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TODO
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TODO
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2-19-20
Implement a method of finding richness.
- Use carrying capacity as a variable
Method of outputing effective burst size
Convert everything to snake-case
2-24-20
Carrying capacity on the order of 10E7
- will impact bactouch, phage numbers, burst count
- Double check changeability of burst size
- Email CS for the paper
Burst size tied to carrying capacity
- Reduce VMR
- three burst sizes, coral 50 algae middle barrier 10
- local
Compile list of things accomplished
- Send on Thursday
- How to run script finalized
Separate the Usage from the Internals in the readme
- Folder containing a default values run including output graphs
- Seeds how to input and storage thereof
Send Dr. Luque the classes I had to take as well as short descriptions of methodology
Run 27220202
- no fish interaction with microbe layer
- Burst count as step function
Coral = 50 ; Algae = 30 ; Barrier = 10
Run 2722020
- fish interaction
- Burst count as step function
Coral = 50 ; Algae = 30 ; Barrier = 10
Run 27220201
- fish interaction reduced to growth only
- Burst count as step function
Coral = 100 ; Algae = 60 ; Barrier = 10
Run 27220202
- fish interaction, second term reduced to 0.25
- Burst count as step function
Coral = 100 ; Algae = 60 ; Barrier = 10
- lysogen carrying capacity error fixed
Run 2822020 - Best
- richness ceiling increased to 100 from 10
- Burst Count 100 - 60 - 10
Run 2922020
- Burst 100 - 50 - 5
- Bact-Coral interaction reduced 15 -> 12
Run 2922020 1
- richness changed to 1/(1 - k_mod/k_max) - 1
- results in too high of a richness
Run 2922020 2
- richness changed to (k_mod/k_max)^2
- results in compressed values
Run 2922020 3
- Burst 100 30 5
- R_lys = 2.5
- richness k_mod/k_max
Run 2922020 4
- same as 3 R_lys = 2.0
Run 2922020 5
- fish modifier reduced
- poor results
Run 2922020 6
- fish modifier increased
- continuous burst function
Run 2922020 9
- Continuous burst function
- reduced fish impact
Run 2922020 10
- Step burst function modified by fish impact
Run 2922020 11
- Step burst function modified by inverse fish impact
- bactouch cap increased to 1E8
- inverse trends
Final run
- coral bact interaction reduced from 0.15 to 0.11
TODO
- Auto graph most common outputs
MEETING
3-3-2020
Notes:
- cc changing order of magnitude 7 - 6 based on region
- find steady state parameters. equilibration points and values for each.
- system stability at 60%, 40% naturally
- fish, microbe evolution w/out coral interaction, use outputs
- follow up with CS
- barrier cannot reasonably be highest value
- initial bact. pop change from 0.001 to 0.5
- paper with decay rate change suggests a change of 10^2 in phage decay rate. may also affect burst size
- run simulation with lower bacteria
TODO
PRIORITY - system stability at 60% coral with all interactions running
richness criteria from N* where N* is determined at .5 carrying capacity cc/bac = some max N 0.5N = N*
steady N* or adjustable N* based on ss values of bacteria
add output bucket for matching to github ( default values etc.) with outputs. "Quality Control Test"
New Paper:
- Burst size counts from 5 - 100
- viral decay rate can change from 20 - 0.1 1/Lhr
3-6-2020
- Starting runs with a lower initial fish population
- error in microbial carrying capacities fixed
- what drives down richness in microbes?
- fish growth weighted higher in impact parameter
- phage pop zero? - current build gives number of spec(b*) = k_mod
3-23-2020
- Drive down bacteria and phage pop, VMR is in 100's
- implement abs value for non-handled inputs.