4-Workshop_examples.Rmd

---
title: "Workshop Examples"
author: "Melissa Monk"
date: ''
output:
  pdf_document:
    fig_caption: yes
    includes:
      in_header: header.tex
    keep_tex: yes
    number_sections: yes
    toc: yes
    toc_depth: 4
  html_document:
    toc: yes
    toc_depth: '4'
documentclass: article
fontsize: 12pt
geometry: margin=1in
link-citations: yes
csl: CJFAS.csl
bibliography: BibFile.bib
---

```{r global_options, include=FALSE}
    # set global options for R code chunks: echo=FALSE (don't include source code); 
    # warning=FALSE (suppress R warnings); message=FALSE (suppress R messages)
    # eval = TRUE is default
     knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)

      library(xtable)
      options(xtable.comment = FALSE)  # turns off xtable comments
```

Change some of the YAML settings to see what happens.

Notice, the down arrow at line 25.  If you click this, you can hide the R code chunk.  This is helpful when working through a large document.

On the right side of the R code chunk are additional options, Settings, a down arrow (run previous R code chunks), and a green play button (runs the current chunk).  It's handy to check R code chunks as you go and to debug.  Within the Assessment template, this is also the only way to see variables in your Environment. 



# Epmhasis (R markdown and LaTeX)

*Sebastes*  
_Sebastes_

\emph{Sebastes}

**_Sebastes_**  
__Sebastes__  
\emph{\textbf{Sebastes}}  



# Headers

## Subhead 2
### Subhead 3
#### Subhead 4

*Subhead 5*


# Commenting

<!-- comment here  -->



# Links

[Github](www.github.com)



# Lists

R Markdown are finicky with spacing...     

* Item 1
* Item 2
    + Item 2a
    + Item 2b


 * Item 1
 * Item 2
    + Item 2a
    + Item 2b




Bulleted list
\begin{itemize}[noitemsep,nolistsep,topsep=0pt]

\item \href{https://git-scm.com/book/en/v2/Getting-Started-Installing-Git}{Git}

\item \href{https://cran.r-project.org/bin/windows/base/}{R}

\end{itemize}



Numbered list
\begin{enumerate}[noitemsep,nolistsep,topsep=0pt]

\item \href{https://git-scm.com/book/en/v2/Getting-Started-Installing-Git}{Git}

\item \href{https://cran.r-project.org/bin/windows/base/}{R} 

\end{enumerate}


# References and Citations

We can reference a document section, see Lists in Section \ref{lists}.

Citations: [@Love2002;@Love2002]

Love [-@Love2002]


#Figure from a file
You can use any file extension, including PDFs

![Here's my caption \label{fig:fig_example}](RMarkdownFLow.png)

![Here's my caption 2 \label{fig:fig_example2}](./Figures/RMarkdownFLow1.png)

Figures are referenced using LaTeX syntax \ref{fig:fig_example}.

Put a space between the ] and ( above. Knit the document.  


Now try adding your own picture to the directory, adding it in here, and referencing it.



# R code chunks

You can embed an R code chunk like this:

```{r cars}
summary(cars)

#adsflkasjfaslkdfj
```


Play with the r code chunk options, echo=TRUE, include=FALSE, results='asis'


\FloatBarrier


# Figure from R code chunk

You can also embed plots, for example:

```{r pressure, fig.cap="Figure of something  at $40^\\circ 10^\\prime$. \\label{fig:pressure}"}
plot(pressure)
```

This is inline math mode for Latex  $40^\circ 10^\prime$  

Note, you need extra \\s when using LaTeX syntax within an R code chunk, or when inserting a backslash in R markdown.  The same goes with percent signs and any other LaTeX reserved symbol. You can use  a %  $\%$ 


We can now reference Figure \ref{fig:pressure}.  Note where this text ends up.

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

\FloatBarrier


#Tables



```{r, results='asis'}
#, results='asis', echo=FALSE, include=FALSE, message=FALSE, warning=FALSE
Tab = read.csv('Table_example.csv')

Tab_example = xtable(Tab, 
                   caption=c('This is where you write your caption'),
                   label = 'tab:Table_example',
                   digits=0)  

align(Tab_example) = 'lcrcrcrcrcrc'

print(Tab_example, include.rownames = FALSE, caption.placement = 'top', scalebox=.7)

# print option to try, scalebox = 0.7
# add alignment


```





Try changing the R chunk options above. 

We can now reference Table \ref{tab:Table_example}.

Now, try putting the R code chunk within and HTML comment.



# Create you own table
Either create a .csv file or copy one into the repo folder on your computer.

Now, create a table!







#Math mode

You can use LaTeX math mode both inline and for inserting equations. It's handy for using inline math mode for management measure and lat/long.

Inline looks like this:  $SPR_{40\%}$  
*Note the % sign has a \ when used in math mode, but not in R markdown text.

To get degrees and minutes type: $40^\circ 10^\prime$   



#References