In leca-dev/RFate: FATE with R

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 1.3.5 (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)

leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.