aspenhabitat
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 14 DOI reference(s) in README -
○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.1%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: HARTLabGroup
- License: mit
- Language: TeX
- Default Branch: base
- Size: 112 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 5
Metadata Files
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
- Repositories: 1
- Profile: https://github.com/HARTLabGroup
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GitHub Events
Total
- Release event: 9
- Delete event: 1
- Public event: 1
- Push event: 24
- Create event: 9
Last Year
- Release event: 9
- Delete event: 1
- Public event: 1
- Push event: 24
- Create event: 9