template.Rmd

---
title: "Template"
subtitle: "SUBTITLE"
author: "AUTHORS"
date: "`r format(Sys.Date(), '%d %b %Y')`"
output:
  html_document: 
    df_print: paged
    css: stylesheet.css
    number_sections: yes
    toc: yes
    toc_float: true
    toc_depth: 3
    code_folding: show
editor_options:
  chunk_output_type: console
---

```{r setup, echo = TRUE, message=FALSE, warning=FALSE}
# load libraries
library(tidyverse) 
library(latex2exp)

# source all relevant scripting files
source(file.path("scripts", "plotting_functions.R"))

# global knitting options for automatic saving of all plots as .png and .pdf
knitr::opts_chunk$set(
  dev = c("png", "pdf"), fig.keep = "all",
  dev.args = list(pdf = list(encoding = "WinAnsi", useDingbats = FALSE)),
  fig.path = file.path("fig_output", paste0(gsub("\\.[Rr]md", "", knitr::current_input()), "_"))
)
```

# $\LaTeX$ Math

This is just markdown that can include latex math.

$$
\begin{align}
\dot{x} & = \sigma(y-x) \\
\dot{y} & = \rho x - y - xz \\
\dot{z} & = -\beta z + xy
\end{align}
$$

# Data Table

```{r}
as_tibble(iris)
```

# Export Data

```{r}
iris %>% openxlsx::write.xlsx(file.path("data_output", "iris_dataset.xlsx"))
```

# Simple Plot

```{r "simple_plot", fig.width = 8, fig.height = 6}
iris %>% 
  ggplot() +
  aes(x = Sepal.Length, y = Sepal.Width, color = Species) + 
  geom_point()
```

# Polished Plot

```{r "polished_plot", warning=FALSE, fig.width = 8, fig.height = 6}
iris %>% 
  mutate(
    latex_species = as_factor(Species) %>% 
      fct_recode(
        "$\\left(\\frac{\\textbf{setsoa}}{\\beta^2}\\right)$" = "setosa",
        "$\\int_{\\infinity}\\sqrt[2]_{\\textbf{versicolor}}$" = "versicolor")
  ) %>% 
  ggplot() + 
  aes(Sepal.Length, Sepal.Width, color = latex_species) + 
  geom_point() +
  scale_color_discrete(labels = latex_labeller) +
  facet_wrap(~latex_species, labeller = latex_labeller) +
  labs(x = TeX("my x axis $\\delta^{42}X\\,\\[\U2030\\]$")) + 
  theme_figure(text_size = 16)
```