index.Rmd

---
site: bookdown::bookdown_site
title: '`r yaml::read_yaml("_meta.yml")$book_title`'
author: '`r yaml::read_yaml("_meta.yml")$book_author`'
date: "`r format(Sys.Date(), '%d %B %Y')`"
documentclass: article
classoption: 12pt
bibliography: ["book/bib/references.bib", "book/bib/packages.bib"]
link-citations: yes
github-repo: null
---
```{r Setup, message=FALSE, warning=FALSE, include=FALSE}

# Default to show/hide code in output
knitr::opts_chunk$set(echo = FALSE,
                      message = FALSE,
                      warning = FALSE,
                      fig.pos = "tbp",
                      out.extra = "",
                      out.width = "100%",
                      fig.retina = 2,
                      fig.align = "center")
# knitr and kable/kableExtra options
# set before calling library to ensure correct options by default
options(knitr.kable.NA = '')
options(knitr.table.format = "pipe")
options(kableExtra.auto_format = FALSE)

# Tidyverse packages (remove as appropriate)
#library(magrittr)
library(dplyr)
library(tidyr)
library(ggplot2)
library(purrr)
#library(tibble)
library(stringr)
library(forcats)
library(readr)
#library(readxl)
library(broom)

# other packages
#library(fs)
library(glue)
library(janitor)
library(here)
#library(effectsize)
#library(skimr)
library(ggthemr)
#library(PNWColors) # https://github.com/jakelawlor/pnwcolors
# pal <- PNWColors::pnw_palette(name="Sailboat",n=8,type="discrete")
library(ggtext)
#library(ggsignif)
library(patchwork)
#library(ez)
library(conflicted)
# conflicted::conflict_prefer("cooks.distance.influence.merMod", "car")
conflicted::conflict_prefer("set_names", "purrr")
conflicted::conflict_prefer("filter", "dplyr")
library(knitr)
library(kableExtra)

# set plot theme
ggthemr('greyscale', layout = 'minimal')

# set PDF and word variables to FALSE by default; will be overwritten for 
# appropriate output in next chunk or left as-is for working in RStudio
pdf <- FALSE
word <- FALSE

# read chunks in to include from external code sources - 
# just remember that at SOME point, anything to be used in the final output MUST
# be imported into the index or src files somewhere - so any data creation/import
# chunks in the external code also need to be read in before their output will work

analysis_files <- list.files(path=here::here("analysis"),
                    pattern = "^[^_][0-9a-zA-Z-]+.R$", full.names = TRUE)

for (file in analysis_files) {
  knitr::read_chunk(file)
}

```

```{r detect-output, include=FALSE}

# detect current knitr rendering format
# will output as 'bookdown::pdf_document', 'bookdown::word_document' etc

fmt <- rmarkdown::all_output_formats(knitr::current_input())[1]
pdf <- grepl("pdf", fmt)
word <- grepl("word", fmt)
git <- grepl("gitbook", fmt)

```

```{r float-spacing}

# if(pdf) {
#   plot_default <- knit_hooks$get("plot")
#   knit_hooks$set(plot = function(x, options) { 
#     x <- c("\\vspace{20pt}", plot_default(x, options), "\\vspace{20pt}")
#   })
# }

if(pdf) {
  knit_hooks$set(floatspacer = function(before, options, envir) {
      if (before) {
          "\\vspace{20pt}"
      } else {
          "\\vspace{20pt}"
      }
  })
} else {
  knit_hooks$set(floatspacer = function(before, options, envir) {
      if (before) {
          ""
      } else {
          ""
      }
  })
}

```


```{r word-tocs, eval=FALSE, include=FALSE}

# if rendering to .docx, include blank pages with headings for
# table of contents and lists of figures/tables/appendices
if(word) {
  word_toc <- glue::glue('
\\newpage
::: {{custom-style="Title"}}
Table of Contents
:::
\\newpage
::: {{custom-style="Title"}}
List of Figures
:::
\\newpage
::: {{custom-style="Title"}}
List of Tables
:::
\\newpage
::: {{custom-style="Title"}}
List of Appendices
:::
\\newpage
             ')
} else {
  word_toc <- NULL
}

```

```{r}
if (git) {
  knitr::opts_chunk$set(out.width = "50%")
}
```


```{r, child=if (git) here::here('book', 'src', '_preface.Rmd')}
```