Fill out syllabus and add nyan cat description

.zenodo.json

@@ -0,0 +1,21 @@
+{
+"title": "An Introduction to Writing Reproducible Manuscripts Using RMarkdown",
+"creators": [
+    {
+      "affiliation": "University of Florida",
+      "name": "Hao Ye",
+      "orcid": "0000-0002-8630-1458"
+    }
+],
+    "description": "RMarkdown is a versatile document format that can combine text, R code, figures, and tables together in a single document, and create formatted output as PDFs, MS Word files, slides, websites, and more. This workshop will provide a basic introduction to using RMarkdown, how to insert code, tables, figures, and format references, and an overview of the possible output formats.",
+    "keywords": [
+    "Open Educational Resources",
+    "Research Support Skills",
+    "Reproducible Report",
+    "Literate Programming",
+    "R Markdown"
+  ],
+    "access_right": "open",
+    "license": "CC-BY-4.0",
+    "upload_type": "lesson"
+}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RMDintro
 Title: An Introduction to Writing Reproducible Manuscripts Using RMarkdown
-Version: 0.9.1
+Version: 1.0.0
 Authors@R: 
     person(given = "Hao",
            family = "Ye",

slides/slides.Rmd

@@ -338,10 +338,10 @@ knitr::kable(mtcars[1:4,1:3], format = "markdown")
 # Figures (images)
 
 ```
-![](https://s3-us-west-2.amazonaws.com/webcitation/7eb1102857c5c8b4fcccb53cd2e84520496841f0)
+![Nyan Cat: animated gif of a grey cat with a pop-tart body flying through space and leaving a rainbow trail behind](https://s3-us-west-2.amazonaws.com/webcitation/7eb1102857c5c8b4fcccb53cd2e84520496841f0)
 ```
 
-![](https://s3-us-west-2.amazonaws.com/webcitation/7eb1102857c5c8b4fcccb53cd2e84520496841f0)
+![Nyan Cat: animated gif of a grey cat with a pop-tart body flying through space and leaving a rainbow trail behind](https://s3-us-west-2.amazonaws.com/webcitation/7eb1102857c5c8b4fcccb53cd2e84520496841f0)
 
 ---
 

syllabus.md

@@ -0,0 +1,306 @@
+# Syllabus
+
+* Learning Objectives
+  + describe the principles of reproducible documents
+  + apply markdown syntax to format text
+  + format numerical results in R Markdown
+  + format tables in R Markdown
+  + generate figures in R Markdown
+  + format references in R Markdown
+
+## Reproducible Documents
+
+* Overview
+
+  Reproducible Documents:
+  + a way to write reports that embed text with other outputs:
+    - code, figures, tables
+  + authors only make changes in *one* place
+    - the entire document stays up to date
+    - (instead of redoing an analysis, and copying images and numbers into a separate file)
+* Many Platforms Exist:
+  + [Manubot](https://github.com/manubot/rootstock)
+  + [Stencila](https://stenci.la/)
+  + [Jupyter Notebooks](https://jupyter.org/)
+  **This lesson is a basic intro to [R Markdown](https://rmarkdown.rstudio.com/) !
+(many add-ons exist that extend functionality)**
+
+## How R Markdown Works
+
+* R Markdown Tools
+  + **`rmarkdown`** is the file-format and main interface with R (`*.Rmd`)
+  + **`knitr`** is the underlying engine that runs code
+  + `pandoc` is a software tool that converts markdown documents into other formats
+![A diagram from https://rmarkdown.rstudio.com/lesson-2.html, showing the workflow for R Markdown, where an Rmd file is transformed by `knitr` into a markdown file, and then by `pandoc` into multiple output files."](slides/rmarkdownflow.png)
+* Installation
+  + RStudio comes with `pandoc`.
+    - but it can be [installed separately](https://pandoc.org/installing.html), as well.
+  + The **`rmarkdown`** package includes **`knitr`** as a dependency.
+  For PDF output, you will want LaTeX. The [**`tinytex`** package](https://yihui.org/tinytex/) provides a mechanism for a lightweight LaTeX install:
+    ```r
+    tinytex::install_tinytex()
+    ```
+* Creating Documents
+  1. Create an R Markdown document.
+      - Use the `New R Markdown` file option in RStudio, or create a plaintext file.
+  2. Run the R code
+     ```r
+     rmarkdown::render({document.Rmd})
+     ```
+     **OR**
+
+     Use the `Knit` button in RStudio.
+
+     ![A screenshot of the Knit button in RStudio, which appears as an image of a ball of yarn with a needle in it, next to the text 'Knit' and an optional pulldown menu in the form of a down arrow.](slides/knit-button.png)
+* What happens during knitting?
+
+  For a given `document.Rmd`
+  1. **`knitr`** runs the code chunks and merges the output with the remainder of `document.Rmd` into a markdown file: `document.md`
+  2. `pandoc` converts the markdown into the final outputs.
+
+## Syntax
+
+* Basic Structure
+
+  R Markdown files begin with a header:
+  ```yaml
+  ---
+  title: "An example document"
+  author: "Hao Ye"
+  output: html_document
+  ---
+  ```
+  + this specifies metadata about the document that gets incorporated in the final output
+* A More Complex Header
+  ```yaml
+  ---
+  title: "Chaotic Dynamics"
+  author:
+  - "Hao Ye"
+  - "Gritty"
+  output:
+    html_document:
+      toc: true
+      toc_depth: 2
+  ---
+  ```
+* Syntax: Headings
+  ```
+  # heading 1
+  ## heading 2
+  ### heading 3
+  ```
+  *renders into*
+
+  # heading 1
+  ## heading 2
+  ### heading 3
+
+* Syntax: bullets
+  ```
+  - bullet list
+      + sub-item
+  1. numbered list
+  1. numbered list
+  ```
+  *renders into*
+
+  - bullet list
+    + sub-item
+  1. numbered list
+  1. numbered list
+
+* Syntax: text
+  ```
+   **bold**, __bold__
+   *italic*, _italic_
+   > This is a quote.
+  ```
+  *renders into*
+
+   **bold**, __bold__
+
+   *italic*, _italic_
+
+   > This is a quote
+
+* Links
+  ```
+  Raw URLs:
+  https://cran.r-project.org/
+  
+  And formatted links:
+  [CRAN](https://cran.r-project.org/)
+  ```
+  *renders into*
+
+  Raw URLs:
+  https://cran.r-project.org/
+
+  And formatted links:
+  [CRAN](https://cran.r-project.org/)
+
+## Code Chunks
+
+* Inserting Code
+
+  ````
+  ```{r}
+  1 + 1
+  ```
+  ````
+  *renders into*
+
+  ```r
+  1 + 1
+  ```
+  ```
+  ## [1] 2
+  ```
+
+* Code Chunk Options
+
+  The evaluation of code chunks can be controlled through options, e.g.:
+  ````
+  ```{r, eval = FALSE}
+  1 + 1
+  ```
+  ````
+  *renders into*
+
+  ```
+  1 + 1
+  ```
+
+  See the description of [chunk options](https://yihui.org/knitr/options/) for details.
+
+* Inline code
+  ````
+  The square root of 10 is `r sqrt(10)`.
+  Today's date is `r Sys.Date()`.
+  ````
+  *renders into*
+
+  The square root of 10 is 3.1622777.
+
+  Today's date is 2020-07-23.
+
+* Other Coding Languages
+
+  **`knitr`** supports other programming languages.
+
+  See [Section 2.7](https://bookdown.org/yihui/rmarkdown/language-engines.html) of the R Markdown book for details.
+
+* Tables (markdown)
+
+  ```
+  | Tables        | Are           | Cool  |
+  | ------------- |:-------------:| -----:|
+  | col 3 is      | right-aligned | $1600 |
+  | col 2 is      | centered      |   $12 |
+  | zebra stripes | are neat      |    $1 |
+  ```
+  *renders into*
+
+  | Tables        | Are           | Cool  |
+  | ------------- |:-------------:| -----:|
+  | col 3 is      | right-aligned | $1600 |
+  | col 2 is      | centered      |   $12 |
+  | zebra stripes | are neat      |    $1 |
+
+
+* Tables (R code)
+
+  ````
+  ```{r, results="asis"}
+  knitr::kable(mtcars[1:4,1:3], 
+               format = "markdown")
+  ```
+  ````
+  *renders into*
+
+  |               |  mpg| cyl| disp|
+  |:--------------|----:|---:|----:|
+  |Mazda RX4      | 21.0|   6|  160|
+  |Mazda RX4 Wag  | 21.0|   6|  160|
+  |Datsun 710     | 22.8|   4|  108|
+  |Hornet 4 Drive | 21.4|   6|  258|
+
+
+* Figures (images)
+  ```
+  ![Nyan Cat: animated gif of a grey cat with a pop-tart body flying through space and leaving a rainbow trail behind](https://s3-us-west-2.amazonaws.com/webcitation/7eb1102857c5c8b4fcccb53cd2e84520496841f0)
+  ```
+
+  ![Nyan Cat: animated gif of a grey cat with a pop-tart body flying through space and leaving a rainbow trail behind](https://s3-us-west-2.amazonaws.com/webcitation/7eb1102857c5c8b4fcccb53cd2e84520496841f0)
+
+* Figures (code)
+  ```
+  plot(mpg ~ disp, data = mtcars, 
+       cex = 2, cex.lab = 2, cex.axis = 2)
+  ```
+
+  ![](plot.png)
+
+* References
+  + Get your citations into a `.bib` format. (plain-text bibtex, most reference managers can output a list in this way)
+  + Add metadata to the header about the file and the *style* of citations
+  + Insert citations using `[@{bibentry}]`, where `{bibentry}` is the unique identifier for the reference in the bibliography.
+    - see also the [`citr` add-in](https://github.com/crsh/citr).
+* References (`.bib`)
+  `refs.bib`:
+  ```
+  @article{Barkai_1988,
+  	Author = {Amos Barkai and Christopher McQuaid},
+  	Journal = {Science},
+  	Number = {4875},
+  	Pages = {62-64},
+  	Title = {Predator-prey role reversal in a marine benthic ecosystem},
+  	Volume = {242},
+  	Year = {1988}}
+  ```
+* References (YAML header)
+  ```{yaml}
+  ---
+  title: "An example document"
+  author: "Hao Ye"
+  output: html_document
+  bibliography: refs.bib
+  csl: methods-in-ecology-and-evolution.csl
+  ---
+  ```
+  Find Citation Style Language (CSL) files at
+  + https://github.com/citation-style-language/styles
+  + https://www.zotero.org/styles
+
+* References (usage)
+  ```
+  Sometimes whelks eat lobsters [@Barkai_1998].
+  ```
+  *renders into*
+
+  Sometimes whelks eat lobsters (Barkai and McQuaid, 1988).
+
+  ### References
+
+  1. Barkai, A. and C. McQuaid (1988). "Predator-prey role reversal in a marine benthic ecosystem". In: *Science* 242.4875, pp. 62-64.
+
+## Extensions
+
+* Basic Output Formats
+  + `html_document` - a single HTML file
+  + `pdf_document` - a single PDF file (requires a LaTeX installation, see the [**`tinytex`** package](https://yihui.org/tinytex/))
+  + `word_document` - a single MS Word file
+  + `github_document` - markdown for rendering in GitHub
+* Other Formats
+  MANY packages build on R Markdown to do more complex things:
+  + [thesisdown](https://github.com/ismayc/thesisdown) has thesis templates
+  + [blogdown](https://bookdown.org/yihui/blogdown/) for websites
+  + [xaringan](https://github.com/yihui/xaringan) for interactive slides  
+  (what this uses)
+* Thanks
+  + Let me know what content you'd like to see
+  + Contact me for additional questions or consultation requests!
+  + Check back in on the libguide for more modules and contact info:
+    - https://guides.uflib.ufl.edu/reproducibility
+