Template for using R 'xaringan' package in a 'rosr' project

In rosr: Create Reproducible Research Projects

# Markdown Syntax
# - FORMAT  : *italic*, **bold**, `code`, ~subscript~, ^superscript^, > quote, ^[footnote] # - [](hyperlink)
# - EQUATION: $inline equation$, $$display equation$$, \begin{equation} (\#eq:eq-label)\end(equation), \@ref(eq:eq-label)
# - CITATION: [@bib-entry1; @bib-entry2]
# - FIGURE  : ![](image link), knitr::include_graphics(), \@ref(fig:fig1)
# - TABLE   : knitr::kable(), \@ref(tab:tab1)

oldwd <- getwd()
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE) 
knitr::opts_knit$set(root.dir = dirname(dirname(oldwd)))
require('rosr')

options(htmltools.dir.version = FALSE)

Introduction

This template comes from the R 'xaringan' package and modified by Peng Zhao. It intends to show how to cross refer other files in a 'rosr' project, rather than to show how to use the original template.

---

Methods

Set up

Firstly, we switch off the codes and message display in a manuscript, and set the working directory to the rosr project.

oldwd <- getwd()
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE) 
knitr::opts_knit$set(root.dir = dirname(dirname(oldwd)))

---

Load data

Now we can use the relative path. Let's sync the bib file and run an R script.

source('R/rosr.R')

---

Numbers

As we just ran the source() command, we can use the results from the R/rosr.R. For example, the mean temperature is r temperature degree.

---

Tables

We could insert a table.

aq$Month <- as.factor(aq$Month)
DT::datatable(
  aq, 
  fillContainer = FALSE, options = list(pageLength = 4)
)

---

Figures

Plot the data in a diagram.

plot(aq)

---

We could insert an image.

fig('rosr_R.png')

---

Equations

Use the rosr::eq() function to insert an equation. See Eq. \@ref(eq:sd).

eqs <- 'equation/rosr-eq.Rmd'
eq(eqs, label = 'sd')

Well, xaringan seems not supporting equation labels or cross-reference. Use eq(style = 'display') instead.

eq(eqs, label = 'em', style = 'display')

rosr documentation built on July 2, 2020, 2:28 a.m.