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PhytoFit

Shiny app for viewing satellite chla and modelling phytoplankton blooms

https://github.com/BIO-RSG/PhytoFit

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Shiny app for viewing satellite chla and modelling phytoplankton blooms

Basic Info
  • Host: GitHub
  • Owner: BIO-RSG
  • License: mit
  • Language: HTML
  • Default Branch: master
  • Homepage:
  • Size: 213 MB
Statistics
  • Stars: 7
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 1
Created almost 6 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

PhytoFit

DOI

This app can be used to display satellite chlorophyll concentration, and calculate statistics and model phytoplankton blooms for regions within custom polygons. See below for example in screen capture.

screencap

Public host: https://cioosatlantic.ca/phytofit/

How to cite

In publications, please include acknowledgements to NASA OBPG for the satellite data and the BIO remote sensing group for the application, and use this citation in the references:

Stephanie Clay, Chantelle Layton, & Emmanuel Devred. (2021). BIO-RSG/PhytoFit: First release (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.4770754

BibTeX format: 

@misc{clay21,
  author       = {Clay, Stephanie and Layton, Chantelle and Devred, Emmanuel},
  title        = "PhytoFit",
  howpublished = "\url{https://github.com/BIO-RSG/PhytoFit}",
  year         = 2021
}

Prerequisites

  1. Install the latest versions of R and RStudio.

  2. Install the necessary packages: r install.packages(c("fst", "shiny", "shinyWidgets", "shinyjs", "shinybusy", "leaflet", "leafpm", "quantreg", "minpack.lm", "sp", "ggplot2", "ggpp", "dplyr", "tidyr", "terra", "stringr", "RCurl", "sf", "fs"))

  3. Restart R after the packages have been installed.

Getting started

  1. Download this repository one of two ways:

  • Option 1: Code --> Download ZIP

  • Option 2: Using git (this will make it easier to download updates in the future, by simply using the git pull command): Open git bash terminal, navigate to the folder where you want to download the repository, and type: git clone https://github.com/BIO-RSG/PhytoFit.git

  1. Open the PhytoFit repository in RStudio:
  • File --> Open Project --> Navigate to the PhytoFit folder and open "PhytoFit.Rproj"
  1. Download the datasets of your choice:
  • Open 00_download_new_datasets.R from the PhytoFit folder. Set ask_user=FALSE to download all available datasets, or ask_user=TRUE to ask before downloading each one. Alternatively, you can run the script from the command line like: Rscript [script directory]/00_download_new_datasets.R 'false', filling in the [script directory] with the location where you stored the script. 'false' is the ask_user argument, set to 'true' for prompts.
  1. To update existing datasets:
  • Similar to the download script in step 3, open 00_update_datasets.R and set the ask_user argument, or run from the command line (e.g. Rscript [script directory]/00_update_datasets.R 'false'. This will update the datasets you have already downloaded with the most recent copies (and download any years of data missing from your local directory).

WARNINGS:
- Data files will be downloaded to data/[region]/ subfolders of the PhytoFit repository - Do NOT move them from there or the app will not be able to read them.
- If possible, please keep the data files if you intend to use them in the future, rather than re-downloading them later, to avoid excessive traffic on the ftp server.
- Any data that is < 3 months old is "Near Real Time" (NRT) quality. NRT data is replaced with "Science quality" data after it becomes available, following the 3-month lag. More info here.

Running

Open app.R within RStudio, and click "Run app"

Authors

  • Chantelle Layton - Initial concept, preliminary design, coding, and algorithm development/improvements
  • Stephanie Clay - Final app design and modifications, feature addition, new datasets, maintenance, and algorithm improvements
  • Emmanuel Devred - Scientific support, algorithm development/improvements, review and feature recommendations

Acknowledgments

  • Andrea Hilborn for many valuable suggestions

Links

User guide (In progress)
Chl-a model performance evaluation
References and data sources
Using the raw (binned) data (This is a quick tutorial explaining how the raw satellite chlorophyll data used in PhytoFit can be read into R and manipulated for other purposes)
Code updates affecting the algorithms (Summary of updates that affected the way the bloom metrics are calculated)

Owner

  • Name: SOPhyE (Satellite Ocean Colour and Phytoplankton Ecology Group)
  • Login: BIO-RSG
  • Kind: organization
  • Location: Canada

Remote Sensing Group at the Bedford Institute of Oceanography for DFO Canada

GitHub Events

Total
  • Watch event: 1
  • Push event: 14
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Watch event: 1
  • Push event: 14
  • Pull request event: 1
  • Fork event: 1

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 393
  • Total Committers: 8
  • Avg Commits per committer: 49.125
  • Development Distribution Score (DDS): 0.344
Past Year
  • Commits: 48
  • Committers: 3
  • Avg Commits per committer: 16.0
  • Development Distribution Score (DDS): 0.188
Top Committers
Name Email Commits
Clay S****y@d****a 258
claysa c****h@h****m 99
Default Seadas User s****r@l****t 12
Jeff Cullis j****s@d****a 9
David Fishman d****h@g****m 8
Scott Bruce s****e@m****a 3
Andrea Hilborn a****n@g****m 2
Clay C****A@E****a 2
Committer Domains (Top 20 + Academic)
ent.dfo-mpo.ca: 1 mi.mun.ca: 1 dal.ca: 1 dfo-mpo.gc.ca: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 6
  • Average time to close issues: 14 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 1
  • Total pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jeffcullis (1)
Pull Request Authors
  • sjbruce (4)
  • schckngs (2)
  • claysa (1)
  • jeffcullis (1)
  • davjfish (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 2
proxy.golang.org: github.com/bio-rsg/phytofit
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
proxy.golang.org: github.com/BIO-RSG/PhytoFit
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago

Dependencies

Dockerfile docker
  • rocker/shiny latest build
docker-compose.yml docker
  • cioosatlantic/phytofit latest