100,
required.max_abund_low,
required.max_abund_medium,
required.max_abund_high,
doLight = FALSE,
LIGHT.thresh_medium,
LIGHT.thresh_low,
LIGHT.recruit = TRUE,
LIGHT.saving = TRUE,
doSoil = FALSE,
SOIL.fill_map = TRUE,
SOIL.init,
SOIL.retention,
SOIL.recruit = TRUE,
SOIL.saving = TRUE,
doDispersal = FALSE,
DISPERSAL.mode = 1,
DISPERSAL.saving = FALSE,
doHabSuitability = FALSE,
HABSUIT.mode = 1,
doDisturbances = FALSE,
DIST.no,
DIST.no_sub = 4,
DIST.freq = rep(1, DIST.no),
DIST.prob = rep(1, DIST.no),
DIST.pair = rep(1, DIST.no),
doDrought = FALSE,
DROUGHT.no_sub = 4,
doAliens = FALSE,
ALIEN.freq = 1,
doFire = FALSE,
FIRE.no,
FIRE.no_sub = 4,
FIRE.freq = 1,
FIRE.ignit_mode = 1,
FIRE.ignit_no,
FIRE.ignit_noHist,
FIRE.ignit_logis = c(0.6, 2.5, 0.05),
FIRE.ignit_flammMax,
FIRE.neigh_mode = 1,
FIRE.neigh_CC = c(2, 2, 2, 2),
FIRE.prop_mode = 1,
FIRE.prop_intensity,
FIRE.prop_logis = c(0.6, 2.5, 0.05),
FIRE.quota_mode = 4,
FIRE.quota_max
)a string corresponding to the main directory
or simulation name of the FATE simulation
(optional) default NULL
a string corresponding to the name of the global parameter file to
be created
(optional) default 1.
an integer
corresponding to the number of resources that can be used to parallelize
the FATE simulation
(optional) default FALSE.
If TRUE, pre-existing files inside
name.simulation/DATA/GLOBAL_PARAMETERS folder will be replaced
(optional) default TRUE.
If TRUE, and saving years have been defined within the
Simul_parameters file with the SAVING_YEARS_MAPS flag,
pixel abundances per PFG per stratum are saved
(optional) default TRUE.
If TRUE, and saving years have been defined within the
Simul_parameters file with the SAVING_YEARS_MAPS flag,
pixel abundances per PFG are saved
(optional) default TRUE.
If TRUE, and saving years have been defined within the
Simul_parameters file with the SAVING_YEARS_MAPS flag,
pixel abundances per stratum are saved
an integer corresponding to the number of PFG
an integer corresponding to the number of
height strata
an integer corresponding to the
duration of simulation (in years)
an integer corresponding to the
duration of seeding (in years)
an integer corresponding to the
time interval at which occurs the seeding, and until the seeding duration
is not over (in years)
an integer corresponding to the number
of seeds attributed to each PFG at each time step, and until the seeding
duration is not over
an integer corresponding to the
maximum number of seeds produced each year by a PFG (it can also be
specified within PFG succession files (see
PRE_FATE.params_PFGsuccession)
otherwise this value will be used)
an integer in the order of
1 000 to rescale abundance values of tall PFG
an integer in the order of
1 000 to rescale abundance values of intermediate PFG
an integer in the order of
1 000 to rescale abundance values of small PFG
default FALSE.
If TRUE, light interaction
is activated in the FATE simulation, and associated parameters are
required
(optional)
an integer in the
order of 1 000 to convert PFG abundances in each stratum into light
resources. It corresponds to the limit of abundances above which light
resources are medium. PFG abundances lower than this threshold imply
high amount of light. It is consequently lower than
LIGHT.thresh_low.
(optional)
an integer in the order
of 1 000 to convert PFG abundances in each strata into light
resources. It corresponds to the limit of abundances above which light
resources are low. PFG abundances higher than
LIGHT.thresh_medium and lower than this threshold imply
medium amount of light.
(optional) default TRUE.
If TRUE, recruitment is depending on the tolerance of the PFG to
the pixel light resources within the stratum 0
(optional) default TRUE.
If TRUE, and saving years have been defined within the
Simul_parameters file with the SAVING_YEARS_MAPS flag,
pixel light resources are saved
default FALSE.
If TRUE, soil interaction is
activated in the FATE simulation, and associated parameters
are required
(optional) default TRUE.
If TRUE, soil initialization map is filled with SOIL.init
value ; if FALSE, soil initialization map is defined within the
Simul_parameters file with the SOIL_MASK flag
(optional)
a double corresponding to the
soil value to initialize all pixels when starting the FATE
simulation
(optional)
a double corresponding
to the percentage of soil value of the previous simulation year that will
be kept in the calculation of the soil value of the current simulation year
(optional) default TRUE.
If TRUE, recruitment is depending on the tolerance of the PFG to
the pixel soil resources
(optional) default TRUE.
If TRUE, and saving years have been defined within the
Simul_parameters file with the SAVING_YEARS_MAPS flag,
pixel soil resources are saved
default FALSE.
If TRUE, seed dispersal
is activated in the FATE simulation, and associated parameters are
required
(optional)
an integer corresponding
to the way of simulating the seed dispersal for each PFG, either packets
kernel (1), exponential kernel (2) or exponential kernel with
probability (3)
(optional) default TRUE.
If TRUE, and saving years have been defined within the
Simul_parameters file with the SAVING_YEARS_MAPS flag,
pixel dispersed seeds per PFG are saved
default FALSE.
If TRUE, habitat
suitability is activated in the FATE simulation, and associated
parameters are required
(optional)
an integer
corresponding to the way of simulating the habitat suitability variation
between years for each PFG, either random (1) or PFG specific
(2)
default FALSE.
If TRUE, disturbances
are applied in the FATE simulation, and associated parameters are
required
(optional)
an integer corresponding to the
number of disturbances
(optional)
an integer corresponding to
the number of way a PFG could react to a disturbance
(optional)
a vector of integer
corresponding to the frequency of each disturbance (in years)
(optional)
a vector of double
corresponding to the probability of each pixel to be impacted by each
disturbance (between 0 and 1)
(optional)
a vector of integer
corresponding to the disturbance paired identification : which disturbances
will be impacted within the same pixels selected to fullfill the
DIST.prob condition
default FALSE.
If TRUE, drought
disturbances are applied in the FATE simulation, and associated
parameters are required
(optional)
an integer corresponding
to the number of way a PFG could react to a drought disturbance
default FALSE.
If TRUE, invasive plant
introduction is activated in the FATE simulation, and associated
parameters are required
(optional)
a vector of integer
corresponding to the frequency of each introduction (in years)
default FALSE.
If TRUE, fire
disturbances are applied in the FATE simulation, and associated
parameters are required
(optional)
an integer corresponding to the
number of fire disturbances
(optional)
an integer corresponding to
the number of way a PFG could react to a fire disturbance
(optional)
a vector of integer
corresponding to the frequency of each fire disturbance (in years)
(optional)
an integer
corresponding to the way of simulating the fire(s) ignition each year,
either random (1, 2 or 3), according to cell conditions
(4) or through a map (5)
(optional) (required if
FIRE.ignit_mode = 1 or 2)
an integer corresponding to the
number of fires starting each year
(optional) (required if
FIRE.ignit_mode = 3)
a vector of integer
corresponding to historical number of fires
(optional) (required if
FIRE.ignit_mode = 4)
a vector of 3 values to parameterize
the logistic probability function :
asymptote of the function curve
time where the slope starts to increase
speed of slope increase
(optional) (required if
FIRE.ignit_mode = 4)
an integer corresponding to the
maximum flammmability of PFG
(optional)
an integer
corresponding to the way of finding neighboring cells each year,
either 8 adjacent (1) or with cookie cutter (2 or 3)
(optional) (required if
FIRE.neigh_mode = 2 or 3)
a vector of 4 values
corresponding to the extent of cookie cutter :
number of cells towards north
number of cells towards east
number of cells towards south
number of cells towards west
(optional)
an integer
corresponding to the way of simulating the fire(s) propagation each year,
either fire intensity (1), % of plants consumed (2), maximum
amount of resources (3 or 4), or according to cell conditions
(5)
(optional) (required if
FIRE.prop_mode = 1)
a vector of double
corresponding to the intensity or probability of dispersal of each fire
disturbance (between 0 and 1)
(optional) (required if
FIRE.prop_mode = 5)
a vector of 3 values to parameterize
the logistic probability function :
asymptote of the function curve
time where the slope starts to increase
speed of slope increase
(optional)
an integer
corresponding to the way of ending the fire(s) spread each year,
either maximum steps (1), maximum amount of resources (2),
maximum cells (3), or keep going (4)
(optional) (required if
FIRE.quota_mode = 1, 2 or 3)
an integer corresponding to
the maximum quantity limit (either steps, resources, cells)
A .txt file into the
name.simulation/DATA/GLOBAL_PARAMETERS directory with the following
parameters :
NO_CPU
SAVING_ABUND_PFG_STRATUM
SAVING_ABUND_PFG
SAVING_ABUND_STRATUM
NO_PFG
NO_STRATA
SIMULATION_DURATION
SEEDING_DURATION
SEEDING_TIMESTEP
SEEDING_INPUT
POTENTIAL_FECUNDITY
MAX_ABUND_LOW
MAX_ABUND_MEDIUM
MAX_ABUND_HIGH
If the simulation includes light interaction :
DO_LIGHT_INTERACTION
LIGHT_THRESH_MEDIUM
LIGHT_THRESH_LOW
LIGHT_RECRUITMENT
LIGHT_SAVING
If the simulation includes soil interaction :
DO_SOIL_INTERACTION
SOIL_FILL_MAP
SOIL_INIT
SOIL_RETENTION
SOIL_RECRUITMENT
SOIL_SAVING
If the simulation includes dispersal :
DO_DISPERSAL
DISPERSAL_MODE
DISPERSAL_SAVING
If the simulation includes habitat suitability :
DO_HAB_SUITABILITY
HABSUIT_MODE
If the simulation includes disturbances :
DO_DISTURBANCES
DIST_NO
DIST_NOSUB
DIST_FREQ
DIST_PROB
DIST_PAIR
If the simulation includes drought disturbance :
DO_DROUGHT_DISTURBANCE
DROUGHT_NOSUB
If the simulation includes aliens introduction :
DO_ALIENS_INTRODUCTION
ALIENS_FREQ
If the simulation includes fire disturbance :
DO_FIRE_DISTURBANCE
FIRE_NO
FIRE_NOSUB
FIRE_FREQ
FIRE_IGNIT_MODE
FIRE_IGNIT_NO
FIRE_IGNIT_NOHIST
FIRE_IGNIT_LOGIS
FIRE_IGNIT_FLAMMMAX
FIRE_NEIGH_MODE
FIRE_NEIGH_CC
FIRE_PROP_MODE
FIRE_PROP_INTENSITY
FIRE_PROP_LOGIS
FIRE_QUOTA_MODE
FIRE_QUOTA_MAX
The core module of FATE requires several parameters to
define general characteristics of the simulation :
the number of plant functional groups that will be
included into the simulation.
This number should match with the
number of files that will be given to parameterize the different
activated modules with the characteristics of each group (SUCC,
DISP, ...).
the number of height strata that will be used into the
succession module.
This number should match with the maximum number
of strata possible defined into the PFG SUCC files.
the number of seeds produced each year by
each mature individual.
Maximal number of seeds produced per pixel
is limited by PFG maximum abundance, meaning that maximum fecundity
per PFG per pixel is equal to
\(MaxAbund * \text{required.potential_fecundity}\)
abundance regulation thresholds for
tall / intermediate / small PFG within a pixel (in `FATE` arbitrary
abundance units).
Each PFG is assigned with one of these 3 values (see
PRE_FATE.params_PFGsuccession) to be a broad proxy of the
amount of space it can occupy within a pixel (herbaceous should be more
numerous than phanerophytes). These thresholds help regulate the PFG
fecundity :
$$fecundity = min(matAbund, MaxAbund) * \text{required.potential_fecundity}$$
and recruitment happens only if :
$$totAbund < MaxAbund * (1 + ImmSize)$$
the duration of simulation (in years)
the duration of seeding (in years)
the time interval at which occurs the seeding, and until the seeding duration is not over (in years)
the number of seeds dispersed for each PFG at each
time step, and until the seeding duration is not over
The other modules of FATE can be activated within this
file, and if so, some additional parameters will be required :
= to influence seed recruitment and plant mortality according
to PFG preferences for light conditions
(see
PRE_FATE.params_PFGlight)
= light resources are calculated as a proxy of PFG abundances within each
height stratum
To transform PFG abundances into light resources :
$$abund_{\text{ PFG}_{all}\text{, }\text{Stratum}_k} <
\text{LIGHT.thresh_medium} \;\; \Leftrightarrow \;\;
light_{\text{ Stratum}_k} = \text{High}$$
$$\text{LIGHT.thresh_medium } < abund_{\text{ PFG}_{all}\text{, }\text{Stratum}_k} < \text{LIGHT.thresh_low} \\ \Leftrightarrow \;\; light_{\text{ Stratum}_k} = \text{Medium}$$
$$abund_{\text{ PFG}_{all}\text{, }\text{Stratum}_k} >
\text{LIGHT.thresh_low} \;\; \Leftrightarrow \;\;
light_{\text{ Stratum}_k} = \text{Low}$$
As light resources are directly obtained from PFG abundances,
LIGHT.thresh_medium and LIGHT.thresh_low parameters should
be on the same scale than required.max_abund_low,
required.max_abund_medium and required.max_abund_high
parameters from the core module.
= to influence seed recruitment and plant mortality
according to PFG preferences for soil conditions
(see
PRE_FATE.params_PFGsoil)
= soil composition is calculated as the weighted mean of each PFG's
contribution with a possible retention of the soil value of the previous
simulation year
$$Soil_y + \text{SOIL.retention} * (Soil_{y-1} - Soil_y)$$
with
$$Soil_y = \sum abund_{\text{ PFG}_i\text{, }y} *
\text{contrib}_{\text{ PFG}_i}$$
= to allow plants to disperse seeds according to 3
user-defined distances
(see PRE_FATE.params_PFGdispersal)
Three modes of dispersal (DISPERSAL.mode) are available :
packets kernel :
homogeneous dispersal of 50% of the seeds within the
d50 circle
dispersal of 49% of the seeds within the d99 - d50
ring with the same concentration as in the first circle but by pairs
of pixel (see Boulangeat et al, 2014)
dispersal of 1% of the seeds within the ldd - d99 ring
into one random pixel
exponential kernel : seeds are dispersed within each
concentric circle (d50, d99 and ldd) according to
a decreasing exponential density law (lambda = 1)
exponential kernel with probability : seeds are dispersed
within each concentric circle (d50, d99 and ldd)
according to a decreasing exponential density law (lambda = 1) and a
continuous decreasing probability with distance
= to influence plants fecundity and seed
recruitment according to PFG preferences for habitat conditions
= filter based on maps given for each PFG within the
Simul_parameters file with the PFG_HAB_MASK flag
(see
PRE_FATE.params_simulParameters)
These maps must contain values between 0 and 1 corresponding
to the probability of presence of the PFG in each pixel. Each year
(timestep), this value will be compared to a reference value, and if
superior, the PFG will be able to grow and survive.
Two methods to define this habitat suitability reference value are
available (HABSUIT.mode) :
random : for each pixel, the reference value is drawn from a uniform distribution, and the same value is used for each PFG within this pixel.
PFG specific : for each PFG, a mean value and a
standard deviation value are drawn from a uniform distribution. For
each pixel and for each PFG, the reference value is drawn from a
normal distribution of parameters the mean and standard deviation of
the PFG.
= to influence plant mortality and / or resprouting
according to PFG tolerances to these events
(see
PRE_FATE.params_PFGdisturbance)
= defined for events such as mowing, grazing, but also urbanization,
crops, etc
= filter based on maps given for each disturbance within the
Simul_parameters file with the DIST_MASK flag
(see
PRE_FATE.params_simulParameters)
These maps must contain values between 0 and 1 defining the
impact zone of each perturbation and its intensity. The user will have to
define how each PFG will be impacted depending on age and life stage, and
this will be weighted by the intensity value.
the number of different disturbances
the number of way a PFG could react to a perturbation
the frequency of each disturbance (in years)
the probability of each pixel to be impacted by each
disturbance (between 0 and 1)
which disturbances will be impacted within the same
pixels randomly selected if DIST.prob < 1
= to experience extreme events with a direct and a
delayed response on PFG
= based on a map given within the Simul_parameters file with the
DROUGHT_MASK flag
(see
PRE_FATE.params_simulParameters)
This map must contain values representing proxies for drought intensity,
like moisture values, in the sense that the lower the values, the higher
the chance of experiencing a drought event. Developed canopy closure helps
to reduce these values. The intensity of the drought event (moderate or
severe) is determined based on thresholds defined for each PFG according
to, for example, their moisture preference, as well as the number of
cumulated consecutive years during which the PFG experienced a drought
(see PRE_FATE.params_PFGdrought).
if \(di_y > \text{threshold.MOD}_{\text{ PFG}_i}\), the counter of cumulated consecutive years of drought experienced by the PFG will decrease : $$\text{counter}_{\text{ PFG}_i} = \text{counter}_{\text{ PFG}_i} - \text{counter.RECOVERY}_{\text{ PFG}_i}$$
if \(\text{threshold.SEV}_{\text{ PFG}_i} < di_y < \text{threshold.MOD}_{\text{ PFG}_i}\)
if \(di_y < \text{threshold.SEV}_{\text{ PFG}_i} \;\; \text{ & } \;\; \text{counter}_{\text{ PFG}_i} = 0\)
then fecundity and recruitment are set to 0 for this year, and
counter is incremented : \(\text{counter}_{\text{ PFG}_i} ++\)
if \(di_y < \text{threshold.SEV}_{\text{ PFG}_i} \;\; \text{ & } \;\; \text{counter.SENS}_{\text{ PFG}_i} \leq \text{counter}_{\text{ PFG}_i} < \text{counter.CUM}_{\text{ PFG}_i}\)
if \(\text{counter}_{\text{ PFG}_i} \geq \text{counter.CUM}_{\text{ PFG}_i}\)
then PFG experiences immediate drought-related mortality ;
and the year after, fecundity and recruitment will be set to 0
and PFG will experience delayed drought-related mortality.
As for the disturbances module, the user will have to define how each PFG will be impacted depending on age and life stage.
!not required!
= 2, the
immediate and delayed responses
the number of way a PFG could react to each of these two perturbations
!not required!
the map of
drought intensity proxy defined within the Simul_parameters file
with the DROUGHT_MASK flag, as well as the
DROUGHT_CHANGEMASK_YEARS and DROUGHT_CHANGEMASK_FILES
flags, make it possible to manage the frequency and the variation of
drought values (see PRE_FATE.params_simulParameters)
= to add new PFG during the simulation
= defined for events such as invasive introduction, colonization, but also
new crops development, reintroduction, etc
= filter based on maps given for each PFG within the
Simul_parameters file with the PFG_MASK_ALIENS flag
(see
PRE_FATE.params_simulParameters)
These maps, containing either 0 or 1, define the
introduction areas.
If the habitat suitability filter is on,
suitability maps will also be needed for these new groups.
the frequency of each introduction (in years)
= to influence plant mortality and / or resprouting according
to PFG tolerances to these events (see
PRE_FATE.params_PFGdisturbance)
Fire extreme events are broken down into 4 steps representing their
life cycle, so to speak. Each of these steps can be parameterized
according to different available options :
Five methods to define the cells that are going to burn
first, and from which the fire will potentially spread, are available
(FIRE.ignit_mode) :
Random (fixed) : FIRE.ignit_no positions are
drawn randomly over the area
Random (normal distribution) : ignit_no positions
are drawn randomly over the area, with
$$\text{ignit_no} \sim N(\text{FIRE.ignit_no}, 1 +
\frac{\text{FIRE.ignit_no}}{10})$$
Random (historic distribution) : ignit_no positions
are drawn randomly over the area, with
$$\text{ignit_no} \sim \text{FIRE.ignit_noHist}
[\;\; U(1, length(\text{FIRE.ignit_noHist})) \;\;]$$
Probability
(Li et al. 1997 Ecology Modelling)
: each cell can be a fire start with a probability (probLi)
taking into account a baseline probability (BL), the PFG
composition and abundances (fuel), and a drought index
(DI, only if values between 0 and 1, given within
the Simul_parameters file with the DROUGHT_MASK flag
(see PRE_FATE.params_simulParameters)) :
$$probLi_y = \text{BL}_y * \text{fuel}_y * (-DI)$$ with
$$\text{BL}_y = \frac{\text{FIRE.ignit_logis}[1]}{1 +
e^{\text{FIRE.ignit_logis}[2] - \text{FIRE.ignit_logis}[3] * TSLF_y}}$$
$$\text{fuel}_y = \sum \frac{\text{FLAMM}_{\text{ PFG}_i}}
{\text{FIRE.ignit_flammMax}} * \frac{abund_{\text{ PFG}_i\text{, }y}}
{abund_{\text{ PFG}_{all}\text{, }y}}$$
Map !no neighbours, propagation, quota steps!
Each cell specified by the map given within the
Simul_parameters file with the FIRE_MASK flag and
containing either 0 or 1 to define the starting
positions (see PRE_FATE.params_simulParameters)
Three methods to define the
neighboring cells of the cell currently burning, and to which the fire
will potentially spread, are available (FIRE.neigh_mode) :
8 neighbours : all the 8 adjacent cells can potentially be impacted by fire, and propagation will determine which ones are effectively affected.
Extent (fixed) !no propagation step!
All
cells contained within the rectangle defined by the cookie
cutter extent (FIRE.neigh_CC) are impacted by fire
Extent (random) !no propagation step!
All
cells contained within the rectangle defined by the cookie
cutter extent (neigh_CC) are impacted by fire, with
$$neigh\_CC_y \in \sum U(1, \text{FIRE.neigh_CC}_i)$$
Five methods to define which cells among the
neighboring cells will actually burn are available
(FIRE.prop_mode) :
Probability (fire intensity) : a probability is
assigned to the cell currently burning corresponding to the
concerned fire intensity (FIRE.prop_intensity) and compared to a
number drawn randomly for each neighbor cell
Probability (% of plants consumed) : a probability is
assigned to the cell currently burning linked to the percentage
of PFG killed by the concerned fire (prob) and compared to a
number drawn randomly for each neighbor cell
$$\text{prob}_y = \sum \text{KilledIndiv}_{\text{ PFG}_i} *
\frac{abund_{\text{ PFG}_i\text{, }y}}
{abund_{\text{ PFG}_{all}\text{, }y}}$$
Maximum amount (PFG) : the cell(s) with the maximum
amount of plants weighted by their flammability (fuel) will
burn
$$\text{fuel}_y = \sum \text{FLAMM}_{\text{ PFG}_i} *
abund_{\text{ PFG}_i\text{, }y}$$
Maximum amount (soil) : if the soil module was activated, the cell(s) with the maximum amount of soil will burn
Probability
(Li et al. 1997 Ecology Modelling)
: a probability is assigned to the cell currently burning
taking into account a baseline probability (BL), the PFG
composition and abundances (fuel), the elevation and slope
(given within the Simul_parameters file with the
ELEVATION_MASK and SLOPE_MASK flags (see
PRE_FATE.params_simulParameters)), and a drought index
(DI, only if values between 0 and 1, given within
the Simul_parameters file with the DROUGHT_MASK flag
(see PRE_FATE.params_simulParameters)) :
$$probLi_y = \text{BL}_y * \text{fuel}_y * (-DI) * probSlope$$ with
$$\text{BL}_y = \frac{\text{FIRE.prop_logis}[1]}{1 +
e^{\text{FIRE.prop_logis}[2] - \text{FIRE.prop_logis}[3] * TSLF_y}}$$
$$\text{fuel}_y = \sum \frac{\text{FLAMM}_{\text{ PFG}_i}}
{\text{FIRE.ignit_flammMax}} * \frac{abund_{\text{ PFG}_i\text{, }y}}
{abund_{\text{ PFG}_{all}\text{, }y}}$$
$$\text{if going up, } probSlope = 1 + 0.001 * \text{SLOPE}$$
$$\text{if going down, } probSlope = 1 + 0.001 *
max(-30.0,-\text{SLOPE})$$
Four methods to define when the fire will stop
spreading are available (FIRE.quota_mode) :
Maximum step : after a fixed number of steps
(FIRE.quota_max)
Maximum amount : when a fixed amount of PFG is consumed
(FIRE.quota_max)
Maximum cells : when a fixed amount of cells is
consumed (FIRE.quota_max)
Keep going : as long as it remains a fire that manages to spread
As for the disturbances module, the user will have to define how each PFG will be impacted depending on age and life stage.
the number of different fire disturbances
the number of way a PFG could react to a perturbation
the frequency of each fire disturbance
(in years)
## Create a skeleton folder with the default name ('FATE_simulation') ------------------------
PRE_FATE.skeletonDirectory()
## Create a Global_parameters file------------------------------------------------------------
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 3
, required.no_strata = 5
, required.simul_duration = 500
, required.seeding_duration = 50
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.potential_fecundity = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000
, doLight = TRUE
, LIGHT.thresh_medium = 4000
, LIGHT.thresh_low = 7000
, doDispersal = TRUE
, DISPERSAL.mode = 1
, doHabSuitability = TRUE
, HABSUIT.mode = 1)
## Create SEVERAL Global_parameters files ----------------------------------------------------
PRE_FATE.params_globalParameters(name.simulation = "FATE_simulation"
, required.no_PFG = 3
, required.no_strata = 5
, required.simul_duration = 500
, required.seeding_duration = 50
, required.seeding_timestep = 1
, required.seeding_input = 100
, required.potential_fecundity = 100
, required.max_abund_low = 3000
, required.max_abund_medium = 5000
, required.max_abund_high = 9000
, doLight = TRUE
, LIGHT.thresh_medium = 4000
, LIGHT.thresh_low = 7000
, doDispersal = TRUE
, DISPERSAL.mode = 1
, doHabSuitability = TRUE
, HABSUIT.mode = c(1,2))