index.Rmd

---
title: "Data Science In RStudio"
author: "Andrew P. Lapointe"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
bibliography: styles/LabBible.bib #[book.bib, packages.bib]
csl: styles/spectroscopy-letters.csl
#biblio-style: apalike
link-citations: yes
linkcolor: blue
citecolor: red
urlcolor: blue
github-repo: alapo/learnR
cover-image: "images/cover.png"
description: "This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook."
---

# Index

## Things to add

Signe recommended students run a live tutorial in [swirl](https://swirlstats.com/students.html)

## Documentation for Author

```{r global_options2, include=FALSE}
# setwd("G:/My Drive/Projects/fNIRS_guide/example2/bookdown-demo-master")
# library(knitr)
knitr::opts_chunk$set(fig.align='center',
                      #fig.pos = 'H',
                      eval = FALSE, 
                      fig.path = 'images/',
                      echo = TRUE,
                      warning = FALSE,
                      message = FALSE,
                      include = TRUE,
                      out.width = "100%") # needed or else homer image goes off the page when rendering to pdf

```

```{r, echo=FALSE}
#knitr::include_graphics("G:/My Drive/Projects/fNIRS_guide/example2/bookdown-demo-master/images/cover.png")
# pacman::p_load(readxl,psych,dplyr,ggplot2, apastats, data.table, gridExtra, effects,kableExtra,Hmisc, plotly,grid,captioner,stringr,citr)
```

## Andrew's Notes / Ramblings

To render the book used the following code, you must do this before knitting the GitBook (webpage)

```{r}
bookdown::render_book("index.Rmd", "bookdown::gitbook")
bookdown::render_book("index.Rmd", "bookdown::pdf_book", encoding="UTF-8")
bookdown::render_book("index.Rmd", "bookdown::epub_book")
```

The `_output.yml` contains the header arguments. I would but them here so its cleaner and easier to read the code.

## To Do

-   Is there a way I can have matlab code syntax highlighted properly? Maybe [here](https://dotnet.github.io/docfx/spec/docfx_flavored_markdown.html?tabs=tabid-1%2Ctabid-a)

-   Get Camera to take nice pictures

-   Get example dataset that I can run through

-   Can I export this to github.io? The GitHub Repository for this guidebook can be found [here](https://github.com/alapo/fnirs)

-   Add highlight arg to `_output.yml`

-   Upload the MATLAB packages required to GitHub directory


-   [ ] Implement [Open Review](https://benmarwick.github.io/bookdown-ort/intro.html) which will allow people to make comments. An example can be seen [here](https://benmarwick.github.io/bookdown-ort/)

-   [x] Finish my changes

-   [ ] Push my commits to GitHub

-   [ ] Open a pull request

-   [x] Cleaned the main directory to make it easier to interpret for beginners

For Chapter \@ref(datawrangling)

-   [ ] steal logo from [here](https://bioconnector.github.io/workshops/r-dplyr-yeast.html). It would be great to have a logo here that was cowboy themed
-   [ ] [These](https://github.com/gadenbuie/tidyexplain) animations would be great at explaining some key concepts

## Title word cloud

Titles: inquiry-based R for researchers in a hurry Reproducible science

## Copy from Chapter 1 Example

You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter `\@ref(intro)`. If you do not manually label them, there will be automatic labels anyway, e.g., Chapter `\@ref(methods)`.

Figures and tables with captions will be placed in `figure` and `table` environments, respectively.

```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'}
par(mar = c(4, 4, .1, .1))
plot(pressure, type = 'b', pch = 19)
```

Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure `\@ref(fig:nice-fig)`. Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table `\@ref(tab:nice-tab)`.

```{r nice-tab, tidy=FALSE}
knitr::kable(
  head(iris, 20), caption = 'Here is a nice table!',
  booktabs = TRUE
)
```

You can write citations, too. For example, we are using the **bookdown** package in this sample book, which was built on top of R Markdown and **knitr** .

## MATLAB Highlighting

``` {.matlab}
% This is a comment in MATLAB
function y = average(x)
if ~isvector(x)
   error('Input must be a vector')
end
y = sum(x)/length(x); 
end
```

So could [this](https://amber.rbind.io/blog/2017/11/15/syntax-highlighting/)

## CSS / Templates

-	https://bookdown.org/yihui/bookdown/templates.html
-	[CSS course](https://rstudio4edu.github.io/rstudio4edu-book/css-crash.html#css-crash)
-	[Blogdown Themes](https://bookdown.org/yihui/blogdown/themes.html)

## Misc code/data

    gitbook(fig_caption = TRUE, number_sections = TRUE, self_contained = FALSE, 
       lib_dir = "libs", pandoc_args = NULL, ..., template = "default", 
       split_by = c("chapter", "chapter+number", "section", "section+number", 
           "rmd", "none"), split_bib = TRUE, config = list(), table_css = TRUE)

## Other Resources

Book called [Just Enough R](https://benwhalley.github.io/just-enough-r/datasets-dataframes.html)

To test the normality of your data you can use a few different methods

-   <http://www.sthda.com/english/wiki/normality-test-in-r>
-   <https://rstudio-pubs-static.s3.amazonaws.com/2002_1f803b2bc84c46008d3599a07867a95a.html>

1.  Plot your data
2.  Check skewness and kurtosis
3.  Shapiro test.

There should be a section on general access to your df. How to manipulate it effectively (perhaps in the data wrangling section) This would include things like using `df$colname to access a column`

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