FishSET GUI Quickstart Guide
2024-08-07
Source:vignettes/FishSET_GUI_Quickstart_Guide.Rmd
FishSET_GUI_Quickstart_Guide.Rmd
Introduction
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.
FishSET 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: nmfs.fishset@noaa.gov
This document walks through the steps of:
- Opening the FishSET GUI
- Using the FishSET GUI
- Using the Report template to generate a report.
Opening the FishSET GUI
- To open the FishSET GUI run the following lines of code in RStudio:
-
run_fishset_gui()
Using the FishSET GUI
Upload Data
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.
Data Quality Evaluation
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.
Explore the Data
Data Exploration
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.
Simple Analyses
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.
Map Viewer
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.
Compute New Variables
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.
Fleet Assignment and Summary
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.
Fleet assignment
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.
Fleet Summary
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.
Define Alternative Fishing Choices
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.
Expected Catch/Revenue
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.
Models
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.
Policy
Zone Closure
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.
Run Policy
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.
Generating reports
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.