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@@ -4,20 +4,6 @@ IBASAM (Individual Based Atlantic SAlmon Model) is a simulation model, developed
 
 # MODEL DESCRIPTION
 
-IBASAM was developed to cover the entire life cycle of S. salar. Thereby processes can be split into specific phases of the life cycle depending on the yearly events and the phases at which they happen. We structured the model in 8 submodels corresponding to life cycle events and processes:
-1. [Reproduction and redd creation](reproduction.md)
-2. Emergence from the redds and individual birth
-3. Genetic coding and transmission
-4. Growth
-5. Survival
-6. Smoltification
-7. Maturation
-8. Migrations
-
-Growth and survival can be split into specific phases depending on the yearly events of the life cycle in the two time steps (summer and winter). The computational order of life cycle events and processes, together with their length (in days) when relevant, are presented in Table 1.
-
-![cycle](cycle.png)
-
 In the river phase, individuals grew in weight according to individual and stage-dependent growth capacity and influenced by water temperature, population density and river flow. Growth increments in weight were then allocated to fat reserves (Fat) or somatic growth through an increase in body length depending on a variable individual propensity to accumulate fat. Survival in the river was phase dependent, with higher mortality for maturing individuals and during winter. The triggering of sea migration was size dependent 6 months before the run. The smoltification process allows an individual that was in the river (‘parr’) to become physiologically ready to run into the sea (as ‘smolt’). The probability of smolting for an individual followed a reaction norm based on its body length.
 
 Once at sea, individuals grew in weight following a Gompertz function depending on specific individual characteristics and overall oceanic conditions. In this function, a NoiseSeat factor represented a daily environmental condition for growth. In the absence of EC, NoiseSeat was simply a normal random number centred on MeanNoiseSea = 1 and of variance 0 1. With EC, MeanNoiseSea decreased through time and NoiseSeat was a normal random number with variance 0 1 but centred on the MeanNoiseSea of the year. Each replicate of simulations had consequently different environmental conditions. Fat and body length accumulation were allocated as in the river phase. Survival at sea was size dependent with a clear disadvantage for small individuals.
@@ -30,10 +16,22 @@ Fishery mortality on returning individuals was simulated by the removal of a pro
 
 The reproduction events were simulated according to relevant S. salar literature (Fleming 1996). The mating system allowed mature male parr to fertilize a fraction of the eggs. It selected anadromous males following size dominance while allowing satellite males to fertilize a significant fraction of the eggs. The number of egg per female was size dependent. Egg-to-emergence survival was water temperature, river flow and density dependent.
 
-# BIOLOGICAL PROCESSES
-IBASAM is made of 8 submodels representing fundamental biological processes :
+## Biological processes
+IBASAM was developed to cover the entire life cycle of S. salar. Thereby processes can be split into specific phases of the life cycle depending on the yearly events and the phases at which they happen. We structured the model in 8 submodels (SM) corresponding to life cycle events and processes:
+1. [Reproduction and redd creation](reproduction.md)
+2. [Emergence from the redds and individual birth](Emergence.md)
+3. [Genetic coding and transmission](Genetic.md)
+4. [Growth](Growth.md)
+5. [Survival](Survival.md)
+6. [Smoltification](Smoltification.md)
+7. [Maturation](Maturation.md)
+8. [Migrations](Migrations.md)
 
+Growth and survival can be split into specific phases depending on the yearly events of the life cycle in the two time steps (summer and winter). The computational order of life cycle events and processes, together with their length (in days) when relevant, are presented in Table 1.
 
-It also includes 2 environmental submodels :  
+![cycle](cycle.png)
+
+# Environmental submodels  
 10. River climate (Water temperature and flow)  
 11. Ocean climate
+