Merge branch 'datacarpentry:main' into main

Author: kristi-sara

CONTRIBUTING.md

@@ -1,151 +1,121 @@
-# Contributing
-
-[Software Carpentry][swc-site] and [Data Carpentry][dc-site] are open source projects,
-and we welcome contributions of all kinds:
-new lessons,
-fixes to existing material,
-bug reports,
-and reviews of proposed changes are all welcome.
-
-## Contributor Agreement
-
-By contributing,
-you agree that we may redistribute your work under [our license](LICENSE.md).
-In exchange,
-we will address your issues and/or assess your change proposal as promptly as we can,
-and help you become a member of our community.
-Everyone involved in [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
-agrees to abide by our [code of conduct](CONDUCT.md).
-
-## How to Contribute
-
-The easiest way to get started is to file an issue
-to tell us about a spelling mistake,
-some awkward wording,
-or a factual error.
-This is a good way to introduce yourself
-and to meet some of our community members.
-
-1.  If you do not have a [GitHub][github] account,
-    you can [send us comments by email][contact].
-    However,
-    we will be able to respond more quickly if you use one of the other methods described below.
-
-2.  If you have a [GitHub][github] account,
-    or are willing to [create one][github-join],
-    but do not know how to use Git,
-    you can report problems or suggest improvements by [creating an issue][issues].
-    This allows us to assign the item to someone
-    and to respond to it in a threaded discussion.
-
-3.  If you are comfortable with Git,
-    and would like to add or change material,
-    you can submit a pull request (PR).
-    Instructions for doing this are [included below](#using-github).
-
-## Where to Contribute
-
-1.  If you wish to change this lesson,
-    please work in <https://github.com/swcarpentry/shell-novice>,
-    which can be viewed at <https://swcarpentry.github.io/shell-novice>.
-
-2.  If you wish to change the example lesson,
-    please work in <https://github.com/carpentries/lesson-example>,
-    which documents the format of our lessons
-    and can be viewed at <https://carpentries.github.io/lesson-example>.
-
-3.  If you wish to change the template used for workshop websites,
-    please work in <https://github.com/carpentries/workshop-template>.
-    The home page of that repository explains how to set up workshop websites,
-    while the extra pages in <https://carpentries.github.io/workshop-template>
-    provide more background on our design choices.
-
-4.  If you wish to change CSS style files, tools,
-    or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
-    please work in <https://github.com/carpentries/styles>.
-
-## What to Contribute
-
-There are many ways to contribute,
-from writing new exercises and improving existing ones
-to updating or filling in the documentation
-and submitting [bug reports][issues]
-about things that don't work, aren't clear, or are missing.
-If you are looking for ideas,
-please see [the list of issues for this repository][issues],
-or the issues for [Data Carpentry][dc-issues]
-and [Software Carpentry][swc-issues] projects.
-
-Comments on issues and reviews of pull requests are just as welcome:
-we are smarter together than we are on our own.
-Reviews from novices and newcomers are particularly valuable:
-it's easy for people who have been using these lessons for a while
-to forget how impenetrable some of this material can be,
-so fresh eyes are always welcome.
-
-## What *Not* to Contribute
-
-Our lessons already contain more material than we can cover in a typical workshop,
-so we are usually *not* looking for more concepts or tools to add to them.
-As a rule,
-if you want to introduce a new idea,
-you must (a) estimate how long it will take to teach
-and (b) explain what you would take out to make room for it.
-The first encourages contributors to be honest about requirements;
-the second, to think hard about priorities.
-
-We are also not looking for exercises or other material that only run on one platform.
-Our workshops typically contain a mixture of Windows, macOS, and Linux users;
-in order to be usable,
-our lessons must run equally well on all three.
-
-## Using GitHub
-
-If you choose to contribute via GitHub,
-you may want to look at
-[How to Contribute to an Open Source Project on GitHub][how-contribute].
-In brief:
-
-1.  The published copy of the lesson is in the `gh-pages` branch of the repository
-    (so that GitHub will regenerate it automatically).
-    Please create all branches from that,
-    and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
-    before starting work.
-    Please do *not* work directly in your `gh-pages` branch,
-    since that will make it difficult for you to work on other contributions.
-
-2.  We use [GitHub flow][github-flow] to manage changes:
-    1.  Create a new branch in your desktop copy of this repository for each significant change.
-    2.  Commit the change in that branch.
-    3.  Push that branch to your fork of this repository on GitHub.
-    4.  Submit a pull request from that branch to the [master repository][repo].
-    5.  If you receive feedback,
-        make changes on your desktop and push to your branch on GitHub:
-        the pull request will update automatically.
-
-Each lesson has two maintainers who review issues and pull requests
-or encourage others to do so.
-The maintainers are community volunteers,
-and have final say over what gets merged into the lesson.
-
-## Other Resources
-
-General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
-happens on the [discussion mailing list][discuss-list],
-which everyone is welcome to join.
-You can also [reach us by email][contact].
-
-[contact]: mailto:admin@software-carpentry.org
+## Contributing
+
+[The Carpentries][cp-site] ([Software Carpentry][swc-site], [Data
+Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source
+projects, and we welcome contributions of all kinds: new lessons, fixes to
+existing material, bug reports, and reviews of proposed changes are all
+welcome.
+
+### Contributor Agreement
+
+By contributing, you agree that we may redistribute your work under [our
+license](LICENSE.md). In exchange, we will address your issues and/or assess
+your change proposal as promptly as we can, and help you become a member of our
+community. Everyone involved in [The Carpentries][cp-site] agrees to abide by
+our [code of conduct](CODE_OF_CONDUCT.md).
+
+### How to Contribute
+
+The easiest way to get started is to file an issue to tell us about a spelling
+mistake, some awkward wording, or a factual error. This is a good way to
+introduce yourself and to meet some of our community members.
+
+1. If you do not have a [GitHub][github] account, you can [send us comments by
+   email][contact]. However, we will be able to respond more quickly if you use
+   one of the other methods described below.
+
+2. If you have a [GitHub][github] account, or are willing to [create
+   one][github-join], but do not know how to use Git, you can report problems
+   or suggest improvements by [creating an issue][issues]. This allows us to
+   assign the item to someone and to respond to it in a threaded discussion.
+
+3. If you are comfortable with Git, and would like to add or change material,
+   you can submit a pull request (PR). Instructions for doing this are
+   [included below](#using-github).
+
+Note: if you want to build the website locally, please refer to [The Workbench
+documentation][template-doc].
+
+### Where to Contribute
+
+1. If you wish to change this lesson, add issues and pull requests here.
+2. If you wish to change the template used for workshop websites, please refer
+   to [The Workbench documentation][template-doc].
+
+
+### What to Contribute
+
+There are many ways to contribute, from writing new exercises and improving
+existing ones to updating or filling in the documentation and submitting [bug
+reports][issues] about things that do not work, are not clear, or are missing.
+If you are looking for ideas, please see [the list of issues for this
+repository][repo], or the issues for [Data Carpentry][dc-issues], [Library
+Carpentry][lc-issues], and [Software Carpentry][swc-issues] projects.
+
+Comments on issues and reviews of pull requests are just as welcome: we are
+smarter together than we are on our own. **Reviews from novices and newcomers
+are particularly valuable**: it's easy for people who have been using these
+lessons for a while to forget how impenetrable some of this material can be, so
+fresh eyes are always welcome.
+
+### What *Not* to Contribute
+
+Our lessons already contain more material than we can cover in a typical
+workshop, so we are usually *not* looking for more concepts or tools to add to
+them. As a rule, if you want to introduce a new idea, you must (a) estimate how
+long it will take to teach and (b) explain what you would take out to make room
+for it. The first encourages contributors to be honest about requirements; the
+second, to think hard about priorities.
+
+We are also not looking for exercises or other material that only run on one
+platform. Our workshops typically contain a mixture of Windows, macOS, and
+Linux users; in order to be usable, our lessons must run equally well on all
+three.
+
+### Using GitHub
+
+If you choose to contribute via GitHub, you may want to look at [How to
+Contribute to an Open Source Project on GitHub][how-contribute]. In brief, we
+use [GitHub flow][github-flow] to manage changes:
+
+1. Create a new branch in your desktop copy of this repository for each
+   significant change.
+2. Commit the change in that branch.
+3. Push that branch to your fork of this repository on GitHub.
+4. Submit a pull request from that branch to the [upstream repository][repo].
+5. If you receive feedback, make changes on your desktop and push to your
+   branch on GitHub: the pull request will update automatically.
+
+NB: The published copy of the lesson is usually in the `main` branch.
+
+Each lesson has a team of maintainers who review issues and pull requests or
+encourage others to do so. The maintainers are community volunteers, and have
+final say over what gets merged into the lesson.
+
+### Other Resources
+
+The Carpentries is a global organisation with volunteers and learners all over
+the world. We share values of inclusivity and a passion for sharing knowledge,
+teaching and learning. There are several ways to connect with The Carpentries
+community listed at <https://carpentries.org/connect/> including via social
+media, slack, newsletters, and email lists. You can also [reach us by
+email][contact].
+
+[repo]: https://github.com/datacarpentry/r-raster-vector-geospatial
+[contact]: mailto:team@carpentries.org
+[cp-site]: https://carpentries.org/
 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
-[dc-lessons]: http://datacarpentry.org/lessons/
-[dc-site]: http://datacarpentry.org/
-[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
-[github]: http://github.com
+[dc-lessons]: https://datacarpentry.org/lessons/
+[dc-site]: https://datacarpentry.org/
+[discuss-list]: https://lists.software-carpentry.org/listinfo/discuss
+[github]: https://github.com
 [github-flow]: https://guides.github.com/introduction/flow/
 [github-join]: https://github.com/join
 [how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
-[issues]: https://github.com/swcarpentry/shell-novice/issues/
-[repo]: https://github.com/swcarpentry/shell-novice/
+[issues]: https://carpentries.org/help-wanted-issues/
+[lc-issues]: https://github.com/issues?q=user%3ALibraryCarpentry
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: http://software-carpentry.org/lessons/
-[swc-site]: http://software-carpentry.org/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
+[lc-site]: https://librarycarpentry.org/
+[template-doc]: https://carpentries.github.io/workbench/

episodes/03-raster-reproject-in-r.Rmd

@@ -318,14 +318,14 @@ DSM_hill_SJER_WGS <-
     rast("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_DSMhill_WGS84.tif")
 
 # reproject raster
-DTM_hill_UTMZ18N_SJER <- project(DSM_hill_SJER_WGS,
+DSM_hill_UTMZ18N_SJER <- project(DSM_hill_SJER_WGS,
                                  crs(DSM_SJER),
                                  res = 1)
 
 # convert to data.frames
 DSM_SJER_df <- as.data.frame(DSM_SJER, xy = TRUE)
 
-DSM_hill_SJER_df <- as.data.frame(DTM_hill_UTMZ18N_SJER, xy = TRUE)
+DSM_hill_SJER_df <- as.data.frame(DSM_hill_UTMZ18N_SJER, xy = TRUE)
 
 ggplot() +
      geom_raster(data = DSM_hill_SJER_df, 

episodes/07-vector-shapefile-attributes-in-r.Rmd

@@ -32,10 +32,11 @@ library(sf)
 
 ```{r load-data, echo=FALSE, results="hide"}
 # learners will have this data loaded from previous episodes
-point_HARV <- st_read("data/NEON-DS-Site-Layout-Files/HARV/HARVtower_UTM18N.shp")
+point_HARV <-
+    st_read("data/NEON-DS-Site-Layout-Files/HARV/HARVtower_UTM18N.shp")
 lines_HARV <- st_read("data/NEON-DS-Site-Layout-Files/HARV/HARV_roads.shp")
-aoi_boundary_HARV <- st_read(
-  "data/NEON-DS-Site-Layout-Files/HARV/HarClip_UTMZ18.shp")
+aoi_boundary_HARV <-
+    st_read("data/NEON-DS-Site-Layout-Files/HARV/HarClip_UTMZ18.shp")
 ```
 
 ::::::::::::::::::::::::::::::::::::::::::  prereq
@@ -490,33 +491,29 @@ other lines can be black.
 
 ## Answers
 
-First we need to make sure that the `BicyclesHo` attribute is a factor and
-check how many levels it has.
+First we explore the `BicyclesHo` attribute to learn the values that correspond
+to the roads we need.
 
 ```{r}
-lines_HARV$BicyclesHo <- as.factor(lines_HARV$BicyclesHo)
-class(lines_HARV$BicyclesHo)
-levels(lines_HARV$BicyclesHo)
+lines_HARV %>%
+  pull(BicyclesHo) %>%
+  unique()
 ```
 
-Next, we will create a new object `lines_removeNA` that removes missing values.
+Now, we can create a data frame with only those roads where bicycles and horses 
+are allowed.
 
 ```{r}
-lines_removeNA <- lines_HARV[!is.na(lines_HARV$BicyclesHo),]
+lines_showHarv <-
+  lines_HARV %>%
+  filter(BicyclesHo == "Bicycles and Horses Allowed")
+
 ```
 
-In our plot, we will set colors so that only the allowed roads are magenta, and
-we will set line width so that the first factor level is thicker than the
-others.
+Finally, we plot the needed roads after setting them to magenta and a thicker 
+line width.
 
 ```{r harv-paths-bike-horses, fig.cap="Roads and trails in the area highlighting paths where horses and bikes are allowed."}
-# First, create a data frame with only those roads where bicycles and horses
-# are allowed
-lines_showHarv <-
-  lines_removeNA %>%
-  filter(BicyclesHo == "Bicycles and Horses Allowed")
-
-# Next, visualise using ggplot
 ggplot() +
   geom_sf(data = lines_HARV) +
   geom_sf(data = lines_showHarv, aes(color = BicyclesHo), size = 2) +