PRE_FATE - build parameter files

The different type of parameters and flags

FATE requires a quite large number of parameters, which are stored into .txt files, presented to and recovered by the software.
These parameters can be of 3 types :

1. Filenames, to guide the application to other parameter files that should be read
2. These filenames either correspond to :
   • other parameter files that contain values to be actually read and used
   • raster files, with the extension .tif (lighter) or .img

To enumerate these settings, 2 types of flag can be found and used within the parameter files :

1. To give one or several links to other files containing parameter values or to raster files : --PARAM_NAME--

   --GLOBAL_PARAMS--
   FATE_simulation/DATA/GLOBAL_PARAMETERS/Global_parameters_V1.txt
   --MASK--
   FATE_simulation/DATA/MASK/mask.tif
   --PFG_PARAMS_LIFE_HISTORY--
   FATE_simulation/DATA/PFGS/SUCC/SUCC_PFG1.txt
   FATE_simulation/DATA/PFGS/SUCC/SUCC_PFG2.txt
   ...
   

In this way, each parameter can have several values (filenames), and each line corresponds to a value.
The transition to a new parameter is made thanks to the presence of a new flag on the next line.

2. To give parameter values : PARAM_NAME

   NAME H2_dryGrass
   MATURITY 3
   LONGEVITY 11
   MAX_ABUNDANCE 1
   CHANG_STR_AGES 0 10000 10000 10000 10000
   ...
   

Each line corresponds to a parameter, given by the flag (parameter name in capital letters) followed by all values linked to this flag on the same line. Each value has to be separated from another by a space.

Which files for which settings ?

The function PRE_FATE.skeletonDirectory allows to create a user-friendly directory tree to store all parameter files and data.

1. Simulation parameterization

• Global parameters : related to the simulation definition
  (number of PFG and strata, simulation duration, computer resources, manage abundance values, modules loaded…)
  with the function PRE_FATE.params_globalParameters
• Years to save abundance raster maps and simulation outputs with the function PRE_FATE.params_saveYears
• Years and files to change rasters for the succession, habitat suitability or disturbance modules
  with the function PRE_FATE.params_changingYears

2. For each PFG : behavior and characteristics

• Succession files : related to the life history with the function PRE_FATE.params_PFGsuccession
• Dispersal files : related to the dispersal ability with the function PRE_FATE.params_PFGdispersal
• Light files : related to the light interaction with the function PRE_FATE.params_PFGlight
• Soil files : related to the soil interaction with the function PRE_FATE.params_PFGsoil
• Disturbance files : related to the response to perturbations in terms of resprouting and mortality
  with the function PRE_FATE.params_PFGdisturbance
• Drought files : related to the response to drought in terms of resprouting and mortality
  with the function PRE_FATE.params_PFGdrought

3. Parameter management

• SimulParameters file : containing all links to the files created with the previous functions.
  This is the file that will be given as the only argument to the FATE function.
  It can be created with the function PRE_FATE.params_simulParameters
• Multiple set of files : to duplicate simulation folder and scan global parameters space with Latin Hypercube Sampling.
  Folders can be created with the function PRE_FATE.params_multipleSet