markdown source builds

Auto-generated via {sandpaper}
Source  : f402c81
Branch  : main
Author  : Erin Becker <erinstellabecker@gmail.com>
Time    : 2023-10-20 13:22:31 +0000
Message : Merge pull request datacarpentry#877 from klgallagher/main

Formatting changes to episodes

CITATION.md

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+# CITATION
+
+
+```{.warning}
+Warning in system("update-copyright.py"): error in running command
+```
+
+## 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.
+
+[http://esapubs.org/archive/ecol/E090/118/](http://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:
+
+
+```{.warning}
+Warning in file(con, "r"): cannot open file 'AUTHORS': No such file or
+directory
+```
+
+```{.error}
+Error in file(con, "r"): cannot open the connection
+```
+
+or as a BibTeX entry:
+
+
+```{.warning}
+Warning in file(con, "r"): cannot open file 'AUTHORS': No such file or
+directory
+```
+
+```{.error}
+Error in file(con, "r"): cannot open the connection
+```
+
+

CONDUCT.md

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+# Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people
+who contribute through reporting issues, posting feature requests, updating
+documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual
+language or imagery, derogatory comments or personal attacks, trolling, public
+or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to
+our [Code of Conduct](https://software-carpentry.org/conduct/). Project
+maintainers who do not follow the Code of Conduct may be removed from the
+project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by following our [reporting guidelines](https://software-carpentry.org/CoC-reporting/).
+
+

LICENSE.md

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+# LICENSE
+
+### Instructional Material
+
+All Data Carpentry instructional material is made available under
+the Creative Commons Attribution license. You are free:
+
+- to **Share**\---to copy, distribute and transmit the work
+- to **Remix**\---to adapt the work
+
+Under the following conditions:
+
+- **Attribution**\---You must attribute the work using "Copyright (c)
+  Data Carpentry" (but not in any way that suggests that we
+  endorse you or your use of the work).  Where practical, you must
+  also include a hyperlink to [https://datacarpentry.org](https://datacarpentry.org).
+
+With the understanding that:
+
+- **Waiver**\---Any of the above conditions can be waived if you get
+  permission from the copyright holder.
+- **Other Rights**\---In no way are any of the following rights
+  affected by the license:
+  - Your fair dealing or fair use rights;
+  - The author's moral rights;
+  - Rights other persons may have either in the work itself or in
+    how the work is used, such as publicity or privacy rights.  \*
+- **Notice**\---For any reuse or distribution, you must make clear to
+  others the license terms of this work. The best way to do this is
+  with a link to
+  [https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/).
+
+For the full legal text of this license, please see
+[https://creativecommons.org/licenses/by/4.0/legalcode](https://creativecommons.org/licenses/by/4.0/legalcode).
+
+### Software
+
+Except where otherwise noted, the example programs and other software
+provided by Data Carpentry are made available under the
+[OSI](https://opensource.org)\-approved
+[MIT license](https://opensource.org/licenses/mit-license.html).
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+

NEWS.md

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+## R-ecology-lesson v2017.04.0
+
+Initial release of the Data Carpentry R ecology lesson.

config.yaml

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+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'dc'
+
+# Overall title for pages.
+title: 'Data Analysis and Visualisation in R for Ecologists'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: '2015-04-02'
+
+# Comma-separated list of keywords for the lesson
+keywords: 'software, data, lesson, The Carpentries'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'stable'
+
+# License of the lesson materials (recommended CC-BY 4.0)
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/datacarpentry/R-ecology-lesson'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: 'curriculum@carpentries.org'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes: 
+- 00-before-we-start.Rmd
+- 01-intro-to-r.Rmd
+- 02-starting-with-data.Rmd
+- 03-dplyr.Rmd
+- 04-visualization-ggplot2.Rmd
+- 05-r-and-databases.Rmd
+
+# Information for Learners
+learners: 
+- reference.md
+
+# Information for Instructors
+instructors: 
+- instructor-notes.md
+
+# Learner Profiles
+profiles: 
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+
+
+url: 'https://datacarpentry.github.io/R-ecology-lesson'