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Atlnts 155 retune planktivores #70

Merged
merged 27 commits into from
Oct 20, 2020
Merged

Atlnts 155 retune planktivores #70

merged 27 commits into from
Oct 20, 2020

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jcaracappa1
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New Functions/Scripts

  1. get_param_kdenr.R : Retrieves all fixed recruitment (KDENR_XXX) parameters from at_biology.prm
  2. plot_realized_foodweb.R : Function to create visualization of realized foodweb from dietcheck.txt
  3. plot_species_biomass.R : Short function to get a detailed/age-structured view for a single species biomass

Altered Functions/Scripts

  1. make_atlantis_diagnostic_figures.R:
    Changed paramater file name reference to be based on param.ls object
    Add plot_consumption to function
  2. plot_detailed_diet.R:
    Added total biomass to view
    Changes to figure formatting
  3. plot_overall_predation.R: Add total consumption and domain-wide biomass to panel view
  4. plot_run_comparisons.r : Option to remove "Rel*" groups
  5. test post-processing.R: Add plot.consumption flag

Parameter Changes

  1. pPREY of all groups on all filter feeders, planktivores, and higher predators on bacteria reduced or eliminated
  2. pPREY for all planktivores altered to prefer zooplankton over detritus and bacteria
  3. Assimilation Efficiency on live prey (E_XXX) of HER,MAK,MEN,ANC, and GOO reduced
  4. Recruitment rates on ISQ, LSQ, and NSH reduced
  5. Recruitment for all higher predatory fish tuned to reduce all groups biomass to within 5x initial conditions for the first 15 years. Groups that had StockSmart recruitment timeseries available were tuned from median recruitment over all available data.

@jcaracappa1
First Attempt at Fixing
e815848 
E_MEN -> 0.35
E_MEN -> 0.35
E_HER -> 0.3
EDL_MEN -> 0.1

Remove BB consumption by benthic filter feeders
Remove ANC consumption on meiobenthos
@jcaracappa1
PlantivFix 2 at_biology update
c126769 
- Reduced early herring mum and C
- Increased mum_ZL to 0.2
- Reduced MEN and ANC predation on BB to 0
- Slightly decreased peak biomass for MEN,MAK,ANC,HER
- Increased biomass for ZM and ZS
@jcaracappa1
Removed bacterial/detritus consumption from planktivores
357b3aa 
- HER,MEN,ANC,benthic filter feeders, red crab, ZL,ZM,ZS pPREY of DL/DR set to 0.001
- ZL cannibalism ZL:ZL set to 0.01
@jcaracappa1
Planktiv Fix 4
d350c56 
- Decreased ZL:ZL predation to 0.001 - solved cannibilsm early on
- Dropped MEN DL predation to 0 eliminates bacterial consumption
-Does not resolve crashing of MEN,MAK, and HER but diets okay
@jcaracappa1
Change how parameters are read into plotting function
c0fd515
@jcaracappa1
Reworked Functions to Better Calculate Consumption
f148e1a
@jcaracappa1
Updated for new param.ls usage
c6b9f1f
@jcaracappa1
Merge pull request #67 from NOAA-EDAB/master
aa8f2dc 
Add Migration into RetunePlanktivores
@jcaracappa1
Detailed plot for single species biomass by age class
c14f6d4
@jcaracappa1
Sort prey groups alphabetically
a1bc94f
@jcaracappa1
separate consumption plots
8f12ad0 
-gets arround issue with max num of ggplot colors for diet plots...
@jcaracappa1
RetunePlanktiv6
07a146a 
- Decrease RCB consumption of shellfish and self
- Decrease shellfish consumption of detritus
- Decrease BO cannibalism
- Decrease ANC and HER BB consumption
- Decrease predation on HER by WPF and FLA
@jcaracappa1
RetunePlanktiv7
5c00bca 
- Remove shellfish, zooplankton, and crab consumption of HER
@jcaracappa1
Function to plot food web from dietcheck.txt
20bea08
@jcaracappa1
More color options
f794baf
@jcaracappa1
Spreadsheet to help keep track of groups
1fa19f8
@jcaracappa1
Updated for RemovePred3
1c684b1 
- Reset KDENR (fixed recruits) to long-term avg from StockSmart dataset
- Reduced additional groups' KDNER if biomass still too high
@jcaracappa1
Pulls fixed recruitment from at_biology.prm
f5071ba
@jcaracappa1
Updated Recruitment fro RemovePred3
20fcfd1 
- Set to longterm avg from assessment recruits dataset
- Increased HER and TYL
- Decreased other groups that were too high
@jcaracappa1
Updated for ReducePred4
53460a1 
- Attempt to fix crashing fish groups
@jcaracappa1
ReducePred5
2444b68 
Focus on getting first 15 yrs within 5x init
Reduce mum/C for RCB
Increase mum for ZM,ZS,ZL
@jcaracappa1
RemovePred6
526a855 
- Last try to reduce beginning groups
- Any groups that don't change in first 15 yrs, deem not a recruitment issue
- Increase Zoo and RCB growth
@jcaracappa1
Edit example
9da2777
@jcaracappa1
update example
d90e693
@jcaracappa1
Flag to remove "REL*" groups
55982ce
@jcaracappa1
Final update to RemovePred
0812167 
- Return all groups who weren't able to be reduced to within 5x init biomass in first 15 years with original recruitment value from RM
- Reset zooplankton mum values to values chosen by RM (need to be tuned along with planktivores)
@jcaracappa1
Final Tuning for Predator Reduction
a1a7afb
@jcaracappa1
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@andybeet @gambler1650 Not everything is perfect, but most of the ~45 middle predator fish groups are within 5x init biomass for the first 15 years. This should be enough to go back to getting HER,MAK,MEN,and ANC stable

@RGamble1
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Looks good to me...

@RGamble1 RGamble1 merged commit fb327d6 into master Oct 20, 2020
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2 participants
@jcaracappa1 @RGamble1