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afs_database_code's Introduction

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AFS Standard Fish Data App

The primary purpose of this application is to display data collected across North America on fish species, using a standardized collection approach and resulting comparable metrics by AFS. Additionally, users can upload their own data to compare to the provided standardized data.

Link to the deployed app: https://viz.datascience.arizona.edu/afs-standard-fish-data/

Repository file organization

Dashboard

  • app/app.R: file that generates dashboard showing standardized fish data and allows user to upload data to compare
  • app/standardized_fish_data.csv: standardized fish data file
  • app/R/functions.R: functions to calculate three metrics of interest
  • app/www/AFS_sponsor_3.png: image file with sponsor logo displayed on dashboard "About" page
  • app/example_user_upload_data.csv: simulated example data to show how user uploaded datasets should be formatted

Data prep

  • app/process_user_data.Rmd: generates example user upload data (user_example.csv) shown in app; shows development of metric calculations
  • app/user_example.csv: example user upload data
  • app/download_map_data.R: code to download the EPA Ecoregions data used in app map
  • analysis_scripts: folder with scripts to prepare standardized data; newer version of this is in app/R/functions.R
  • input_examples: folder containing additional user upload example datasets

Package versions & dependences

  • renv folder
  • renv.lock
  • .Rprofile

Repository metadata

  • .gitignore
  • AFS_database_code.Rproj
  • LICENSE
  • README.md
  • CITATION.cff

How to cite

Please use the citation below if you use or modify this tool for research purposes.

Tracy, E., Guo, J., Riemer, K., & Bonar, S. (2023). Code for "AFS Standard Fish Data App" (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.8169922

How to contribute

If you would like to suggest or make changes to this app, there are a few ways to do so. You can reach out via email to Scott Bonar or the CCT Data Science team with suggestions.You can also create an issue describing a problem with the code or improvements under the "Issues" tab.

If you can make changes to the code yourself, feel free to fork this repo and make a pull request. To run the code locally, follow the instructions in run_locally.md. It will be necessary to download the ecoregions map data by running app/download_map_data.R. Additionally, running the app locally requires the standardized fish records location data file app/sites.csv, which is not available in the repo due to sensitive information. Package versions and dependencies are tracked with renv.

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erinetracy avatar jessicaguo avatar kristinariemer avatar

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afs_database_code's Issues

Make more plot improvements

  • Display calculated UU numbers (e.g., on blue bars)
  • Put horizontal dashed line at 50 and 100 on relative weight plot
  • Relative weight, make sure all categories show up even with no data
  • Change “proportional size distribution to add “categories”
  • Change second plot caption to relative weight by psdc
  • Y-axis relative weight label should be (Wr)
  • For figure captions, move them back to below the plots and remove “graph”
  • CPUE graph change “and individual points” to “and any individual points”
  • Check color blindness for plots
  • Clarify N meanings and move to legend
  • Make all "N" instances italic
  • Change CPUE legend

Add plot improvements

For relative weight plot:

  • Change to points only
  • Replace percentiles with SE error bars

Others:

  • Change Gabelhouse x-axis label to "Proportional size distribution"
  • Remove unnecessary legend from frequency plot
  • Add captions to all plots
  • Comparison frequency plot add UU box
  • Display calculated UU numbers (e.g., on blue bars)

Remove usage of `sp` package

Getting this note related to the ongoing deprecation of some spatial R packages:

The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)

Update About page

  • Add picture(s) of fish
  • Add link to Scott's website / book chapter? / project?
  • Add definition of "N"
  • Add translation instructions
  • Add link to GH repo

Update upload instructions tab

From Erin 6/4/2024:

  • The column headers should be changed to method and effort from method name and effort type just to not cause confusion since those are the column headers we want in the example data csv.
  • Gill_net_fall is listed twice and 1 of those should be gill_net_spring
  • In the description for this can you include that gill_net_spring should be gill netting done Jan - Jun (1-6) and gill net fall should be July - Dec (7-12).
  • Tow_barge_electrofishing should be area m2 like backpack electrofishing and snorkeling

Update README

Bottom of README still references this being a fork of an upstream repo. That needs updating.

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