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=================================   Weaver ReadMe   =================================
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Steps for running the simulations:

1. Modify "run_params" as desired, using your favourite text editor (care with the JSON syntax!).
2. Open a new Terminal window. If you are using Ubuntu just go to Applications->Accesories->Terminal.
3. Change to the directory where the program is placed, using "cd". For example: "cd ~/Weaver_0.9.1"
4. Finally, run the simulation typing "./weaver". It will generate all the output files in folders.


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#################################   Version 0.9.1   #################################
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The configuration file "run_params" is a JSON file which contains
all the information and parameters needed for running the simulations.

A new child has been added recently at the end of the file. It
contains the simulation name and all the output file names. As
an example:



"simulation": 
	(...)
	"outputs" : {
		"simulationName": "low_T",
		"summaryFilename": "dailySummary_w_preds.txt",
		"encountersMatrixFilename": "encountersMatrix.txt",
		"predationsMatrixFilename": "predationsMatrix.txt",
		"nodesMatrixFilename": "nodesMatrix.txt"
	}



The program will create a new folder named after the value of 
"simulationName" whenever a new simulation is run, and will place
all the files related to this new simulation inside the new folder.



#####################################################################################
#################################   Version 0.9.2   #################################
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- The variability of the restriction coeficient per trait has been added. 
- The correlation coeficient can be specified per modules now.
- Now each species contains its own chromosomes generator, therefore each species has
their own set of possible alleles.

The "genetics" child has been modified for each species and the "genetics" child below
the "simulation" child has been deleted. Now it should look like this:

{
"world": {
 	"soil": {
		(...)
  	},
  	"life": {
  		"fungi": [
  			(...)
  		],
  		"animals": [
	  		{	
			(...)
			"genetics" : {
				"randomnessMode": "0",
				"numberOfLoci": "20",
				"numberOfAlleles": "10",
				"numberOfTraits": "13",
				"numberOfTraitsPerModule": "3",
				"positiveModule": [0,0,1,0,1],
				"restrictPerTrait": [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1],
				"correlationCoeficientRHOPerModule": [0.1, 0.1, 0.1, 0.1, 0.1]
			},

These values are applied orderly. This way it is not as flexible as desired, but still usable.

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#################################   Version 0.9.2   #################################
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- Chemostat effect was added. This implementation increases the ammount of fungi depending on two parameters defined:

{
"world": {
 	"soil": {
		(...)
   		"increaseForChemostatEffect": "0.5",	#Percentage of the capacity of the cell, to be added.
   		"thresholdForChemostatEffect": "500.0"	#Chemostat effect triggers when the total biomass is below this threshold.


- Animals are now printed both at the beginning and ending of each day.


