EwECaps

A repository that takes Ecopath with Ecosim with Ecospace output and calculates the ecosystem caps for the system under various types of calculations. The current example is from the Gulf of America Ecospace model.

The repository has two R files: functions.R and caps_from_ewe.R. To run, open the R project ("Ecosystem Caps") and the caps_from_ewe.R file. This file will automatically source the functions.R file. There are 4 dependencies: dplyr, tidyr, ggplot2, stringr. The code is designed to be run straight through. The user must manually input several items to properly run the file (shown below). It is recommended that the user make the adjustments and the run the full file so the final table is appropriately output without duplicate information.

Manual Intervention Items

1. L6: A group info table that has the following structure, where Residency determines if the animal is resident or not, SEDAR determines if the animal is a SEDAR assessed species, and Landings_Prop is the proportion of catches that are landings, since Ecospace_Annual_Average_Catch.csv is both landings and dead discards. This can be adjusted in anyway you need to slice your groups. You would just need to give an appropriate dataframe to the "keep_df" parameter in the "ecosystem_caps_avg...()" function. An example of adding a subset df to those functions can be seen in lines 93 & 99 of the main R file.

Group_Name	Residency	SEDAR	Landings_Prop
Blacktip shark	Resident	SEDAR	0.609
Dusky shark	Resident	SEDAR	0.979
Sandbar shark	Resident	NO	0.561
Large coastal sharks	Resident	SEDAR	0.490
Large oceanic sharks	Transient	NO	1.000

2. L17-21: Incoporate your model's specific characteristics (start_year, model domain area in km, Ecospace scenario name).
3. L30: Adjust the group names to aggregate the relevant multi-stanza groups in your model. We want to aggregate multi-stanza groups to create a single cap per species.
4. L73 & 173: After plotting (L68 & 170), the user should check the plots and identify those that could not be fit properly (i.e., linear ASPt - Bt relationship, negative [u-shaped] parabolic function, negative predicted BMSY).

Example Plots This production function fit well

This production function did not fit well and the MSY was derived from both an average ASP and landings

Final Result Table Click to view Clean CSV Version

Type	Scenario	BMSY	MSY	MSY_BMSY	Prop_MSY	Prop_BMSY
All Species	Landings and Discards - Avg. ASP	66232880	696232.2	0.0105119	0.9655596	0.0450564
All Species	Landings and Discards - Avg. Harvest	66181366	697028.8	0.0105321	0.9644561	0.0450914
Harvested Species	Landings and Discards - Avg. ASP	6946543	649263.6	0.0934657	0.9934190	0.3439321
Harvested Species	Landings and Discards - Avg. Catch	6987793	669765.9	0.0958480	0.9630093	0.3419018
SEDAR Species	Landings and Discards - Avg. ASP	1484211	505194.4	0.3403790	0.9982705	0.9965861
SEDAR Species	Landings and Discards - Avg. Catch	1484234	505180.6	0.3403645	0.9982978	0.9965707
Resident Species	Landings and Discards - Avg. ASP	66101601	674752.2	0.0102078	0.9641046	0.0432751
Resident Species	Landings and Discards - Avg. Catch	66041400	675306.9	0.0102255	0.9633128	0.0433146
All Species	Landings Only - Avg. ASP	66186604	678096.9	0.0102452	0.9664056	0.0443847
All Species	Landings Only - Avg. Harvest	66134854	678894.6	0.0102653	0.9652701	0.0444194
Harvested Species	Landings Only - Avg. ASP	6900267	631128.3	0.0914643	0.9951284	0.3394939
Harvested Species	Landings Only - Avg. Catch	6941281	651631.7	0.0938777	0.9638170	0.3374879
SEDAR Species	Landings Only - Avg. ASP	1480389	498508.7	0.3367417	0.9983906	0.9963989
SEDAR Species	Landings Only - Avg. Catch	1480176	498496.0	0.3367815	0.9984161	0.9965423
Resident Species	Landings Only - Avg. ASP	66055263	656870.1	0.0099443	0.9649516	0.0426000
Resident Species	Landings Only - Avg. Catch	65994826	657425.8	0.0099618	0.9641359	0.0426390