Parameterize Scallop fleet

[andybeet]

Test case: Parameterize Scallop fleet using effort whilst another single fleet usesforced catch

Forced effort

time series file similar to the total_catch.ts file

1. How to integrate the two forcing file data? How does that work? Forced catch for some species, forced effort for others. Can you simply omit species from from the catch.ts file and add them to an effort ts file (as long as the meta data describes this)?

   • Yes, but better option is to zero out catch in forcing file for SCA and zero out all effort in effort file for all other fleets
   • Global effort.ts was not available as an option, only box specific effort ts files had been coded for. The branch AtlantisImposedEffort has been created off 6681 to allow for global effort

     The new parameter per fishery is XXXX_imposeeffort (Where XXXX is the fishery code)

     0 = No imposed effort 1 = Global effort (single time series file) 2 = Spatial effort (per box)

     You also need to add the parameter flagimpose_effort_hdistrib. This only has an effect if you pick impose global effort. 0 = CPUE based allocation (on day 1 only uses effort_hdistrib per fishery) 1 = Imposed effort uses effort_hdistrib per fishery to do the spatial allocation 2 = Imposed effort uses effort_hdistrib and the relative distribution of the biomass of the fishery’s target species

2. Box specific forcing of effort by fleet. Requires 30 ts files all formatted similarly. Also need to include metadata in the forcing.prm file

   • Scripts made to create and manipulate these files

3. Can you force catch, for Scallop, for part of the time, say first 20 yrs, then use effort after some time point? Would this just involve including Scallop in both files? If not then just have constant effort as part of the time series over initial period of the run.

   • Yes, i think so, Zero out effort in effort file for early years and zero out catch in latter years. Need to check this by looking at catch by fleet output. However to do this you'd need to double the number of fleets and define one to be effort based the other forced catch. Doubles effort. Better to just use constant effort over initial period, although no guarentee catch will be constant since it will depend on abundance and age structure +

4. Alternatively use contant effort through time with seasonal scalars (parameters in the harvest flle, no forcing). This is limiting and prevents lookng at scenarios with changes in effort through time based on things like management or climate

NOTE:: Current state - we can not currently run the model with a single global forcing file (segmentation error) until we update the version with the code updates The model currently can not handle a single forced effort file (like catch), it has to be box specific effort. As an alternative we are resorting to constant total effort

Harvest equation (in atlantis terms)

Harvest = Effort YYY_sweptarea f(selcurve_YYY,sel_XXX) management_scalar (vertical overlap positional availability) g(habitat overlap, q_XXX) * Biomass (1-p(escapement) )

where escapement = h(flagesacpement_XXX, p_escape_XXX ,ka_escape_XXX ,kb_escape_XXX) Effort is a forced time series we supply, either total effort or box level effort (effortmodel=11) or Effort is fixed (effortmodel = 9) where catch is proportional to population density (biomass)

Parameter changes

Effort

• [x] YYY_effortmodel. All values = 0.
  • Changed SCA fleet to 11, indicating forcing file.

Alternative: effortmodel =9. Fixed total effort

• [x] YYY_Effort - days day-1. (This is a scalar per fishery. Fixed total effort per year)
• [ ] Effort_vdistribYYY - A vector (length 4, number of layers) giving relative distribution of effort for fishery YYY across the vertical layers in each box. Currently all = [0 0 0 0] . (Function of YYY_Effort?)
  • Find out which layer is bottom and set to 1 for SCA. [1 0 0 0]?
  • [x] Effort_hdistribYYYd - A vector (length 30, number of boxes) setting relative effort per box by the fishery YYY for each quarter of the year (1 to 4). It is used in combination with YYY_Effort to get the actual final effort per box in days per day.
  • For effortmodel = 9, these only apply during the burn in period (specified in run.prm, tburnday parameter), after which effort based on biomass density.
  • Function of YYY_Effort. May need to specify boxes for SCA
• [ ] use MPAs to define fishery footprint (MPAYYY) and flagmpa=1, YYY_flagmpa

Catch

• [x] flagimposecatch_SCA Changed to 0
• [x] flagincidmort (value = 0, no bycatch) then specify target species in target_YYY
• [x] target_YYY A Boolean vector indicating which species are targeted by the fishery YYY. The vector should have as many entries as there are values in the functional_group.csv file. 1- species is targeted, 0 – species is not targeted
  • Vector of 0's for fleet target_SCA. With value = 1 for SCA (62nd position in vector represents SCA)
• [ ] flag_access_thru_wc_XXX (at_harvest.prm) Whether a fishery has access to fish in the entire water column (e.g. do trawl doors remain open as the gear moves up/down through the water column there by interacting with species who do not live at the depth the trawl is most actively being towed). Currenlty set to 1
• [x] XXX_flagdempelfishery (at_harvest.prm) Demersal fishery = 1, Pelagic fishery = 0. (Dynamic fishing). All Values = 0 (Even though some fleets are pelagic) Changed to 1
• [x] flaghabitat_XXX - Habitat scalar. Vector (length 28, number of fleets). All Values = 0. No additional scalar applied to q_XXX.
• [ ] habitat_XXX (at_biology.prm) Binary array indicating if fishing is excluded from certain habitats. Each species is described by a vector of 11 (types of habitat) values. Habitat typs: SCA, QHG, CLA, BFF, MA, SG, MB, reef, flat, soft, canyon. Does a value of zero indicate fishing is excluded? Current model has text indicating which habitats each group prefers. Value of 1 = group lives on habitat. Need to sort this out
• [ ] XXX_mindepth,XXX_maxdepth (at_biology.prm) Min and max depth fishery operates. All mindepth values = 0 Maxdepth values most are 5000 or 1900. Some 255,800,25,50,100,200
• [x] XXX_sweptarea (at_harvest.prm) (Proportion of?) total volume of cell the fishery can sweep. All Values = 0.
  • Changed to 0.1 (10%)

Selectivity & Catchability

• [x] q_XXX. Catchability of species XXX. Proportion of biomass (constant across all age groups). Since flaghabitat_XXX = 0 for all fleets this is a simple multiplier. Currenly all set to zero fro all fleets.
  • Changed SCA fleet (5th position) to value = 1
• [x] sel_XXX. Scallops have 1 size class. Currently Set to 1 (Proportion selected)
• [x] selcurve_YYY. Currenlty set to 0 (constant selectivity)

NOTE: from 15.4 It might be easier to track the fishing outcomes if catchability or escapement are modified one at a time. So, for example, the catchability can be set to 1, but escapement can be set to a different age or length specific proportion. Alternatively, the user might want no escapement and modify the available biomass through catchability only. Finally, the simplest option would include no escapement and 100% catchability; then the available biomass of the target and bycatch species of fishery YYY, in the swept volume of the cell, would only be limited by the fishery’s gear selectivity.

Escapement

Currently, provisions made for escapement but all fisheries set to No escapement

• [x] flagescapement_XXX (at_harvest.prm) No escapement (0) constant escapement (1, provide proportions in p_escape_XXX), size-based escapement (2, provide Ka_escape_XXX, Kb_escape_XXX) Values = 1
• [x] p_escape_XXX (at_harvest.prm) Vector of proportions. All Values = 0 (p_escape = ka.Length + kb)
• [x] Ka_escape_XXX,Kb_escape_XXX - All values = 0

Management scalars

• [x] YYY_flagmanage All Values = 0. No management scalars wiill be applied

With these settings the Harvest should collapse to something like:

Harvest = Effort 0.1 Biomass

Therefore included estimated Effort in forcing file Effort = 10*Harvest/Biomass

Calibration tips

1. Estimate effort from data and keep fixed in box.ts files
2. YYY_sweptarea to get in ball park
3. q_XXX and sel_XXX to fine tune (using selcurve_YYY = 2 (logistic))
4. Turn on fleet of interest, turn off others using YYY_tStart

[andybeet]

added most of this to atlantiscas vignette