FishSET is a set of statistical programming and data management tools developed to improve fishery modeling. The tools standardize data management and organization, enable the use of location choice models to provide input into fishery management, and provide various other modeling and visualization tools.
The FishSET toolbox is provided as a set of R functions that can be run in an R console or here in this FishSET Graphical User Interface (FishSET GUI).
In addition to this Quickstart Guide, check out the FishSET video tutorial that walks through the GUI.
The FishSET GUI is a user-friendly interface that guides users through the steps necessary to run discrete choice models. The FishSET GUI requires no knowledge of coding or the R programming language as all steps to prepare and run discrete choice models can be run in a graphical user interface.
The FishSET GUI is divided into tabs to guide users through functions from uploading and exploring data to running models and simulating policy scenarios. All data are automatically saved to a local SQLite database on the users computer (data not shared with other users or FishSET developers) called the FishSET database when first loaded. The database is housed in the project’s directory withing the FishSET R package directory (FishSETFolder). Modified versions of the data can be saved to the FishSET database in the Data Quality Evaluation and Compute New Variables tabs. Plots and table outputs are saved in an output folder within the project’s directory. Function calls, including input parameters, are saved to the Logs folder within the project’s directory. The Quickstart Guide subtab provides further assistance on using the FishSET GUI.
This document includes basic instructions on how to use the FishSET GUI. Refer to the FishSET User Manual for information on installing R software and to the main page of this website for FishSET installation instructions.
For questions and comments please contact: [email protected]
This document walks through the steps of:
library(FishSET)
run_fishset_gui()
The Upload Data tab is used to load data (primary, port,
spatial, gridded, and auxiliary) from local files on your computer or
from the FishSET database. Follow the instructions provided in the left
side panel of the GUI.
See Chapter 4 of the FishSET User Manual for more information on the different types of data.
If including confidentiality checks: - Click the
Confidentiality button (appears after loading data). -
Check the Check for confidentiality box. -
Select vessel identifier variable from the dropdown menu. -
Select a Rule (n: rule of n or k:
majority allocation). - Select a Threshold value such as 3
for rule of n or 90% for majority allocation. - Click Save
and repeat if more confidentiality rules are needed. - Click the
Close button when finished.
The Data Quality and Evaluation tab is used to identify
and correct common data quality issues such as erroneous outliers,
missing values (NA or NaN), and coordinates that occur on land. Use the
radio buttons in the left side panel to navigate between data quality
and control functions. After running each function, click on the ‘Save
data to FishSET database’ button to save changes.
See the recommended data quality checks in Chapter 4 of the FishSET User Manual.
The Data Exploration tab is used to view, filter, and
explore the data tables. Use the input options in the left side panel to
select tables and plots to view.
The table view can be used to directly filter/edit datasets, and any
changes made to the tables will be logged for reproducibility. Click on
the Save data to FishSET database to save any changes.
Also, plots generated in the GUI will be automatically saved in the project’s output folder in the FishSETFolder directory.
For more details see Chapter 6 of the FishSET User Manual.
The Simple Analyses tab is used to run correlation
analysis and simple linear regressions between variables in the primary
table. Tables and plots generated here will be automatically save to the
project’s output folder in the FishSETFolder directory.
For more details see Chapter 6 of the FishSET User Manual.
The Map Viewer tab is used to view the spatial
distribution of hauls. Use the input options in the left side panel to
plot hauls as points or paths using start and end locations.
Required: 1. Spatial data file. 2. Zone identifier variable in primary dataset.
For more details see Chapter 6 of the FishSET User Manual.
The Compute New Variables tab is used to transform or
derive new variables. There are a variety of predefined functions to
chose from in the dropdown menus in the side panel. Importantly, this is
where users can create centroid tables (in the “Spatial functions”
options), which can be used to represent alternative locations in
discrete choice models. After creating a new variable, click
Save data to FishSET database to save new variables.
The Fleet Assignment and Summary tab is used to define
fleets and explore data at a fleet level. There are two subtabs, fleet
assignment and fleet summary.
Define fleets and apply fleet definitions to the primary dataset.
Follow the instructions in the left side panel of the GUI. Use the
Save table to FishSET database at the bottom of the side
panel to save fleet definitions prior to fleet assignments. Then select
Fleet assignment from the Select task dropdown
menu, load the fleet definition table at the bottom of the left side
panel and assign fleets.
The Fleet Summary subtab is used to generate tables and
plots that summarize data by fleets.
For more details see Chapter 6 of the FishSET User Manual.
The Define Alternative Fishing Choices tab is used to
define how the distance matrix between observed fishing locations and
alternative fishing locations should be calculated.
Prior to selecting input options, click on
Save final table to FishSET database and follow
instructions. This step is to ensure that alternative choices and
following steps for setting up the discrete choice model can be
completed successfully.
Then, select options from the drop down menus. In the
Include zones with more observations than input box, insert
the minimum number of observations needed for a zone to be included in
the model. Click Save choices in the left side panel to
save alternative choice table.
See Chapter 8 of the FishSET User Manual for more information on defining alternative choices and model development.
The Expected Catch/Revenue tab is used to calculate the
expected catch or revenue matrix for alternative fishing zones (zones
where fishing could have happened but did not). A catch variable is
required, and include a price or value variable if you want expected
revenue. Select input options in the left side panel. In addition, users
can select from a number of default matrices in the main panel
(checkboxes for these options are at the bottom of the page).
See Chapter 8 of the FishSET User Manual for more information about how expected catch/revenue is calculated and model development.
The Models tab is used to design/run discrete choice
models, compare outputs between models, and quantify model robustness.
FishSET includes default likelihood functions to chose from. Conditional
logit models require an expected catch matrix. EPMs require price
data.
See Chapter 8 of the FishSET User Manual for more information on model development.
The Zone closure tab is used to design spatial closures,
and required for the Run Policy tab. Simply select which
zones to close and provide a name for the scenario.
The Run Policy tab is used to simulate redistributed
fishing effort and calculate welfare changes following implementation of
the policy scenarios. Select input options from the left side panel -
including the number of simulations (“Betadraws”) to run.
For more information on simulating policy scenarios see Chapter 9 of the FishSET User Manual.
The Bookmark Choices tabs is used to store choices and
actions made in the FishSET GUI and enable choices and actions to be
reloaded at a later date.
NOTE: This tab is still underdevelopment (7/17/2024)
FishSET includes a report template that guides users through the process of writing a reproducible report and inserting output from the FishSET GUI into the report.
This report cannot be written in the FishSET GUI. It must be opened and edited in RStudio. Locate the template in the FishSETFolder > [project folder] > doc subdirectory. Instructions for filling in the report are included in the template file.