class: center, middle, inverse, title-slide # Customized RMarkdown documents ## Introduction to RStudio and RMarkdown ### Yebelay Berehan ### Email: <code><yebelay.ma@gmail.com></code> ### 2022-04-01 --- <div> <style type="text/css">.xaringan-extra-logo { width: 90px; height: 85px; z-index: 0; background-image: url(logo.png); background-size: contain; background-repeat: no-repeat; position: absolute; top:1em;right:1em; } </style> <script>(function () { let tries = 0 function addLogo () { if (typeof slideshow === 'undefined') { tries += 1 if (tries < 10) { setTimeout(addLogo, 100) } } else { document.querySelectorAll('.remark-slide-content:not(.title-slide):not(.inverse):not(.hide_logo)') .forEach(function (slide) { const logo = document.createElement('div') logo.classList = 'xaringan-extra-logo' logo.href = null slide.appendChild(logo) }) } } document.addEventListener('DOMContentLoaded', addLogo) })()</script> </div> # Outline * Introduction to R, Rstudio, and coding * R Markdown * R Markdown Outputs * Creating R Markdown documents --- # `R Markdown` ## Install the rmarkdown package in R - Install from CRAN ```r install.packages('rmarkdown') ``` Or install the development version, from GitHub ```r if (!requireNamespace("devtools")) install.packages('devtools') devtools::install_github('rstudio/rmarkdown') ``` --- # Basics - A single R Markdown file used + to both save and execute code, - to generate high quality reports that can be shared with an audience. - R Markdown was designed for easier reproducibility, since both the computing code and narratives are in the same document, and results are automatically generated from the source code. - R Markdown supports dozens of static and dynamic/ interactive output formats. - Below is a minimal R Markdown document, which should be a plain-text file, with the conventional extension .Rmd : --- # R Markdown Headers The header of an .Rmd file is a [YAML](http://yaml.org/) code block, and everything else is part of the main document. ```{} --- title: " R markdown " author: "Yebelay Berehan" date: "April 01, 2022" output: html_document --- ``` - To mess with global formatting, [you can modify the header](http://rmarkdown.rstudio.com/html_document_format.html)². .footnote[[2] Be careful though, YAML is space-sensitive; indents matter!] ```{} output: html_document: theme: readable ``` --- # con 1. You can create a new Rmd file from the menu **File -> New File -> R Markdown**. 2. There are three basic components of an R Markdown document: the metadata, text, and code. 3. The metadata is written between the pair of three dashes `---` . 4. A code chunk starts with three backticks like ````{r}` where r indicates the language name, and ends with three backticks. 5. You can write chunk options in the curly braces (e.g., set the figure height to 5 inches: ````{r, fig.height=5}` ). 6. An inline R code expression starts with `r` and `ends with a backtick`. 7. The usual way to compile an R Markdown document is to click the Knit button, and the corresponding keyboard shortcut is `Ctrl + Shift + K`. --- # R Markdown Documents Let's try making an R Markdown file: 1. Choose *File > New File > R Markdown...* 1. Make sure *HTML Output* is .p2-green[selected] and click OK 1. Save the file somewhere, call it `my_first_rmd.Rmd` 1. Click the *Knit HTML* button 1. Watch the progress in the R Markdown pane, then gaze upon your result! You may also open up the file in your computer's browser if you so desire, using the *Open in Browser* button at the top of the preview window. --- # Output formats - There are two types of output formats in the rmarkdown package: documents, and presentations. - Some available formats are listed below: * `beamer_presentation` * `html_document` * `latex_document` * `word_document` * `pdf_document` * `powerpoint_presentation` etc. - There are multiple output formats in a dropdown menu behind the Rstudio Knit button. --- - Each output format is often accompanied with several format options. - All these options are documented on the R package help pages. - Type `?rmarkdown::html_document` to open the help page of the html_document format. - The values from R to YAML, e.g., html_document(toc = TRUE, toc_depth = 2, dev = 'svg') can be written in YAML as: ```{} output: html_document: toc: true toc_depth: 2 dev: 'svg' ``` --- - Character strings in YAML often do not require the quotes(e.g., dev: 'svg' and dev: svg are the same), unless they contain special characters, such as the colon : . - If you are not sure if a string should be quoted or not, test it with the yaml package, e.g., ```{} cat(yaml::as.yaml(list(title = 'A Wonderful Day', subtitle = 'hygge: a quality of coziness'))) ``` renders: * `title:` A Wonderful Day * `subtitle:` "hygge: a quality of coziness" - Note that the subtitle in the above example is quoted because of the colon. --- ## Markdown syntax - The text in an R Markdown document is written with the Markdown syntax. ## Inline formatting - Inline *`text`* will be italic if surrounded by underscores or asterisks,(` _text_` or `*text*`). - **`Bold`** text is produced using a pair of double asterisks ( `**text**` ). - A pair of tildes (~) like `X~2~` renders `\(x_2\)` . - A pair of carets (^) like `X^2^` produce a superscript `\(X^2\)`. - To mark text as inline code , use a pair of backticks, e.g., `code` . --- # R Markdown Syntax .pull-left[ ## Output **bold/strong emphasis** *italic/normal emphasis* ## Head ## Subheader ### Subsubheader > Block quote from famous person ] .pull-right[ ## Syntax ``` - **bold/strong emphasis** - *italic/normal emphasis* - `# Header` - ## Subheader - ### Subsubheader ``` ``` > Block quote from famous person ``` ] --- # Formulae and Syntax .pull-left[ ## Output 1. Write LaTeX math expressions inside a pair of dollar signs, e.g. `\(\alpha+\beta\)` or 1. `\(y= \left( \frac{2}{3} \right)^2\)` right up in there. 1. Display style with double dollars `(\begin{equation} ... \end{equation})`: `$$\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i$$` ] .pull-right[ ## Syntax ``` 1. `\(\alpha+\beta\)` 2. `\(y= \left(\frac{2}{3} \right)^2\)` 3. $$\frac{1}{n}\sum_{i=1}^{n}x_i =\bar{x}_n$$` ``` ] --- - Hyperlinks are created using the syntax `[text](link)`. + `[RStudio](https://www.rstudio.com)`. - The syntax for images is similar: just add an exclamation mark. + `![alt text or image title] (path/to/image)`. - Footnotes are put inside the square brackets after a caret ^[]. + ^[This is a footnote.] . - There are multiple ways to insert citations, and we recommend that you use BibTeX databases, because they work better when the output format is LaTeX/PDF. - The key idea is that when you have a BibTeX database (a plain-text file with the conventional filename extension .bib ) that contains entries like: --- ```{} @Manual{R-base,title = {R: A Language and Environment for Statistical Computing}, author = {{R Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2017}, url = {https://www.R-project.org/},} ``` - You may add a field named bibliography to the YAML metadata, and set its value to the path of the BibTeX file. - Then in Markdown, you may use `@R-base` or `[@Rbase]` to reference the BibTeX entry. - Pandoc will automatically generated a list of references in the end of the document. ## Blockquotes are written after `>` > "If the Statistics are boring, then you have got the wrong numbers." AH, Tufte Writes --- # Math expressions - Inline LaTeX equations can be written in a pair of dollar signs using the LaTeX syntax, e.g., .pull-left[ ``` 1. $f(k) = {n\choose k} p^{k} (1-p)^{n-k}$ - Also can be written in a pair of double dollar signs, 2. $$f(k) = {n\choose k} p^{k} (1-p)^{n-k}$$` 3. $\begin{array}{ccc} x_{11} & x_{12} & x_{13}\\ x_{21} & x_{22} & x_{23} \end{array}$ ``` ] .pull-right[ ## Output 1. `\(f(k) = {n\choose k} p^{k} (1-p)^{n-k}\)` 2. `$$f(k) = {n\choose k} p^{k} (1-p)^{n-k}$$` 3. `$$\begin{array}{ccc} x_{11} & x_{12} & x_{13}\\ x_{21} & x_{22} & x_{23} \end{array}$$` ] --- # Math expressions .pull-left[ ##Syntax ``` 1. `$$X = \begin{bmatrix}1 & x_{1}\\ 1 & x_{2}\\ 1 & x_{3} \end{bmatrix}$$` 2. `$$\Theta = \begin{pmatrix} \alpha & \beta\\ \gamma & \delta \end{pmatrix}$$` 3. `$$\begin{vmatrix} a & b\\ c & d \end{vmatrix}=ad-bc$$` ``` ] .pull-right[ ## Output 1. `$$X = \begin{bmatrix}1 & x_{1}\\ 1 & x_{2}\\ 1 & x_{3} \end{bmatrix}$$` 2. `$$\Theta = \begin{pmatrix}\alpha & \beta\\ \gamma & \delta \end{pmatrix}$$` 3. `$$\begin{vmatrix}a & b\\ c & d \end{vmatrix}=ad-bc$$` ] --- # R code chunks and inline R code - You can insert an R code chunk either using the RStudio toolbar (the Insert button) or the keyboard shortcut `Ctrl + Alt + I`. - There are a lot of things you can do in a code chunk: you can produce text output, tables, or graphics. - You have fine control over all these output via chunk options, which can be provided inside the curly braces ````{r}`. - For example, you can choose hide text output via the chunk option `results= 'hide'` , or set the figure height to 4 inches via `fig.height = 4`. - Chunk options are separated by commas, e.g., ````{r, chunk-label, results='hide', fig.height=4}`. - There are a large number of chunk options in knitr documented at <https://yihui.name/knitr/options>. We list a subset of them below: --- # Chunk Options Chunks have options that control what happens with their code, such as: * `echo=FALSE`: Keeps R code from being shown in the document * `eval=FALSE`: Shows R code in the document without running it * `include=FALSE`: Hides all output but still runs code (good for `setup` chunks where you load packages!) * `results='hide'`: Hides R's (non-plot) output from the document * `cache=TRUE`: Saves results of running that chunk so if it takes a while, you won't have to re-run it each time you re-knit the document * `fig.height=5, fig.width=5`: modify the dimensions of any plots that are generated in the chunk (units are in inches) Some of these can be modified using the gear-shaped *Modify Chunk Options* button in each chunk. [There are a *lot* of other options, however](https://yihui.name/knitr/options/). --- - `fig.width and fig.height:` The size of R plots in inches. `fig.dim = c(6, 4) means fig.width = 6 and fig.height = 4`. - `out.width and out.height:` The output size of R plots in the output document, `out.width = '80%' means 80% of the page width`. - `fig.align:` The alignment of plots. It can be 'left' , center , or 'right' . - `fig.cap:` The figure caption. - If a certain option needs to be frequently set to a value in multiple code chunks, you can consider setting it globally in the first code chunk of your document, e.g., ```{} knitr::opts_chunk$set(fig.width = 8, collapse = TRUE) ``` --- # Figures - By default, figures produced by R code will be placed immediately after the code chunk they were generated from. For example: .pull-left[ ```r plot(cars, pch = 18) ```  ] .pull-right[ - You can provide a figure caption using fig.cap in the chunk options. - If the document output format supports the option `fig_caption: true` + (e.g., the output format rmarkdown::html_document ), the R plots will be placed into figure environments. + In the case of PDF output, such figures will be automatically numbered. ] --- You may wish to fine-tune the positions once the content is complete using the fig.pos chunk option (e.g., fig.pos = 'h') . To place multiple figures side-by-side from the same code chunk, you can use the fig.hold='hold' option along with the out.width option. .pull-left[ <img src="RMarkdown-presentation_files/figure-html/unnamed-chunk-4-1.png" width="35%" /><img src="RMarkdown-presentation_files/figure-html/unnamed-chunk-4-2.png" width="35%" /> ] .pull-right[ ```{} ```{r fig.show="hold", out.width="35%"} par(mar = c(4, 4, .1, .1)) plot(cars, pch = 19) plot(pressure, pch = 17) ``` ``` ] - If you want to include a graphic that is not generated from R code, you may use the `knitr::include_graphics()` function, which gives you more control over the attributes of the image than the Markdown syntax of ``. ```r knitr::include_graphics('images/hex-rmarkdown.png') ``` --- # Tables - The easiest way to include tables is by using `knitr::kable()`, which can create tables for HTML, PDF and Word outputs. Table captions can be included by passing caption to the function, .small[ ```r knitr::kable(iris[1:4, ], caption = 'My first Table') ``` Table: My first Table | Sepal.Length| Sepal.Width| Petal.Length| Petal.Width|Species | |------------:|-----------:|------------:|-----------:|:-------| | 5.1| 3.5| 1.4| 0.2|setosa | | 4.9| 3.0| 1.4| 0.2|setosa | | 4.7| 3.2| 1.3| 0.2|setosa | | 4.6| 3.1| 1.5| 0.2|setosa | ] - For LaTeX/PDF output formats, you will need to use the LaTeX package longtable, by adding `\usepackage{longtable}` to your LaTeX preamble, and passing `longtable =TRUE to kable()` to break tables across multiple pages. --- - kableExtra package, provides functions to customize the appearance of PDF and HTML tables. - You may also consider the pander package. There are several other packages for producing tables, .pull-left[ - kableExtra - formattable - DT - pander - huxtable - reactable - flextable ] .pull-right[ - ftextra - pixiedust - tangram - ztable - condformat - stargazer - xtable ] --- # Example .pull-left[ .small[ ```r library(gtsummary) # make dataset trial2 <- trial %>% select(age, grade, response, trt) # summarize the data with our package Table1 <- trial2 %>% tbl_summary(by = trt) %>% add_n() %>% add_p() %>% modify_header(label = "**Variable**") %>% bold_labels() ``` ]] .pull-right[ .small[ <div id="zkruhyzsiv" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>html { font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif; } #zkruhyzsiv .gt_table { display: table; border-collapse: collapse; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; 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text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #zkruhyzsiv .gt_column_spanner_outer:first-child { padding-left: 0; } #zkruhyzsiv .gt_column_spanner_outer:last-child { padding-right: 0; } #zkruhyzsiv .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #zkruhyzsiv .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; } #zkruhyzsiv .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #zkruhyzsiv .gt_from_md > :first-child { margin-top: 0; } #zkruhyzsiv .gt_from_md > :last-child { margin-bottom: 0; } #zkruhyzsiv .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #zkruhyzsiv .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #zkruhyzsiv .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #zkruhyzsiv .gt_row_group_first td { border-top-width: 2px; } #zkruhyzsiv .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #zkruhyzsiv .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #zkruhyzsiv .gt_first_summary_row.thick { border-top-width: 2px; } #zkruhyzsiv .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #zkruhyzsiv .gt_grand_summary_row { color: #333333; 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padding-left: 5px; padding-right: 5px; } #zkruhyzsiv .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #zkruhyzsiv .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #zkruhyzsiv .gt_left { text-align: left; } #zkruhyzsiv .gt_center { text-align: center; } #zkruhyzsiv .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #zkruhyzsiv .gt_font_normal { font-weight: normal; } #zkruhyzsiv .gt_font_bold { font-weight: bold; } #zkruhyzsiv .gt_font_italic { font-style: italic; } #zkruhyzsiv .gt_super { font-size: 65%; } #zkruhyzsiv .gt_footnote_marks { font-style: italic; font-weight: normal; font-size: 75%; vertical-align: 0.4em; } #zkruhyzsiv .gt_asterisk { font-size: 100%; vertical-align: 0; } #zkruhyzsiv .gt_slash_mark { font-size: 0.7em; line-height: 0.7em; vertical-align: 0.15em; } #zkruhyzsiv .gt_fraction_numerator { font-size: 0.6em; line-height: 0.6em; vertical-align: 0.45em; } #zkruhyzsiv .gt_fraction_denominator { font-size: 0.6em; line-height: 0.6em; vertical-align: -0.05em; } </style> <table class="gt_table"> <thead class="gt_col_headings"> <tr> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1"><strong>Variable</strong></th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>N</strong></th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>Drug A</strong>, N = 98<sup class="gt_footnote_marks">1</sup></th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>Drug B</strong>, N = 102<sup class="gt_footnote_marks">1</sup></th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>p-value</strong><sup class="gt_footnote_marks">2</sup></th> </tr> </thead> <tbody class="gt_table_body"> <tr><td class="gt_row gt_left" style="font-weight: bold;">Age</td> <td class="gt_row gt_center">189</td> <td class="gt_row gt_center">46 (37, 59)</td> <td class="gt_row gt_center">48 (39, 56)</td> <td class="gt_row gt_center">0.7</td></tr> <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Unknown</td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center">7</td> <td class="gt_row gt_center">4</td> <td class="gt_row gt_center"></td></tr> <tr><td class="gt_row gt_left" style="font-weight: bold;">Grade</td> <td class="gt_row gt_center">200</td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center">0.9</td></tr> <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">I</td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center">35 (36%)</td> <td class="gt_row gt_center">33 (32%)</td> <td class="gt_row gt_center"></td></tr> <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">II</td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center">32 (33%)</td> <td class="gt_row gt_center">36 (35%)</td> <td class="gt_row gt_center"></td></tr> <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">III</td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center">31 (32%)</td> <td class="gt_row gt_center">33 (32%)</td> <td class="gt_row gt_center"></td></tr> <tr><td class="gt_row gt_left" style="font-weight: bold;">Tumor Response</td> <td class="gt_row gt_center">193</td> <td class="gt_row gt_center">28 (29%)</td> <td class="gt_row gt_center">33 (34%)</td> <td class="gt_row gt_center">0.5</td></tr> <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Unknown</td> <td class="gt_row gt_center"></td> <td class="gt_row gt_center">3</td> <td class="gt_row gt_center">4</td> <td class="gt_row gt_center"></td></tr> </tbody> <tfoot class="gt_footnotes"> <tr> <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks">1</sup> Median (IQR); n (%)</td> </tr> <tr> <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks">2</sup> Wilcoxon rank sum test; Pearson's Chi-squared test</td> </tr> </tfoot> </table> </div> ]] --- # Example cont'd .pull-left[ .small[ ```r library(huxtable) trial2 %>% cross_tab(trt ~ ., method = 2) %>% theme_pubh() ``` ]] .pull-right[ .small[ <table class="huxtable" style="border-collapse: collapse; border: 0px; margin-bottom: 2em; margin-top: 2em; width: 80%; margin-left: auto; margin-right: auto; " id="tab:unnamed-chunk-9"> <col><col><col><col><tr> <th colspan="2" style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;"> </th><th style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;"> </th><th style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;"> </th></tr> <tr> <th style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;"> </th><th style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;">Drug A</th><th style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;">Drug B</th><th style="vertical-align: top; text-align: center; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0pt 0pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: bold;">Total</th></tr> <tr> <td style="vertical-align: top; text-align: center; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td><td style="vertical-align: top; text-align: center; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">(N=98)</td><td style="vertical-align: top; text-align: center; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">(N=102)</td><td style="vertical-align: top; text-align: center; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">(N=200)</td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: bold;">Age </td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">46.0 [37.0;59.0]</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">48.0 [39.0;56.0]</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">47.0 [38.0;57.0]</td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">Grade </td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"> - I </td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">35 (35.7%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">33 (32.4%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">68 (34.0%)</td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"> - II </td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">32 (32.7%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">36 (35.3%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">68 (34.0%)</td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"> - III </td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">31 (31.6%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">33 (32.4%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">64 (32.0%)</td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">Tumor Response</td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"></td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"> - 0 </td><td style="vertical-align: top; text-align: right; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">67 (70.5%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">65 (66.3%)</td><td style="vertical-align: top; text-align: left; white-space: normal; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">132 (68.4%)</td></tr> <tr> <td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: normal;"> - 1 </td><td style="vertical-align: top; text-align: right; white-space: normal; border-style: solid solid solid solid; border-width: 0pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">28 (29.5%)</td><td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">33 (33.7%)</td><td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0pt 0pt 0.4pt 0pt; padding: 3pt 6pt 3pt 6pt; font-weight: normal;">61 (31.6%)</td></tr> </table> ]] --- # Documents **HTML document** - The very original version of Markdown was invented mainly to write HTML content more easily. - To create an HTML document from R Markdown, you specify the html_document output format in the YAML metadata of your document: ```{} --- title: R markdown author: Yebelay B date: 2022-07-01 output: html_document: toc: true toc_depth: 2 --- ``` - You can add a table of contents using the toc option and specify the depth of headers that it applies to using the `toc_depth` option. --- # Section numbering - You can add section numbering to headers using the `number_sections` option. ```{} --- output: html_document: toc: true number_sections: true --- ``` - If the table of contents depth is not explicitly specified, it defaults to 3 (meaning that all level 1, 2, and 3 headers will be included in the table of contents). --- # Appearance and style - There are several options that control the appearance of HTML documents: theme specifies include + default, cerulean, journal, flatly, readable, spacelab, united, cosmo, lumen, paper, sandstone, simplex, and yeti. - highlight specifies the syntax highlighting style. - Supported styles include default , tango , pygments , kate , monochrome , espresso , zenburn, haddock, and textmate. Pass null to prevent syntax highlighting. ```{} --- output: html_document: theme: united highlight: tango --- ``` --- # Custom CSS - You can add your own CSS to an HTML document using the css option: ```{} --- output: html_document: css: styles.css --- ``` - If you want to provide all of the styles for the document from your own CSS you set the theme (and potentially highlight ) to null: ```{} --- output: html_document: theme: null highlight: null css: styles.css --- ``` --- # Figure options - There are a number of options that affect the output of figures within HTML documents: fig_width and fig_height can be used to control the default figure width and height (7x5 is used by default). - `fig_retina` specifies the scaling to perform for retina displays (defaults to 2, which currently works for all widely used retina displays). Set to null to prevent retina scaling. - `fig_caption` controls whether figures are rendered with captions. ```{} --- title: " R markdown " output: html_document: fig_width: 7 fig_height: 6 fig_caption: true --- ``` --- # Data frame printing - You can enhance the default display of data frames via the `df_print` option. - The possible values of the `df_print` option for the `html_document` format. - **default** : Call the `print.data.frame` generic method - **kable** : Use the `knitr::kable` function - **Tibble** : Use the `tibble::print.tbl_df` function - **Paged** : Use `rmarkdown::print.paged_df` to create a pageable table --- # Paged printing - When the `df_print` option is set to paged, tables are printed as HTML tables with support for pagination over rows and columns. ```{} --- title: "Motor Trend Car Road Tests" output: html_document: df_print: paged --- ``` ```r mtcars ``` --- - `max.print:` The number of rows to print. - `rows.print:` The number of rows to display. - `cols.print:` The number of columns to display. - `cols.min.print:` The minimum number of columns to display. - `pages.print:` The number of pages to display under page navigation. - `paged.print:` When set to FALSE turns off paged tables. - `rownames.print:` When set to FALSE turns off row names. - These options are specified in each chunk like below ```{r, cols.print=3, rows.print=3} mtcars ``` --- # Advanced customization ### Keeping Markdown - When knitr processes an R Markdown input file, it creates a Markdown ( *.md ) file that is subsequently transformed into HTML by Pandoc. - If you want to keep a copy of the Markdown file after rendering, you can do so using the keep_md option: ```{} --- title: "R markdown" output: html_document: keep_md: true --- ``` --- ## Includes - You can do more advanced customization of output by including additional HTML content or by replacing the core Pandoc template entirely. - To include content in the document header or before or after the document body, you use the includes option as follows: ```{} --- output: html_document: includes: in_header: header.html before_body: doc_prefix.html after_body: doc_suffix.html --- ``` --- # PDF document - T to generate PDF output, you will need to install LaTeX or install TinyTeX for Rmarkdwon users. ```r install.packages("tinytex") tinytex::install_tinytex() # install TinyTeX ``` - To create a PDF document from R Markdown, you specify the `pdf_document` output format in the YAML metadata: ```{} --- title: " R markdown " author: Yebelay B date: 2022-04-01 output: pdf_document --- ``` - Within R Markdown documents that generate PDF output, you can use raw LaTeX, and even define LaTeX macros. --- You can add section numbering to headers using the number_sections option: ```{} --- title: " R markdown " output: pdf_document: toc: true number_sections: true --- ``` If you are familiar with LaTeX, number_sections: true means `\section{}` , and number_sections: false means `\section*{}` for sections in LaTeX (it also applies to other levels of sections such as `\chapter{}` , and `\subsection{}` ). --- ## Figure options - There are a number of options that affect the output of figures within PDF documents: `fig_width` and `fig_height` can be used to control the default figure width and height. - `fig_crop` controls whether the pdfcrop utility, if available in your system, is automatically applied to PDF figures. - If your graphics device is postscript , we recommend that you disable this feature. - `fig_caption` controls whether figures are rendered with captions. ```{} --- output: pdf_document: fig_width: 7 fig_height: 6 fig_caption: true --- ``` --- # Data frame printing - You can enhance the default display of data frames via the df_print option. - Valid values are presented - The possible values of the df_print option for the pdf_document format. - `default`: Call the print.data.frame generic method - `kable`: Use the knitr::kable() function - `tibble`: Use the tibble::print.tbl_df() function ```{} --- title: " R markdown " output: pdf_document: df_print: kable --- ``` --- # Syntax highlighting - The highlight option specifies the syntax highlighting style. - Its usage in pdf_document is the same as html_document. ```{} --- title: " R markdown " output: pdf_document: highlight: tango --- ``` **LaTeX options** - Many aspects of the LaTeX template used to create PDF documents can be customized using top-level YAML metadata. ```{} --- title: "Introduction to Rmarkdown" output: pdf_document fontsize: 11pt geometry: margin=1in --- ``` --- - Available top-level YAML metadata variables for LaTeX output. * `lang`: Document language code * `fontsize`: Font size (e.g., 10pt , 11pt , or 12pt ) * `documentclass`: LaTeX document class (e.g., article ) * `classoption`: Options for documentclass (e.g., oneside ) * `geometry`: Options for geometry class (e.g., margin=1in ) * `mainfont, sansfont,monofont, mathfont`: Document fonts and works only with xelatex and lualatex. * `linkcolor, urlcolor,citecolor`: Color for internal, external, and citation links **LaTeX packages for citations** - To use one of these packages, just set the option citation_package to be natbib or biblatex, ```{} --- output: pdf_document: citation_package: natbib --- ``` --- # Advanced customization **LaTeX engine** - By default, PDF documents are rendered using pdflatex. - You can specify an alternate engine using the latex_engine option. Available engines are pdflatex , xelatex , and lualatex . ```{} --- title: " R markdown " output: pdf_document: latex_engine: xelatex --- ``` - The main reasons you may want to use xelatex or lualatex are: + (1) They support Unicode better; + (2) It is easier to make use of system fonts. --- **Includes** - You can do more advanced customization of PDF output by including additional LaTeX directives and/or content or by replacing the core Pandoc template entirely. - To include content in the document header or before/after the document body, you use the includes option as follows ```{} --- title: " R markdown " output: pdf_document: includes: in_header: preamble.tex before_body: doc-prefix.tex after_body: doc-suffix.tex --- ``` --- # Word document - To create a Word document from R Markdown, you specify the word_document output format in the YAML metadata of your document ```{} --- title: " R markdown " author: Yebelay B date: April 01, 2022 output: word_document --- ``` - The most notable feature of Word documents is the Word template, which is also known as the "style reference document". - You can specify a document to be used as a style reference in producing a *.docx file (a Word document). - This will allow you to customize things such as margins and other formatting characteristics. --- - For best results, the reference document should be a modified version of a .docx file produced using rmarkdown or Pandoc. - The path of such a document can be passed to the reference_docx argument of the word_document format. Pass "default" to use the default styles. ```{} --- title: " R markdown " output: word_document: reference_docx: my-styles.docx --- ``` - For more on how to create and use a reference document, you may watch this short video: <https://vimeo.com/110804387>, or read this detailed article: <https://rmarkdown.rstudio.com/articles_docx.html>. --- # Presentations - For documents, the basic units are often sections. - For presentations, the basic units are slides. - A section in the Markdown source document often indicates a new slide in the presentation formats. - In this chapter, we introduce the built-in presentation formats in the rmarkdown package. ## Beamer presentation - To create a Beamer presentation from R Markdown, you specify the `beamer_presentation` output format in the `YAML metadata` of your document. - You can create a slide show broken up into sections by using the `# and ##` heading tags (you can also create a new slide without a header using a horizontal rule `( --- )`. --- ```{} --- title: "Introduction to R Markdown" author: "Yebelay Berelie" date: '2022-04-01' output: "beamer_presentation" --- ``` ```{} # In the morning ## Getting up - Turn off alarm - Get out of bed ```{r, cars, fig.cap="A scatterplot.", echo=FALSE}`''` plot(cars) ``` - Within R Markdown documents that generate PDF output, you can use raw LaTeX and even define LaTeX macros. --- # Themes - You can specify Beamer themes using the theme, colortheme, and fonttheme options. ```{} --- output: beamer_presentation: theme: "AnnArbor" colortheme: "dolphin" fonttheme: "structurebold" --- ``` - You can find a list of possible themes and color themes at <https://hartwork.org/beamer-theme-matrix/>. --- # Thank You!!