NEWS

Package releases

Original version was FATE-HD, developed and used in papers such as Boulangeat 2014, Barros 2017 or Carboni 2018 (see FATE tutorial - Publications). It was only C++ code, and all modules were linked together (LIGHT, DISPERSAL, HABSUIT, SEEDING, DISTURBANCE).

Refinements to the model, and integration of the C++ code within an R package, as well as new modules development, were meant to facilitate the use and spread of the FATE model.

Version 1.4.1 (november 2025)

• 1.4.1 :
  • remove only the last / in name.simulation parameter
  • add doRichness, doCover, doLeinster, doCWM parameters in POST_FATE.graphic_mapPFG function
    + doRichness via binary maps directly
    + correct the .zip step
• 1.4.0 (august) :
  • update SimulMap::UpdateSimulationParameters function
  • add SEED in global parameters (instead of chrono::system_clock::now().time_since_epoch().count(), impacting dispersal, disturbance probability, envsuitRef) and m_RNG parameter in SimulMap
  • switch from std::mt19937 to std::default_random_engine to generate random numbers
  • move all random number generation out of pragma loops (dispersal, disturbances)
  • For dispersal :
    • move random number generation out of Disp::DoDispersalPacket to SimulMap::DoDispersal
    • fix initialization of rand arrays (with resize / clear / reserve / emplace_back functions)
  • For disturbances :
    • add DIST_CHANGEFREQ_FILES and DIST_CHANGEFREQ_YEARS in global parameters
    • change applyDist way of working, correct modulo, and add applyRand
    • always perform random number generation, even when the disturbance is not to be applied, or is PAIRED with another, not to change the RNG count and match simulations with same seed but different use of disturbances

Version 1.3.6 (june 2025)

• 1.3.6 :
  • fix .adaptMaps when files have same extension
  • fix MAX_ABUND with as.integer in PFG succession files
  • remove required.max_abund_low, medium and high parameters in global parameters function
  • weight abundances by SHADE_FACTOR for soil contribution (TEST)
  • remove phyloclim dependency by integrating niche.overlap function within the package
  • change unsigned to int (maskCells and cellID parameters related, Spatial.h, Legion::addCohort() and Legion::reduceCohort()) and remove useless static_cast<int>
  • change raster maps encoding from GDT_UInt16 to GDT_UInt32, and from GUInt16 to GUInt32
  • change some for loop from .size() to range-based
  • clean and add correct getters and setters to Logger and call only on saving years
  • remove elements from boost archive (to make it lighter)

Version 1.3.5 (june 2024)

• 1.3.5 :
  • do not need dispersal to have seeding
  • transform SHADE_FACTOR from int to double
  • remove MAX_ABUND_LOW, MAX_ABUND_MEDIUM, MAX_ABUND_HIGH in global parameters
  • addition of MAX_ABUND parameter within PFG succession files (see FATE tutorial - Modules)
  • update DROUGHT module code
• 1.3.4 :
  • switch between int / unsigned to remove warnings (compilation)
  • change variable names (from m_Dispersed to m_IsSeeded, MaxRecruit to Light/SoilActiveGerm, m_DormBreaks to m_ActiveSeeds)
  • change PFG parameter names related to drought (see FATE tutorial - Modules)
  • update Makevars.win and winlibs to compile on Windows with R 4.4.0 and RTools44

Version 1.3.3 (november 2023)

• 1.3.3 : addition of DIST_PROB and DIST_PAIR parameters within DIST module (see FATE tutorial - Modules)
• 1.3.2 :
  • include PFG loop inside SuFate::DoDisturbance() (optimization)
  • remove call to Legion::pickupCohorts() from Legion::reduceCohort() function, and add Legion::reduceCohort() function targeting directly a specified cohort (seg fault)
  • take into account Germinant LIGHT_TOL values in SuFate::CheckSurvival() function
• 1.3.1 : change scale from 0:10 to 0:100 for
  IMM_SIZE, ACTIVE_GERM, LIGHT_TOL, SOIL_TOL, PROP_KILLED, ACTIVATED_SEED, FATES parameters
• 1.3.0 : addition of LIGHT_RECRUITMENT parameter within LIGHT module,
  and --SOIL_MASK--, SOIL_FILL_MAP and SOIL_RECRUITMENT parameters within SOIL module (see FATE tutorial - Modules)

Version 1.2.0 (april 2023)

• compatibility with PROJ8
• change BOOST files to update BH package from version 1.75 to 1.81
• optimization of SimulMap with unswitching
• minor corrections

Version 1.1.0 (may 2022)

• addition of SHADE_FACTOR parameter within LIGHT module (see FATE tutorial - Modules)
• corrections to seeding recruitment, and environment calculation in LIGHT module (height strata)

Version 1.0.0 (june 2021)

• all steps included in one tool (PRE-FATE, FATE, POST-FATE), that can be easily installed on all OS (Mac, Unix, Windows)
• a simplification of some structural equations of the model (see FATE tutorial - Modelling framework)
• 8 modules that can be turned on/off (see FATE tutorial - Modules)
• a shiny interface for those who prefer to visually explore the parameters (see SHINY interface page)
• a complete documentation and manual, with meaningful examples from real dataset (see Manual & Examples page)