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Default_Quest.Evolvix.txt

You can copy and paste this code into Evolvix 0.3.0 and it should run. This toy model demonstrates some of what Evolvix can do today.

!L This is a one-line comment that ends automatically with the line.
!L Use the following nestable comment symbols for commenting out code
!-- !-- comment in comment --! --!
!L See the Evolvix Manual that comes with every installation for more details.



Evolvix Quest DoubleOscillation_Dynamics (

Question :
"""What do the dynamics of two independent oscillators look like?"""

""" Detailed comments on the one-line summary given above:

Combine the following two models and observe joint timeseries and phase diagrams,
Purely for demonstrating what you can already get out of an Evolvix model now.

Model1:
Predator-prey dynamics ("Lynx, Hares") based on parameters estimated from
real Hare-Lynx time series. For details, see the tutorial by Jacob Goldfinger,
2013-08, in the Evolvix manual.

Model2:
Some oscillating populations ("Foxes, Rabbits") showing stronger stochasticity.
Based on eq 3.18 and fig 4.17, p76, p141 in Otto&Day (2007) "A biologists guide
to mathematical modeling in ecology and evolution", Princeton Univ. Press.

The rest of this InfoBlock does not contain serious content.
It merely demonstrates how more details could be organized
without offending the parser.
Use reStructuredText inside of such InfoBlocks, see here for a QuickReference:
http://docutils.sourceforge.net/docs/user/rst/quickref.html
Why? We plan to provide automatic documentation generation capabilities
for such InfoBlocks, to help you ensure those after you can still understand
what you were modeling.

Use "triple-double quotes" to make it easier to use normal 'quotes' "" in
the Details section of InfoBlocks. This Detail's section is about to end here.
The following meta-information helps chronicle aspects of revision history.
"""

Modified by Laurence_Loewe on 2014-11-03 version v0r2c3 !L added more Units
Modified by Laurence_Loewe on 2014-10-03 version v0r2c2
Reviewed by Laurence_Loewe on 2014-07-17 version v0r2c1
Modified by Laurence_Loewe on 2014-07-17 version v0r2c1
Created by Jacob_Goldfinger on 2013-08-01 version v0r2c0

)


!L Simulate stochastically until 100 :["years"]
Simulate deterministically until 100 :["years"]


!L The units below can document a type of source of data. Put in "quotes" to
!L denote arbitrary units; missing quotes will represent SI Units in future versions.

Initial Amount of Lynx = 8500 :["Lynx in NationalPark observed by Method 1"]
Initial Amount of Hares = 26800 :["Hares in NationalPark observed by Method 2"]

Initial Amount of Foxes = 40 :["Foxes in Neighborhood recorded by Cam 3"]
Initial Amount of Rabbits = 150 :["Rabbits in Neighborhood recorded by Cam 4"]



!L Simple high level TimeSeries at default precision:


TimeSeries RelativeChangePrecisionOnly (
Report Separately the Amount of Part Foxes, Rabbits
From 0 :["years"]
Until 100 :["years"]
Report whenever values change by 0.5 [% Relative Difference ]
)

!--
TimeSeries (
Report Separately the Flux of Part Lynx, Hares , Foxes, Rabbits
)
TimeSeries (
Report Simultaneously the Flux of Part Lynx, Hares , Foxes, Rabbits
)
TimeSeries (
Report Simultaneously the Amount of Part
Lynx,Hares, Foxes,Lynx, Lynx,Rabbits, Foxes,Rabbits
)


!L Highly customized special TimeSeries (code examples):


TimeSeries (
Report Separately the Amount of Part Lynx, Hares , Foxes, Rabbits
Report whenever values change by 0.1 0.2 [ RelAbsMix Difference ]
)


TimeSeries FullyCustomized_But_Silly (
Report Separately the Amount of Part Lynx, Hares
From 0 :["years"]
Until 100 :["years"]
Ignore values below 200 :["Individuals"]
Ignore values above 1000 :["Individuals"]
Report whenever values change by 100 [ Absolute Difference]
Report times when crossing values 20, 90, 50
Report values when crossing times 5,22,25,27,30
)

TimeSeries RegularIntervalls (
Report Separately the Amount of Part Lynx, Hares
Report whenever times change by 1 :[ "years" ] !L this is by interval
Report values when crossing times 10, 90
)


--!


!L Model 1 ************************************************************


Action 1 Hares_Breeding (

Hares -----[ Rate = 1.5 :["1/year "] ]-----> 2 Hares
)

Action 2 Lynx_Breeding (

Hares + Lynx -----[ Rate = 0.000045 :["1/year "] ]-----> 2 Lynx
)

Action 3 Lynx_Dying (

Lynx -----[ Rate = 0.225 :["1/year "] ]-----> !L could say "0 Lynx"
)

Action 4 Lynx_Playing_With_Food (

Hares + Lynx -----[ Rate = 0.000225 :["1/year "] ]-----> Lynx
)


!L Model 2 ************************************************************


Action 5 Rabbits_Breeding (

Rabbits ----[ Rate = 0.5 :["1/year "] ]----> 2 Rabbits
)

Action 6 Foxes_Breeding (

Foxes + Rabbits ----[ Rate = 0.0002 :["1/year "] ]----> 2 Foxes
)

Action 7 Foxes_Dying (

Foxes ----[ Rate = 0.1 :["1/year "] ]----> 0 Foxes
)

Action 8 Foxes_Playing_With_Food (

Rabbits + Foxes ----[ Rate = 0.0098 :["1/year "] ]----> Foxes
)