Managing Redband Trout for Climate Resilience

A newer version of the software may be available. See https://code.usgs.gov/wma/vizlab/trout_and_climate/-/releases to view all releases.

This website uses visual storytelling to describe how climate vulnerability for Redband Trout depends on their climate-adaptation.

This repo uses R and Vue.js to build a data visualization website about indicators of vulnerability to water insecurity. In R, there are scripts showing how to fetch, process, and visualize data. The rest of the files build the website.

To access the data from ScienceBase in R

Activate ScienceBase credentials. Note, you only have to do this once to get the data from each release for the first time.

1. Install the latest version of the sbtools package. (Requires sbtools v1.3.0 or newer)
2. Run the code below
3. When prompted, enter your email address as the username
4. Log into https://sciencebase.usgs.gov/manager/ and select "Copy API Token" from the User dropdown menu
5. Copy the Token into the pop up dialog. If this worked, you should get a "TRUE" result in the console.

sbtools::initialize_sciencebase_session()

Fetch data from ScienceBase. The full code to download data for this site is listed in R_src/01_fetch_data.qmd. For example, to fetch data from this data release, use the following code:

Benjamin, J.R., Dunham, J.B., and Penn, C.A., 2023, Simulated growth potential of redband trout in the Donner und Blitzen River Basin, southeastern Oregon, using a bioenergetics model: U.S. Geological Survey data release, https://doi.org/10.5066/P9MAXBZN.

sbtools::item_file_download(sb_id = "65381be6d34ee4b6e05bba62", 
    dest_dir = "R_src/in/sciencebase/", 
    overwrite_file = FALSE)

Other data releases included to produce the figures are:

Sando, R.R., and Schultz, A.R., 2022, Reach-scale predicted annual streamflow permanence probabilities, predicted monthly mean stream temperature for August, and predicted monthly streamflow discharge for stream reaches in the Pacific Northwest, USA (2004-2015) (ver. 2.0, January 2023): U.S. Geological Survey data release, https://doi.org/10.5066/P94SMJKI.

Miller, M.P., Carlisle, D.M., Wolock, D.M., and Wieczorek, M.E., 2018, Natural Monthly Flow Estimates for the Conterminous United States, 1950-2015: U.S. Geological Survey data release, https://doi.org/10.5066/F7CC0ZMG.

Laramie, M.B., Mejia, F.H., Heaston, E.D., and Dunham J.B., 2020, Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022): U.S. Geological Survey data release, https://doi.org/10.5066/P9QZGDMB.

Penn, C.A., Dunham, J.B., Markstrom, S.L., Overstreet, B.T., and Stratton, L.E., 2023, Simulated streamflow and stream temperature in the Donner und Blitzen River Basin, southeastern Oregon, using the Precipitation-Runoff Modeling System (PRMS): U.S. Geological Survey data release, https://doi.org/10.5066/P9WQM25Y.

To recreate the figures

The code to process the data and create the data visualizations are included as R-Markdown scripts in the R_src/ directory. Corresponding data should be stored in the R_src/in/sciencebase/ directory. (Exact pathways to each file are listed in the R-markdown scripts.)

Building the website locally

Clone the repo. In the directory, run npm install to install the required modules. Once the dependencies have been installed, run npm run dev to run locally from your browser.

To build the website locally you'll need npm v20 and node v8.1 or higher installed. To manage multiple versions of npm, you may try using nvm.

Citation

Archer, Althea, Ivey, Leo, Corson-Dosch, Hayley, and Nell, Cee. 2024. Managing redband trout for climate resilience. U.S. Geological Survey software release. Reston, VA. https://doi.org/10.5066/P13UMTRM.