R-ecology-lesson
Data Analysis and Visualization in R for Ecologists.
https://github.com/datacarpentry/R-ecology-lesson
Category: Sustainable Development
Sub Category: Education
Keywords
carpentries data-carpentry data-visualisation data-visualization data-wrangling ecology english lesson open-educational-resources r stable
Keywords from Contributors
beta carpentries-incubator tidyverse spreadsheet data-management fair-principles tibfds sustainable-software geospatial-data carpentries-lab
Last synced: about 8 hours ago
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Repository metadata
Data Analysis and Visualization in R for Ecologists
- Host: GitHub
- URL: https://github.com/datacarpentry/R-ecology-lesson
- Owner: datacarpentry
- License: other
- Created: 2015-04-02T22:11:48.000Z (about 10 years ago)
- Default Branch: main
- Last Pushed: 2025-06-03T14:04:34.000Z (4 days ago)
- Last Synced: 2025-06-04T09:28:16.090Z (3 days ago)
- Topics: carpentries, data-carpentry, data-visualisation, data-visualization, data-wrangling, ecology, english, lesson, open-educational-resources, r, stable
- Language: R
- Homepage: https://datacarpentry.org/R-ecology-lesson/
- Size: 692 MB
- Stars: 322
- Watchers: 32
- Forks: 508
- Open Issues: 24
- Releases: 8
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.Rmd
- License: LICENSE.md
- Citation: CITATION
- Authors: AUTHORS
- Zenodo: .zenodo.json
README.md
Data Carpentry: R for data analysis and visualization of Ecological Data
This is an introduction to R designed for participants with no programming
experience. It can be taught in 3/4 of a day (approximately 6 hours).
It is a redesigned version of the original Data Carpentry lesson.
The initial effort towards this redesign was done by Michael Culshaw-Maurer in another repository in The Carpentries Incubator: https://github.com/carpentries-incubator/R-ecology-lesson (now archived). See Michael's notes while preparing the redesign in the update_plans.md file of that repository.
The lesson starts with information about the R programming language and the RStudio interface. It then moves to loading in data and exploring how to visualise it with ggplot2. The next episode takes learners through an exploration of data frames and some common data cleaning operations, before discussing vectors and factors. The final episode introduces the flow of data in R, and how to combine operations to select, filter, and mutate a data frame.
Providing feedback on this lesson
If you teach this redesigned lesson, please open an issue on this repository to share your experience.
Prerequisites
The lesson assumes no prior knowledge of R or RStudio.
Learners should have R and RStudio installed on their computers. They will also
need to be able to install R packages from CRAN, create directories, and
download files.
See the lesson website
for instructions on installing R, RStudio, and the required R packages.
Contributing
Contributions to the content and development of these lesson are very welcome!
If you would like to contribute, we encourage you to review our contributing guide.
Questions
If you have any questions or feedback, please open an issue, contact the
maintainers, or come chat with us on the
Slack Channel for this lesson.
If you don't already have a Slack account with the Carpentries, you can
create one.
Maintainers
Citation (CITATION)
## Data
Data is from the paper S. K. Morgan Ernest, Thomas J. Valone, and James
H. Brown. 2009. Long-term monitoring and experimental manipulation of a
Chihuahuan Desert ecosystem near Portal, Arizona, USA. Ecology 90:1708.
[https://esapubs.org/archive/ecol/E090/118/](https://esapubs.org/archive/ecol/E090/118/)
A simplified version of this data, suitable for teaching is available on
[figshare](https://doi.org/10.6084/m9.figshare.1314459.v5).
## Lessons
The first workshop was run at NESCent on May 8-9, 2014 with the development and
instruction of lessons by Karen Cranston, Hilmar Lapp, Tracy Teal, and Ethan
White and contributions from Deb Paul and Mike Smorul.
Original materials adapted from SWC Python lessons by Sarah Supp. John Blischak
led the continued development of materials with contributions from Gavin
Simpson, Tracy Teal, Greg Wilson, Diego Barneche, Stephen Turner, and Karthik
Ram. This original material has been modified and expanded by François
Michonneau.
The **`dplyr`** lesson was created by Kara Woo, who copied and modified and
modified from Jeff
Hollister's [materials](https://usepa.github.io/introR/2015/01/14/03-Clean/).
The **`ggplot2`** lesson was initially created by Mateusz Kuzak, Diana Marek,
and Hedi Peterson, during a Hackathon in Espoo, Finland on March 16-17, 2015,
sponsored by the [ELIXIR project](https://elixir-europe.org/).
You can cite this Data Carpentry lesson as follow:
Michonneau F, Teal T, Fournier A, Seok B, Obeng A, Pawlik AN, Conrado AC, Woo K, Lijnzaad
P, Hart T, White EP, Marwick B, Bolker B, Jordan KL, Ashander J, Dashnow H, Hertweck K,
Cuesta SM, Becker EA, Guillou S, Shiklomanov A, Klinges D, Odom GJ, Jean M, Mislan KAS,
Johnson K, Jahn N, Mannheimer S, Pederson S, Pletzer A, Fouilloux A, Switzer C, Bahlai C,
Li D, Kerchner D, Rodriguez-Sanchez F, Rajeg GPW, Ye H, Tavares H, Leinweber K, Peck K,
Lepore ML, Hancock S, Sandmann T, Hodges T, Tirok K, Jean M, Bailey A, von Hardenberg A,
Theobold A, Wright A, Basu A, Johnson C, Voter C, Hulshof C, Bouquin D, Quinn D,
Vanichkina D, Wilson E, Strauss E, Bledsoe E, Gan E, Fishman D, Boehm F, Daskalova G,
Tavares H, Kaupp J, Dunic J, Keane J, Stachelek J, Herr JR, Millar J, Lotterhos K,
Cranston K, Direk K, Tylén K, Chatzidimitriou K, Deer L, Tarkowski L, Chiapello M, Burle
M, Ankenbrand M, Czapanskiy M, Moreno M, Culshaw-Maurer M, Koontz M, Weisner M, Johnston
M, Carchedi N, Burge OR, Harrison P, Humburg P, Pauloo R, Peek R, Elahi R, Cortijo S,
sfn_brt, Umashankar S, Goswami S, Sumedh, Yanco S, Webster T, Reiter T, Pearse W, Li Y
(2025). “datacarpentry/R-ecology-lesson: Data Carpentry: Data Analysis and Visualization
in R for Ecologists, June 2019.” doi:10.5281/zenodo.3264888
<https://doi.org/10.5281/zenodo.3264888>, <https://datacarpentry.org/R-ecology-lesson/>.
or as a BibTeX entry:
@Misc{,
author = {François Michonneau and Tracy Teal and Auriel Fournier and Brian Seok and Adam Obeng and Aleksandra Natalia Pawlik and Ana Costa Conrado and Kara Woo and Philip Lijnzaad and Ted Hart and Ethan P White and Ben Marwick and Ben Bolker and Kari L Jordan and Jaime Ashander and Harriet Dashnow and Kate Hertweck and Sergio Martínez Cuesta and Erin Alison Becker and Stéphane Guillou and Alexey Shiklomanov and David Klinges and Gabriel J. Odom and Martin Jean and K. A. S. Mislan and Kayla Johnson and Najko Jahn and Sara Mannheimer and Steve Pederson and Alex Pletzer and Anne Fouilloux and Callin Switzer and Christie Bahlai and Daijiang Li and Dan Kerchner and Francisco Rodriguez-Sanchez and Gede Primahadi Wijaya Rajeg and Hao Ye and Hugo Tavares and Katrin Leinweber and Kayla Peck and Mauro Luciano Lepore and Stacey Hancock and Thomas Sandmann and Toby Hodges and Katrin Tirok and Martin Jean and Alistair Bailey and Achaz {von Hardenberg} and Allison Theobold and April Wright and Arindam Basu and Carolina Johnson and Carolyn Voter and Catherine Hulshof and Daina Bouquin and Danielle Quinn and Darya Vanichkina and Earle Wilson and Eli Strauss and Ellen Bledsoe and Emilia Gan and Dmytro Fishman and Fred Boehm and Gergana Daskalova and Hugo Tavares and Jake Kaupp and Jillian Dunic and Jonathan Keane and Joseph Stachelek and Joshua R. Herr and Justin Millar and Katie Lotterhos and Karen Cranston and Kenan Direk and Kristian Tylén and Kyriakos Chatzidimitriou and Lachlan Deer and Leszek Tarkowski and Marco Chiapello and Marie-Helene Burle and Markus Ankenbrand and Max Czapanskiy and Melissa Moreno and Michael Culshaw-Maurer and Michael Koontz and Michael Weisner and Myfanwy Johnston and Nick Carchedi and Olivia Rata Burge and Paul Harrison and Peter Humburg and Richard Pauloo and Ryan Peek and Robin Elahi and Sandra Cortijo and {sfn_brt} and Shivshankar Umashankar and Shubhang Goswami and {Sumedh} and Scott Yanco and Tara Webster and Taylor Reiter and Will Pearse and Ye Li},
title = {datacarpentry/R-ecology-lesson: Data Carpentry: Data Analysis and Visualization in R for Ecologists, June 2019},
editor = {Ana Costa Conrado and Auriel M.V. Fournier and Brian Seok and Francois Michonneau},
month = {May},
year = {2025},
url = {https://datacarpentry.org/R-ecology-lesson/},
doi = {10.5281/zenodo.3264888},
}
Owner metadata
- Name: Data Carpentry
- Login: datacarpentry
- Email: [email protected]
- Kind: organization
- Description: Workshops teaching scientists basic skills for retrieving, viewing, managing, and manipulating data in an open and reproducible way.
- Website: https://datacarpentry.org/
- Location:
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/6666450?v=4
- Repositories: 89
- Last ynced at: 2023-03-13T13:55:49.004Z
- Profile URL: https://github.com/datacarpentry
GitHub Events
Total
- Issues event: 5
- Watch event: 9
- Delete event: 20
- Issue comment event: 27
- Push event: 90
- Pull request review comment event: 1
- Pull request event: 28
- Pull request review event: 8
- Fork event: 16
- Create event: 21
Last Year
- Issues event: 5
- Watch event: 9
- Delete event: 20
- Issue comment event: 27
- Push event: 90
- Pull request review comment event: 1
- Pull request event: 28
- Pull request review event: 8
- Fork event: 16
- Create event: 21
Committers metadata
Last synced: 29 days ago
Total Commits: 1,021
Total Committers: 217
Avg Commits per committer: 4.705
Development Distribution Score (DDS): 0.635
Commits in past year: 25
Committers in past year: 5
Avg Commits per committer in past year: 5.0
Development Distribution Score (DDS) in past year: 0.6
| Name | Commits | |
|---|---|---|
| Francois Michonneau | f****u@g****m | 373 |
| Tobias Busch | t****h@g****m | 46 |
| Toby Hodges | t****s@g****m | 31 |
| Katrin Leinweber | K****r@t****u | 27 |
| Brian Seok | s****k@c****u | 27 |
| Adam Obeng | g****b@b****m | 25 |
| zkamvar | z****r | 20 |
| Mateusz Kuzak | m****k@g****m | 15 |
| Katrin Leinweber | 9****r | 14 |
| Tracy Teal | t****l@g****m | 14 |
| Edmund Hart | e****t@g****m | 14 |
| Ana Costa | 2****t | 13 |
| Philip Lijnzaad | p****d@g****m | 12 |
| Kara Woo | w****a@g****m | 12 |
| Ben Marwick | b****k@h****m | 10 |
| maneesha sane | 8****a | 10 |
| Aleksandra Pawlik | a****k@g****m | 9 |
| Auriel M.V. Fournier | a****r@g****m | 9 |
| Matthias Grenié | m****e@h****m | 8 |
| kathy0305 | k****5@h****m | 8 |
| Erin Becker | e****r@c****g | 8 |
| Ben Bolker | b****r@g****m | 8 |
| Ethan White | e****n@w****g | 7 |
| chriseshleman | e****s@g****m | 7 |
| Kari L. Jordan | k****n@m****m | 7 |
| Doug Joubert | d****C | 5 |
| Mark Robinson | m****n@i****h | 5 |
| David | k****d@s****u | 5 |
| Sergio Martínez Cuesta | s****e@g****m | 5 |
| Ruud Steltenpool | g****m@s****m | 5 |
| and 187 more... | ||
Committer domains:
- carpentries.org: 3
- weecology.org: 3
- ufl.edu: 3
- wisc.edu: 2
- msu.edu: 2
- uw.edu: 2
- umich.edu: 2
- ucdavis.edu: 2
- cam.ac.uk: 2
- swansea.ac.uk: 1
- otago.ac.nz: 1
- iimog.org: 1
- mac.com: 1
- geo.uio.no: 1
- idyll.org: 1
- g.harvard.edu: 1
- sub.uni-goettingen.de: 1
- anche.no: 1
- umb.edu: 1
- soton.ac.uk: 1
- bu.edu: 1
- nih.govt: 1
- member.fsf.org: 1
- steltenpower.com: 1
- si.edu: 1
- imls.uzh.ch: 1
- me.com: 1
- binaryeagle.com: 1
- colorado.edu: 1
- tib.eu: 1
- wfu.edu: 1
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- drycafe.net: 1
- illinois.edu: 1
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- mimuw.edu.pl: 1
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- unm.edu: 1
- mail.missouri.edu: 1
- cc.au.dk: 1
- ucdenver.edu: 1
- uchicago.edu: 1
- logarithmic.net: 1
- mail.nih.gov: 1
- slcu.cam.ac.uk: 1
- neoninc.org: 1
- ucsd.edu: 1
- jhu.edu: 1
- utexas.edu: 1
- mcgill.ca: 1
- york.ac.uk: 1
- aol.com: 1
- acadiau.ca: 1
- email.arizona.edu: 1
Issue and Pull Request metadata
Last synced: 1 day ago
Total issues: 99
Total pull requests: 80
Average time to close issues: over 2 years
Average time to close pull requests: 5 months
Total issue authors: 77
Total pull request authors: 40
Average comments per issue: 2.41
Average comments per pull request: 1.76
Merged pull request: 49
Bot issues: 0
Bot pull requests: 0
Past year issues: 9
Past year pull requests: 27
Past year average time to close issues: about 1 month
Past year average time to close pull requests: 12 days
Past year issue authors: 7
Past year pull request authors: 9
Past year average comments per issue: 1.89
Past year average comments per pull request: 1.3
Past year merged pull request: 23
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- tobyhodges (7)
- maneesha (5)
- zkamvar (4)
- ErinBecker (2)
- mikemahoney218 (2)
- Bisaloo (2)
- edbennett (2)
- murraycadzow (2)
- fmichonneau (2)
- rgaiacs (2)
- bienflorencia (2)
- klbarnes20 (2)
- jaxinewolfe (1)
- toms-coding (1)
- estregger (1)
Top Pull Request Authors
- carpentries-bot (17)
- tobyhodges (10)
- zkamvar (9)
- doujouDC (4)
- CarolynKoehn (2)
- ErinBecker (2)
- edbennett (2)
- sgichuki (2)
- wood-chris (1)
- murraycadzow (1)
- Bisaloo (1)
- phyloverse (1)
- BenjaminJPerry (1)
- susanwashko (1)
- sanjayfuloria (1)
Top Issue Labels
- type:clarification (20)
- type:enhancement (17)
- good first issue (12)
- help wanted (11)
- type:discussion (7)
- status:refer to cac (4)
- type:instructor guide (4)
- status:wait (4)
- status:waiting for response (4)
- type:template and tools (3)
- type:formatting (2)
- status:duplicate (2)
- high priority (1)
- type: package cache (1)
- type:accessibility (1)
- type:teaching example (1)
Top Pull Request Labels
- type: package cache (11)
- type: template and tools (6)
- status:in progress (2)
- status:waiting for response (1)
- type:clarification (1)
- type:template and tools (1)
- type:enhancement (1)
- status:wait (1)
Dependencies
- RSQLite * imports
- dbplyr * imports
- gridExtra * imports
- hexbin * imports
- hunspell * imports
- knitr * imports
- patchwork * imports
- remotes * imports
- rmarkdown * imports
- tidyverse * imports
Score: 11.226336128598184