#Stochastic Model

## Folders and Branches
This folder houses the stochastic model created for my masters project. The development of this model was heavily assisted
by Ella Thomson.

The explicit folder contains the functions used for the explicit tau leaping procedure.

The adaptive folder contains the functions used for the adaptive tau leaping procedure (which alternates between explicit and implicit tau leaping). This folder also contains the procedures used in the biological experiments and for matlab programming. 

The most up to date branch is ChangeConstants1

## Functions
The main program file is SSATestAdaptiveV2.m. 

genRj.m is the function containing a list of parameters and constants for the four mitochondrial reactions. All changes should be made to th constants list (since the parameters were optimized for the deterministic model). 

InitializeParametersMito.m allows the user to change the initial amounts of each species. This function also defines the initial time for the reaction (should be kept at 0) and the change of state vectors for each reaction, which are stored in a matrix. All of the following values are returned to the main program. 

#Stochastic Model

## Folders and Branches
This folder houses the stochastic model created for my masters project. The development of this model was heavily assisted
by Ella Thomson.

The explicit folder contains the functions used for the explicit tau leaping procedure.

The adaptive folder contains the functions used for the adaptive tau leaping procedure (which alternates between explicit and implicit tau leaping). This folder also contains the procedures used in the biological experiments and for matlab programming. 

The most up to date branch is ChangeConstants1

## Functions
The main program file is SSATestAdaptiveV2.m. 

genRj.m is the function containing a list of parameters and constants for the four mitochondrial reactions. All changes should be made to th constants list (since the parameters were optimized for the deterministic model). 

InitializeParametersMito.m allows the user to change the initial amounts of each species. This function also defines the initial time for the reaction (should be kept at 0) and the change of state vectors for each reaction, which are stored in a matrix. All of the following values are returned to the main program. 

evalCrit.m is used to define the percentage of the initial amount of a species required for that species to be deemed critical. The value should be in the range of 0.5-5%. 

Add information for evalCrit function description
Add information for evalCrit function description