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multispp_loops

Data and loop tutorial for multi-species multi-site figure production. This can then be repurposed for many types of tasks.

https://github.com/prairie-rex/multispp_loops

Science Score: 31.0%

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Data and loop tutorial for multi-species multi-site figure production. This can then be repurposed for many types of tasks.

Basic Info
  • Host: GitHub
  • Owner: prairie-rex
  • License: cc0-1.0
  • Language: R
  • Default Branch: main
  • Size: 14.5 MB
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  • Watchers: 1
  • Forks: 0
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Created about 4 years ago · Last pushed about 4 years ago
Metadata Files
Readme License Citation

README.md

multispp_loops

Data and loop tutorial for multi-species multi-site figure production. This can then be repurposed for many types of tasks.

This data comes from GBIF.org (27 May 2022) GBIF Occurrence Download https://doi.org/10.15468/dl.vf6fgm. We collected all lupines (Lupinus spp.) in the United States, with coordinate uncertainty less than ~5000 meters. If you utilize this data elsewhere, please use the above citation, see GBIF citation guidelines.

If you are looking for how to make the same figures or run the same analysis on things multiple times, then this code will help you get started!

You won't need to look at the data cleaning file at all, just get started on the markdown!

If you've never heard of loops before, read through the quick loop information section in the markdown.

Owner

  • Name: Kelsey King
  • Login: prairie-rex
  • Kind: user
  • Location: Washington, USA

Citation (citations.txt) 

When using this dataset please use the following citation and pay attention to the rights documented in rights.txt:
Western Carolina University Herbarium (2022). Western Carolina University Herbarium. Occurrence dataset https://doi.org/10.15468/sk26v2 accessed via GBIF.org on 2022-05-27.
Old Dominion University Herbarium (2022). Old Dominion University Herbarium. Occurrence dataset https://doi.org/10.15468/88bd2d accessed via GBIF.org on 2022-05-27.
Bowser M (2022). Kenai National Wildlife Refuge, Alaska (KNWR) Plant specimens (Arctos). Version 1.33. Kenai National Wildlife Refuge. Occurrence dataset https://doi.org/10.15468/ycpd7y accessed via GBIF.org on 2022-05-27.
University of Graz, Institute of Plant Sciences. University of Graz, Institute of Plant Sciences - Herbarium GZU. Occurrence dataset https://doi.org/10.15468/axtkuz accessed via GBIF.org on 2022-05-27.
Bowser M (2022). Kenai National Wildlife Refuge, Alaska (KNWR) Plant observations (Arctos). Version 1.31. Kenai National Wildlife Refuge. Occurrence dataset https://doi.org/10.15468/1gdw2n accessed via GBIF.org on 2022-05-27.
The Royal Botanic Gardens & Domain Trust (2022). National Herbarium of New South Wales (NSW) AVH data. Occurrence dataset https://doi.org/10.15468/jf3yae accessed via GBIF.org on 2022-05-27.
Roberts D (2022). CHAS Botany Collection (Arctos). Version 13.62. Chicago Academy of Sciences. Occurrence dataset https://doi.org/10.15468/ji4vbl accessed via GBIF.org on 2022-05-27.
Tasmanian Museum and Art Gallery (2022). Tasmanian Herbarium (HO) AVH data. Occurrence dataset https://doi.org/10.15468/8wmoeb accessed via GBIF.org on 2022-05-27.
Masaryk University, Department of Botany and Zoology. Masaryk University - Herbarium BRNU. Occurrence dataset https://doi.org/10.15468/soarvd accessed via GBIF.org on 2022-05-27.
Campbell University (2022). Campbell University Herbarium. Occurrence dataset https://doi.org/10.15468/vx3csq accessed via GBIF.org on 2022-05-27.
Rutger's University - Chrysler Herbarium (2022). Rutgers University, Chrysler Herbarium. Occurrence dataset https://doi.org/10.15468/1n787c accessed via GBIF.org on 2022-05-27.
University of Alberta Museums, La France D, Becker-Burns A (2022). University of Alberta Vascular Plant Herbarium (ALTA-VP). Version 10.66. University of Alberta Museums. Occurrence dataset https://doi.org/10.18165/qssyvr accessed via GBIF.org on 2022-05-27.
Staten Island Museum (2022). Staten Island Museum. Occurrence dataset https://doi.org/10.15468/ctqpb5 accessed via GBIF.org on 2022-05-27.
de Vries H, Lemmens M (2022). Observation.org, Nature data from around the World. Observation.org. Occurrence dataset https://doi.org/10.15468/5nilie accessed via GBIF.org on 2022-05-27.
University of South Carolina (2022). University of South Carolina, A. C. Moore Herbarium. Occurrence dataset https://doi.org/10.15468/fmj4at accessed via GBIF.org on 2022-05-27.
Weber State University (2022). Weber State University Herbarium. Occurrence dataset https://doi.org/10.15468/zmt7jk accessed via GBIF.org on 2022-05-27.
Gall L (2022). Botany Division, Yale Peabody Museum. Yale University Peabody Museum. Occurrence dataset https://doi.org/10.15468/hrztgn accessed via GBIF.org on 2022-05-27.
Theodore  M. Sperry Herbarium (2022). Pittsburg State University, Theodore M. Sperry Herbarium. Occurrence dataset https://doi.org/10.15468/adstge accessed via GBIF.org on 2022-05-27.
National Ecological Observatory Network (2022). NEON Biorepository Terrestrial Plant Collection (Herbarium Vouchers). Occurrence dataset https://doi.org/10.15468/bmmg36 accessed via GBIF.org on 2022-05-27.
Natural History Museum (2022). Natural History Museum (London) Collection Specimens. Occurrence dataset https://doi.org/10.5519/0002965 accessed via GBIF.org on 2022-05-27.
Hayden H, Legler B (2022). Vascular Plant Collection, Starkey Experimental Forest Herbarium. Consortium of Pacific Northwest Herbaria. Occurrence dataset https://doi.org/10.15468/v5m8jm accessed via GBIF.org on 2022-05-27.
The University of Vermont Pringle Herbarium (2021). University of Vermont, Pringle Herbarium. Occurrence dataset https://doi.org/10.15468/zsgiog accessed via GBIF.org on 2022-05-27.
University of Washington Burke Museum. Vascular Plant Collection - University of Washington Herbarium (WTU). Occurrence dataset https://doi.org/10.15468/plngb6 accessed via GBIF.org on 2022-05-27.
Jestrow B, Bornhorst K (2022). Fairchild Tropical Botanic Garden (FTG). Fairchild Tropical Botanic Garden. Occurrence dataset https://doi.org/10.15468/hdpruf accessed via GBIF.org on 2022-05-27.
Jennings L (2021). University of British Columbia Herbarium (UBC) - Vascular Plant Collection. Version 16.7. University of British Columbia. Occurrence dataset https://doi.org/10.5886/rtt57cc9 accessed via GBIF.org on 2022-05-27.
Hardy C (2021). MVSC; The James C. Parks Herbarium at Millersville University. Millersville University James C. Parks Herbarium. Occurrence dataset https://doi.org/10.15468/qdatdf accessed via GBIF.org on 2022-05-27.
Mississippi Museum of Natural Science (2022). Mississippi Museum of Natural Science Herbarium. Occurrence dataset https://doi.org/10.15468/ausqtm accessed via GBIF.org on 2022-05-27.
Sagehen Creek Field Station (2022). SCFS - Sagehen Herbarium. Occurrence dataset https://doi.org/10.15468/fl8uov accessed via GBIF.org on 2022-05-27.
naturgucker.de. naturgucker. Occurrence dataset https://doi.org/10.15468/uc1apo accessed via GBIF.org on 2022-05-27.
Centre for Australian National Biodiversity Research (2022). Centre for Australian National Biodiversity Research (CANB) AVH data. Occurrence dataset https://doi.org/10.15468/xycuk7 accessed via GBIF.org on 2022-05-27.
University of North Carolina at Chapel Hill Herbarium (NCU) (2022). University of North Carolina at Chapel Hill Herbarium: Vascular Plants. Occurrence dataset https://doi.org/10.15468/63vxjd accessed via GBIF.org on 2022-05-27.
Dinosaur National Monument (2022). Dinosaur National Monument Herbarium. Occurrence dataset https://doi.org/10.15468/qz8uyh accessed via GBIF.org on 2022-05-27.
AFFOUARD A, JOLY A, LOMBARDO J, CHAMP J, GOEAU H, BONNET P (2020). Pl@ntNet observations. Version 1.2. Pl@ntNet. Occurrence dataset https://doi.org/10.15468/gtebaa accessed via GBIF.org on 2022-05-27.
E.L. Reed Herbarium at Texas Tech University (TTC) (2022). Texas Tech University, E. L. Reed Herbarium. Occurrence dataset https://doi.org/10.15468/uyakmh accessed via GBIF.org on 2022-05-27.
UM Herbarium Data Group, IPT Admin L (2022). University of Michigan Herbarium. Version 1.41. University of Michigan Herbarium. Occurrence dataset https://doi.org/10.15468/nl8bvi accessed via GBIF.org on 2022-05-27.
Mendocino College Coast Center Herbarium (2022). MCCC - Mendocino College Coast Center Herbarium. Occurrence dataset https://doi.org/10.15468/96qq94 accessed via GBIF.org on 2022-05-27.
University of Minnesota Bell Museum (2022). Bell Museum plants. Occurrence dataset https://doi.org/10.15468/bihrxd accessed via GBIF.org on 2022-05-27.
Black Hills State University Herbarium (2022). Black Hills State University Herbarium. Occurrence dataset https://doi.org/10.15468/ptcrqx accessed via GBIF.org on 2022-05-27.
Magnaghi E, Fong J (2022). CAS Botany (BOT). Version 157.387. California Academy of Sciences. Occurrence dataset https://doi.org/10.15468/7gudyo accessed via GBIF.org on 2022-05-27.
Colorado Mesa University (MESA) (2022). Colorado Mesa University, Walter A. Kelley Herbarium. Occurrence dataset https://doi.org/10.15468/wmbcqk accessed via GBIF.org on 2022-05-27.
Morton J M, Berg E, Bowser M, Eskelin T, Laker M, Magness D (2022). Occurrences from Kenai National Wildlife Refuge’s Long Term Ecological Monitoring Program, 1999–2006. Version 1.5. United States Geological Survey. Occurrence dataset https://doi.org/10.15468/73n3w7 accessed via GBIF.org on 2022-05-27.
California State University San Bernardino Herbarium (2022). CSUSB - California State University San Bernardino. Occurrence dataset https://doi.org/10.15468/t885ps accessed via GBIF.org on 2022-05-27.
Kathryn Kalmbach Herbarium (Denver Botanic Gardens) (2022). Kathryn Kalmbach Herbarium. Occurrence dataset https://doi.org/10.15468/axrelr accessed via GBIF.org on 2022-05-27.
Desert Botanical Garden Herbarium (2022). Desert Botanical Garden Herbarium. Occurrence dataset https://doi.org/10.15468/abe1lg accessed via GBIF.org on 2022-05-27.
California State University, Fresno Herbarium (2022). FSC - Fresno State Herbarium. Occurrence dataset https://doi.org/10.15468/puyrj8 accessed via GBIF.org on 2022-05-27.
Utah State University (2022). Intermountain Herbarium (Vascular plants & algae). Occurrence dataset https://doi.org/10.15468/t43wjj accessed via GBIF.org on 2022-05-27.
Capers R (2014). CONN. University of Connecticut. Occurrence dataset https://doi.org/10.15468/w35jmd accessed via GBIF.org on 2022-05-27.
Biological Collections, California State University Northridge (2022). SFV - California State University, Northridge. Occurrence dataset https://doi.org/10.15468/nrcdx7 accessed via GBIF.org on 2022-05-27.
California State University, Long Beach (2022). LOB - California State University, Long Beach Herbarium. Occurrence dataset https://doi.org/10.15468/3y25yl accessed via GBIF.org on 2022-05-27.
Kenneth S. Norris Center for Natural History (2022). UCSC Herbarium - Kenneth S. Norris Center for Natural History, University of California Santa Cruz. Occurrence dataset https://doi.org/10.15468/uavt0t accessed via GBIF.org on 2022-05-27.
Rocky Mountain Biological Laboratory (2022). Rocky Mountain Biological Laboratory. Occurrence dataset https://doi.org/10.15468/j9jnvg accessed via GBIF.org on 2022-05-27.
Carnegie Museums (2022). Carnegie Museum of Natural History Herbarium. Occurrence dataset https://doi.org/10.15468/d51v1f accessed via GBIF.org on 2022-05-27.
University of California, Irvine (2022). IRVC - University of California, Irvine Herbarium. Occurrence dataset https://doi.org/10.15468/svdy2z accessed via GBIF.org on 2022-05-27.
Ramirez J, Watson K, McMillin L, Gjieli E (2022). The New York Botanical Garden Herbarium (NY). Version 1.47. The New York Botanical Garden. Occurrence dataset https://doi.org/10.15468/6e8nje accessed via GBIF.org on 2022-05-27.
Bentley A, Morse C (2022). R. L. McGregor Herbarium Vascular Plants Collection. University of Kansas Biodiversity Institute. Occurrence dataset https://doi.org/10.15468/htptzr accessed via GBIF.org on 2022-05-27.
San Diego State University Herbarium (SDSU) (2022). SDSU - San Diego State University Herbarium. Occurrence dataset https://doi.org/10.15468/8sx2ag accessed via GBIF.org on 2022-05-27.
San Jose State University (2022). SJSU - Carl W. Sharsmith Herbarium, San Jose State University. Occurrence dataset https://doi.org/10.15468/t3a60p accessed via GBIF.org on 2022-05-27.
Mayfield-Meyer T, Zhuang V (2022). UTEP Plants (Arctos). Version 5.64. University of Texas at El Paso Biodiversity Collections. Occurrence dataset https://doi.org/10.15468/yhb6ky accessed via GBIF.org on 2022-05-27.
University of New Mexico Herbarium (UNM) (2022). University of New Mexico Herbarium. Occurrence dataset https://doi.org/10.15468/dlvoyt accessed via GBIF.org on 2022-05-27.
CSU Los Angeles Herbarium (2022). CSLA - Cal State LA Herbarium. Occurrence dataset https://doi.org/10.15468/36qz6p accessed via GBIF.org on 2022-05-27.
UCLA Herbarium (2022). LA - University of California, Los Angeles Herbarium. Occurrence dataset https://doi.org/10.15468/33k42a accessed via GBIF.org on 2022-05-27.
California Department of Food and Agriculture (CDA) (2022). CDA - California Department of Food and Agriculture. Occurrence dataset https://doi.org/10.15468/phc373 accessed via GBIF.org on 2022-05-27.
Arizona State University Biocollections (2022). Arizona State University Vascular Plant Herbarium. Occurrence dataset https://doi.org/10.15468/a2o8vy accessed via GBIF.org on 2022-05-27.
Northern Arizona University (2022). Deaver Herbarium (Northern Arizona University). Occurrence dataset https://doi.org/10.15468/b7tfpa accessed via GBIF.org on 2022-05-27.
Ickert-Bond S (2022). UAM Herbarium (ALA), Vascular Plant Collection (Arctos). Version 38.63. University of Alaska Museum of the North. Occurrence dataset https://doi.org/10.15468/iawody accessed via GBIF.org on 2022-05-27.
AFFOUARD A, JOLY A, LOMBARDO J, CHAMP J, GOEAU H, BONNET P (2020). Pl@ntNet automatically identified occurrences. Version 1.2. Pl@ntNet. Occurrence dataset https://doi.org/10.15468/mma2ec accessed via GBIF.org on 2022-05-27.
University of Colorado Museum of Natural History (2022). University of Colorado Museum of Natural History Herbarium Vascular Plant Collection. Occurrence dataset https://doi.org/10.15468/wyofjv accessed via GBIF.org on 2022-05-27.
Cheadle Center for Biodiversity and Ecological Restoration (2022). UCSB - University of California Santa Barbara Herbarium. Occurrence dataset https://doi.org/10.15468/qpxmw0 accessed via GBIF.org on 2022-05-27.
San Diego Natural History Museum (2022). SD - SD Herbarium, San Diego Natural History Museum. Occurrence dataset https://doi.org/10.15468/lneqwn accessed via GBIF.org on 2022-05-27.
Humboldt State University (2022). HSC - Humboldt State University Vascular Plant Herbarium. Occurrence dataset https://doi.org/10.15468/qguk7r accessed via GBIF.org on 2022-05-27.
Chico State Herbarium (2022). CHSC - CSU Chico, Chico State Herbarium - Vascular Plants. Occurrence dataset https://doi.org/10.15468/ckxw7v accessed via GBIF.org on 2022-05-27.
University of California, Davis (2022). DAV - UC Davis Herbarium. Occurrence dataset https://doi.org/10.15468/on4axg accessed via GBIF.org on 2022-05-27.
California Polytechnic State University, San Luis Obispo (2022). OBI - Robert F. Hoover Herbarium, Cal Poly State University. Occurrence dataset https://doi.org/10.15468/mypdjd accessed via GBIF.org on 2022-05-27.
Oregon State University. Vascular Plant Collection. Occurrence dataset https://doi.org/10.15468/2bmt3a accessed via GBIF.org on 2022-05-27.
Santa Barbara Botanic Garden (2022). SBBG - Clifton Smith Herbarium, Santa Barbara Botanic Garden. Occurrence dataset https://doi.org/10.15468/adb2bb accessed via GBIF.org on 2022-05-27.
Rancho Santa Ana Botanic Garden (2022). RSA - California Botanic Garden Herbarium. Occurrence dataset https://doi.org/10.15468/0yosx9 accessed via GBIF.org on 2022-05-27.
iNaturalist contributors, iNaturalist (2022). iNaturalist Research-grade Observations. iNaturalist.org. Occurrence dataset https://doi.org/10.15468/ab3s5x accessed via GBIF.org on 2022-05-27.

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