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esdm

A user-friendly spatial tool with a web-based interface that allows users to import SDM layers and create and explore ensemble predictions to inform management and explore spatial uncertainties

https://github.com/swfsc/esdm

Science Score: 36.0%

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

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
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    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (17.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A user-friendly spatial tool with a web-based interface that allows users to import SDM layers and create and explore ensemble predictions to inform management and explore spatial uncertainties

Basic Info
Statistics
  • Stars: 11
  • Watchers: 1
  • Forks: 4
  • Open Issues: 4
  • Releases: 9
Created almost 9 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

eSDM

CRAN version R-CMD-check <!-- badges: end -->

eSDM is an R package designed to allow users to create ensembles of predictions from species distribution models (SDMs) made at different spatial scales or with different prediction units. Included in the package is the eSDM GUI, an R Shiny tool that provides the user with a graphical user interface that they can use to import, overlay, and create ensembles of SDM predictions.

Installation

You can install the released version of eSDM from CRAN with:

r install.packages('eSDM')

To install the latest version from GitHub:

``` r

install.packages('devtools')

devtools::installgithub('SWFSC/eSDM', buildvignettes = TRUE) ```

eSDM GUI

You can access the GUI online at https://connect.fisheries.noaa.gov/eSDM. You do not need to have R or RStudio installed to access the GUI online.

To run the GUI locally: install eSDM as described above, and then run the following code in your RStudio console:

r eSDM::eSDM_GUI()

Depending on your internet connection, running the GUI locally may be faster than running it online. If text or images overlap within the GUI, please make the browser window full screen or adjust the text size in your browser (e.g., Ctrl - minus (‘-’) on Windows systems)

Vignettes

``` r

To see the list of available vignettes

browseVignettes("eSDM")

To open a specific vignette

vignette("example-analysis") ```

Manuscript reference

The paper can be obtained here, and is cited as (preferred):

Woodman, S.M., Forney, K.A., Becker, E.A., DeAngelis, M.L., Hazen, E.L., Palacios, D.M., Redfern, J.V. (2019). eSDM: A tool for creating and exploring ensembles of predictions from species distribution and abundance models. Methods Ecol Evol. 2019;10:1923-1933. doi:10.1111/2041-210X.13283

For data used in the example analysis, see https://github.com/SWFSC/eSDM-Data

For code used to create applicable figures from the manuscript: Figure 2, Figure 3, Figure 4, Figure 5

Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

NOAA Fisheries Logo

U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries

Owner

  • Name: Southwest Fisheries Science Center
  • Login: SWFSC
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 907
  • Total Committers: 2
  • Avg Commits per committer: 453.5
  • Development Distribution Score (DDS): 0.223
Past Year
  • Commits: 22
  • Committers: 1
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
smwoodman s****n@n****v 705
Sam Woodman s****3@g****m 202
Committer Domains (Top 20 + Academic)
noaa.gov: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • edzer (1)
  • smwoodman (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 318 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: eSDM

Ensemble Tool for Predictions from Species Distribution Models

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 318 Last month
Rankings
Forks count: 14.9%
Stargazers count: 21.1%
Average: 27.5%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Downloads: 36.6%
Maintainers (1)
sam.woodman@noaa.gov
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • ROCR * imports
  • dplyr >= 0.7 imports
  • magrittr * imports
  • methods * imports
  • purrr * imports
  • rlang * imports
  • sf >= 0.9 imports
  • shiny * imports
  • stats * imports
  • units * imports
  • DT * suggests
  • RColorBrewer * suggests
  • colorRamps * suggests
  • colourpicker * suggests
  • dichromat * suggests
  • knitr * suggests
  • leafem * suggests
  • leaflet * suggests
  • maps * suggests
  • maptools * suggests
  • raster * suggests
  • rmarkdown * suggests
  • shinybusy * suggests
  • shinydashboard * suggests
  • shinyjs * suggests
  • testthat >= 2.1.0 suggests
  • tmap >= 2.3 suggests
  • viridis * suggests
  • zip * suggests