Science Score: 44.0%

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

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
  • DOI references
    Found 14 DOI reference(s) in README
  • Academic publication links
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (7.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: HARTLabGroup
  • License: mit
  • Language: TeX
  • Default Branch: base
  • Size: 112 MB
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  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 5
Created almost 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Code for: Climate-driven decreases in aspen's distribution and opportunities for future expansion across the Southern Rocky Mountains

Description of the project

This repository contains all code for Climate-driven decreases in aspen's distribution and opportunities for future expansion across the Southern Rocky Mountains.

Organization of the project

The project has the following structure:

  • Code: All code written for this project

    • AspenHabitat-MainText.Rmd: An R markdown file with most of the R code. This file also generates a Microsoft Word document with the main text of the manuscript.
    • AspenHabitat-MainText.docx: A Microsoft Word document with the main text of the manuscript.
    • AspenHabitat-Supplement.Rmd: An R markdown with code for some supplemental analyses.
    • AspenHabitat-Supplement.docx: A Microsoft Word document with supplemental figures and tables.
    • GIDS-Downscaling-SJH.R: An R file that performs a multi-step procedure that spatially downscales gridded climate data using GIDS (Gradient and Inverse Distance-Squared) of Nalder and Wein (1998) and Flint and Flint (2012). It was lightly modified from code written by Rodman et al. (2020).
    • Template.docx: A Microsoft Word document used to a style template for generating AspenHabitatModelling.docx
    • references.bib: A BibTeX file containing all information for all references used in the project
  • Documents: All code written for this project

    • ODMAP-Table.xlsx: Documentation of the species distribution modeling methods used herein following standard protocols outlined by Zurell et al. 2020.
    • PredictorScreeningTable.xlsx{.uri}: A table containing predictors screened for inclusion in the models.
  • .gitignore

  • AspenHabitat.Rproj

  • CITATION.cff

  • License.md

  • README.md

  • citationstyle.csl : A Citation Style Language file used to format references in the main text of AspenHabitatModelling.docx

Description of Analyses and Data

Code

Nearly all analyses are can be run from the script AspenHabitat-MainText.Rmd, which references the GIDS-Downscaling-SJH.R script. Supplemental analyses are included in the script AspenHabitat-Supplement.Rmd. All scripts use relative paths with the .rproj file and the here package in R to reference each of the datasets and use them in analyses. To repeat our analyses, this project must be open in R Studio software prior to opening the .rmd document and the here (Müller 2020) and bookdown (Xie 2016, 2025) packages must be installed.

Input data

All input data is publicly available. The main script is structured to download all data from the internet, however we acknowledge that broken URLs are a common issue. Additional users should take note that the code is structured to download data only once. Thus care should be taken when users are interested in replacing input datasets with updated versions. The best approach is to delete the entire directory where the data is stored.

Output data

Maps of the predictions of current and future aspen habitat suitability generated by running the AspenHabitat-MainText.Rmd script are also forthcoming on Dryad.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Citation

Please cite this work following the Citation.cff file

References

Flint, L. E., and A. L. Flint. 2012. Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis. Ecological Processes 1:2.

Müller, K. 2020. here: A Simpler Way to Find Your Files. R package version 1.0.1, https://doi.org/10.32614/CRAN.package.here{.uri}.

Nalder, I. A., and R. W. Wein. 1998. Spatial interpolation of climatic Normals: test of a new method in the Canadian boreal forest. Agricultural and Forest Meteorology 92:211–225.

Rodman, K., T. Veblen, M. Battaglia, M. Chambers, P. Fornwalt, Z. Holden, T. Kolb, J. Ouzts, and M. Rother. 2020, August 18. Data from: A changing climate is snuffing out post-fire recovery in montane forests. Dryad. https://doi.org/10.5061/DRYAD.QZ612JMB7

Xie, Y. 2016. bookdown: Authoring Books and Technical Documents with R Markdown. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 978-1138700109, https://bookdown.org/yihui/bookdown{.uri}.

Xie, Y. 2025. bookdown: Authoring Books and Technical Documents with R Markdown. R package version 0.43, https://github.com/rstudio/bookdown{.uri}.

Zurell, D., Franklin, J., König, C., Bouchet, P.J., Dormann, C.F., Elith, J., Fandos, G., Feng, X., Guillera-Arroita, G., Guisan, A., Lahoz-Monfort, J.J., Leitão, P.J., Park, D.S., Peterson, A.T., Rapacciuolo, G., Schmatz, D.R., Schröder, B., Serra-Diaz, J.M., Thuiller, W., Yates, K.L., Zimmermann, N.E., Merow, C., 2020. A standard protocol for reporting species distribution models. Ecography 43, 1261–1277. https://doi.org/10.1111/ecog.04960

Owner

  • Name: HARTLabGroup
  • Login: HARTLabGroup
  • Kind: organization

Citation (citationstyle.csl)

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    <author>
      <name>Bernhard Hoiß</name>
      <email>bernhard.hoiss@uni-wuerzburg.de</email>
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    <updated>2016-09-10T14:32:31+00:00</updated>
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