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# Welcome to the RuleStudio Editor 
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# This code simulates a Cellular Automaton for diverse purposes.




########## Rules

'inject' -> Rz(Type~Tg,State~F)		@ 0.0
# The inject rule is for use in a perturbation, it will be triggered to add transgenic rhizobia

'Rz_TgDiv' Rz(Type~Tg,State~F) -> Rz(Type~Tg,State~F), Rz(Type~Tg,State~F)		@ 0.3
'Rz_WtDiv' Rz(Type~Wt,State~F) -> Rz(Type~Wt,State~F), Rz(Type~Wt,State~F)		@ 0.2
'Rz_F_Dth' Rz(Type,State~F) ->													@ 0.1
'Rz_S_Dth' Rz(Type,State~S?) ->													@ 0.05
# These rules are for cellular division and cellular death, for WildType and TransGenic strains

'Rz_Sym_1' Rz(Type,State~F), Plnt(S1~F,S2,S3) -> Rz(Type,State~S!1), Plnt(S1~S!1,S2,S3)			@ 0.1
'Rz_Sym_2' Rz(Type,State~F), Plnt(S1,S2~F,S3) -> Rz(Type,State~S!1), Plnt(S1,S2~S!1,S3)			@ 0.1
'Rz_Sym_3' Rz(Type,State~F), Plnt(S1,S2,S3~F) -> Rz(Type,State~S!1), Plnt(S1,S2,S3~S!1)			@ 0.1
# These rules represent the symbiosis process

'Wt_N_Fix' Rz(Type~Wt,State~S?), Carbon() -> Rz(Type~Wt,State~S?), Nitrogen()						@ 0.1
'TG_N_Fix' Rz(Type~Tg,State~S?), Carbon() -> Rz(Type~Tg,State~S?)									@ 0.1
# These rules represent the economy of the niche, supply of C sources in exchange for nitrous compounds
# A more thorough version would have different "weights" to the carbon intake of the rhizobia, however this would require more computing power due to the finer rates

'Plnt_C_P' Plnt(S1,S2,S3) -> Plnt(S1,S2,S3), Carbon()							@ 0.1
# This is the fixation of carbon by plants through photosynthesis

'Plnt_Rep' Plnt(S1~S,S2~S,S3~S), Carbon(), Nitrogen() -> Plnt(S1~F,S2~F,S3~F), Plnt(S1~F,S2~F,S3~F)				@ 0.1
# This rule represents plant reproduction through the use of C and N related compounds

########## Initialize
%init: 300 * Rz(Type~Wt,State~F)
%init: 30 * Plnt(S1~F,S2~F,S3~F)
# We initialize the system with 300 rhizobia and 30 plants


########## Observables
%obs: 'Rz_Wt_F' Rz(Type~Wt,State~F)
%obs: 'Rz_Tg_F' Rz(Type~Tg,State~F)
#%obs: 'Rz_Wt_S' Rz(Type~Wt,State~S?)
%obs: 'N_Wt' Nitrogen()
%obs: 'Plant' Plnt(S1?,S2?,S3?)
#%obs: 'Rz_Tg_S' Rz(Type~Tg,State~S?)



########## Perturbations
%mod: ['Rz_Wt_F'] > 500 do 'Rz_WtDiv' := 0.1
%mod: ['Rz_Tg_F'] > 500 do 'Rz_TgDiv' := 0.1
# These rules are to prevent the system from entering infinite growth, the maximum population under which exponential growth occurs is 500 elements.

#%mod: $T > 10 do 'inject' := 0
%mod: $T > 10 do 'inject' := 500
%mod: ['Rz_Tg_F'] > 300 do 'inject' := 0
# At time 10, we introduce around 300 transgenic rhizobia, or not. This depends on which scenario we are running: pure vs. transgenic