Merge pull request #1114 from ethanwhite/quarto

Add a Quarto lesson

Author: ethanwhite

assignments/r-quarto.md

@@ -0,0 +1,19 @@
+---
+layout: page
+element: assignment
+title: Quarto
+language: R
+exercises: []
+points: []
+---
+
+### Learning Objectives
+
+> Following this assignment students should be able to:
+>
+> - use knitr and rmarkdown to make documents with reproducible analysis
+> - refresh your ability to use obtain, manipulate, and graph tabular and spatial data
+
+{% include reading.html %}
+
+{% include assignment.html %}

lectures/R-quarto.md

@@ -0,0 +1,8 @@
+---
+layout: page
+element: lecture
+title: Quarto
+language: R
+---
+
+1. [Quarto]({{ site.baseurl }}/materials/quarto)

materials/quarto.md

@@ -0,0 +1,205 @@
+---
+layout: page
+element: notes
+title: Quarto
+language: R
+---
+
+### Literate programming
+
+* Combine text, code, figures, tables, etc.
+* Quickly generate websites
+* Automatically generate reports
+* Easy to share results and code with collaborators
+
+### Getting started
+
+```r
+install.packages(c("quarto", "dplyr", "ggplot2", "gt", "readr"))
+```
+
+* `File` -> `New File` -> `Quarto Document`
+* Title: `Portal Population Dynamics`
+* Default Output Format: `HTML`
+* Uncheck `Use visual markdown editor`
+* `Create`
+* Generates a basic stub of a `.qmd` document
+* The material between the `---`'s is called "front matter"
+* Metadata about the document
+* Title, author, and what we want to create from this file by default
+* Delete everything below the second `---`
+
+### Markdown
+
+* Basic approach to formatting text
+* Let's you do
+    * `# Headers`
+    * `*italics*`
+    * `**bold**`
+    * `[links](http://google.com)`
+    * Lists
+        * `*`
+        * `1.`
+
+<pre><code>
+## Concept
+
+Exploration of population dynamic patterns at **The Portal Project**.
+How do counts of rodents like *Dipodomys* species change through time?
+
+In this document I will:
+
+1. Load data from the [Portal Project](https://portal.weecology.org)
+2. Process it into population time series
+3. And make initial visualizations
+</code></pre>
+
+* Easy to read for humans
+* Easy to convert into other things for computers
+
+* Press `Render` to create `HTML` from the document
+* Can also create `pdf` & Word versions of our files
+* Change output to `pdf` or `docx`
+
+* Switch back to html
+* Click the gear icon and select `Preview in Viewer Pane`
+* `Render`
+* This shows the rendered page right in RStudio
+
+* Markdown is common on lots of websites
+* Used to create all of the exercises and lectures in this course
+
+### Visual editor
+
+* We can also view and interact with the markdown in a style similar to a word processor
+* Click `Visual`
+* Markdown is now rendered in the editor
+* Can use the editor bar to make markdown changes
+* UNBOLD: The Portal Project
+* Click `Source`
+* See that it is no longer bolded using **
+
+### R chunks 
+
+* Quarto allows you to include code to run in the document
+* Click on `+C` button, which stands for "add code"
+
+<pre><code>
+## Required Packages
+
+```{r}
+library(dplyr)
+library(ggplot2)
+library(readr)
+```
+</code></pre>
+
+* Can run this code by clicking the green arrow
+* Load the data and look at it
+
+<pre><code>
+## Data
+
+```{r}
+data <- read_csv("https://ndownloader.figshare.com/files/2292172")
+data
+```
+</code></pre>
+
+* If we run the code with the green arrow we'll get a nicely formatted table
+* If we click the Render button the output will be included in the html web page
+
+* You can run code inside your text, too:
+
+```
+The data includes `r length(unique(data$species_id))` species.
+```
+
+### Analysis Example
+
+<pre><code>
+## Analysis
+
+Get the time-series of counts for all species.
+          
+```{r}
+time_series <-
+  data |>
+  group_by(species_id, year) |>
+  summarize(count = n()) |>
+  filter(sum(count) > 200)
+time_series
+```
+</code></pre>
+
+### Including Graphs
+
+* Graphs will be included as figures in the document
+
+<pre><code>
+## Plot the time-series.
+
+```{r}
+ggplot(time_series, aes(x = year, y = count)) +
+  geom_line() +
+  facet_wrap(vars(species_id), scales = "free_y")
+```
+</code></pre>
+
+### Chunk options
+
+* Chunks have lots of useful options
+* Can add them at the start of the chunk using `#| `, the option name, and then the option value
+* `#| echo: false` let's you show the results of the code chunk without showing the code.
+* ADD: `#| echo: false` to plot chunk
+* `#| message: false` will remove messages returned by R
+* ADD: `#| message: false` to package, data, and analysis chunks
+* RENDER
+
+* There are also chunk options to include figure legends and alt text
+* ADD TO FIGURE CHUNK:
+
+```
+#| fig-cap: "Figure 1. Time-series of rodent population dynamics at Portal."
+#| fig-alt: "Time-seris of 12 rodent species showing a range of dynamics from increases to decreases to variable, but not directionally changing, response"
+```
+
+### Tables
+
+* We can also make nicely formated tables using the `gt()` function
+* Let's say we need to know who many total individuals of each species were included in the analysis
+
+<pre><code>
+```{r}
+time_series |>
+  group_by(species_id) |>
+  summarize(total_count = sum(count)) |>
+  gt() |>
+  cols_label(
+      species_id = "Species",
+      total_count = "Total Population"
+      )
+```
+</code></pre>
+
+* You can add a label and then cite the table/figure in the text
+
+```r
+#| label: tbl-total-count
+#| tbl-cap: "Total population counts for each species in the study"
+```
+
+* You can then reference the table in the text using `@tbl-total-count`
+
+### Citations
+
+* `Insert` -> `Citation` -> `From DOI` -> `10.1101/332783` -> `+` -> `Insert`
+* Creates a `bibliography.bib` file with the citations
+* This is called a bibtex file
+* Can now cite papers using [@ernest2018]
+* It will appear as an in-text citation and in a References section at the bottom of the document
+
+### Other Output Formats
+
+* Slides
+* Websites

schedule.md

@@ -6,7 +6,7 @@ assignments: ['Data Entry and Storage', 'Introduction to R and RStudio',
   'Solving Bigger Problems', 'Functions',
   'Making Choices', 'Hurricane Catchup', 'Repeating Things 1', 'Repeating Things 2', 
   'Spatial Data 1', 'Spatial Data 2', 'Version Control',
-  'Fall Break', 'Class Choice']
+  'Fall Break', 'Quarto']
 ---
 
 [Assignment submission & checklist]({{ site.baseurl }}/materials/turn-in-checklist)