Lesson5_rmd.Rmd

---
title: Using RMarkdown for reproducible and neat documents 
author: |
 | Your name here 
 |  
 | Your affiliation here
output:
  html_document: # html options 
    highlight: tango
    code_folding: show
    toc: yes
    toc_depth: 4
    number_sections: no
    toc_float: yes
  pdf_document: # pdf options
    highlight: tango
    template: null
    toc: yes
    toc_depth: 4
    number_sections: false
    fig_width: 4
    fig_height: 5
    fig_caption: true
    df_print: tibble 
    latex_engine: xelatex #pdflatex # lualatex
  word_document: # ms word options
    highlight: tango
    keep_md: yes
    pandoc_args: --smart
    toc: yes
  md_document: # markdown options
    variant: markdown_github 
inludes:
  before_body: before_body.tex
subtitle: 
tags:
- nothing
- nothingness
params: 
  email: "your email here"
  date: !r Sys.Date()
  version: !r getRversion()
classoption: portrait
---

<!-- this enables math encoding in the knitted documents  -->
<script type="text/x-mathjax-config">
  MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "all"} } });
</script>

```{r, set-options, echo = F, cache = T,message=F}
options(width=100)
knitr::opts_chunk$set(
 eval = TRUE, # run all code
 echo = TRUE, # show code chunks in output 
 tidy=TRUE, # make output as tidy
 message = FALSE,  # mask all messages
 warning = FALSE, # mask all warnings 
 size="small" # set code chunk size
)

### run this once  
# tinytex::install_tinytex()

packages <- c("dplyr","ggplot2","plotly","DT","htmlwidgets")

ppp <- lapply(packages,require,character.only=T)
names(ppp) <- packages
if(any(ppp==F)){cbind(packages,ppp);cat("\n\n\n ---> Check packages are loaded properly <--- \n\n\n")}

# knitr::opts_knit$set(root.dir=paste0(params$dir,"/")) # set working dir
# setwd(paste0(params$dir,"/")) # for running just in R not knitr
```

\newpage   

Date: `r params$date`  
R version: `r params$version`  
*Corresponding author: `r params$email`  

\newpage    
 
# Overview

This document showcases how to create and use `RMarkdown` documents.    

You can write in **bold** and *italicised* text (in _two_ different __ways__).  

You can write in-line `code` if you want to differentiate between when you are typing normally or highlighting `model parameters`, for example.    

Equations like this $t' = \gamma(t - vx/c^{2})$, to appear within text lines.  

Create links to your [website](https://github.com/darwinanddavis).  

Make footnotes^[Here is the footnote you created earlier, automatically formatted].    

# You can easily create headings. This is the same font size as the 'Overview' above    

## Then move down in font size    

### Like this subheading  

#### And this fourth order heading   

Insert line breaks <br>  between text like this    

Insert a horizontal line break using five asterisks ('*****')  

*****        

(There is also a page break here. Best seen in PDF. Check the raw Rmd file to see the code)  

The raw Rmd file also has the code for inserting user comments, 
<!-- To do this, place the cursor on the text and type 'Cmd/Ctl + Shift + C' -->

\newpage    

## Define equations      

Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum ($\pi$) and energy ($Ej$) having amplitudes $a(\pi,Ej)$ (from^[Efthimiades, S., Physical meaning and derivation of Schrodinger and Dirac equations, Department of Natural Sciences, Fordham University. [doi: d34464566](https://arxiv.org/vc/quant-ph/papers/0607/0607001v1.pdf).])     

$$  
\phi n(r,t) =  
  \sum_{i, j} a(p_{i},E_{j})
  e^{
  \frac{i}
  {h}
  (p_{i} \cdot r - E_{j}t) 
}
$$
\    

## Embed images/gifs:  

![Great power is pretty boring](https://github.com/darwinanddavis/EmoRyCodingClub/raw/master/docs/img/opm.jpg).        

\newpage  

## Create, alter, and embed plots    
```{r,echo=F,eval=T}
set.seed(12)
N <- 2000
rr <- rnorm(N)
plot(rr,pch=20,main="Some random data")
```

Figure 1. Example of a stock plot embedded into a PDF from RMarkdown.   

\newpage  

## Show plots with associated code  
```{r,echo=T,eval=T}
require(viridis)
bm <- 0
par(las=1,bty="n"); xlim <- c(-5,5);ylim <- c(0,0.5)
set.seed(12)
N <- 2000
rr <- rnorm(N); rr2 <- rnorm(N^2); rr3 <- rnorm(N+0.3)
rrd <- density(rr);rrd2 <- density(rr2);rrd3 <- density(rr3)
main <- paste0(N," points but plot better");xlab <- "Points in space"
if(bm==1){
  layout(matrix(c(rep(1,3),2:4), 2, 3, byrow = TRUE));sc <- 1
  plot(rr,las=1,bty="n",col=adjustcolor(viridis(N),0.5),pch=20,cex=runif(10,1,5),
       main=main,xlab=xlab)
for(r in list(rrd,rrd2,rrd3)){
  plot(r,xlim=xlim,ylim=ylim,main="")
  polygon(r,col=adjustcolor(viridis(250)[sc],0.5),border=viridis(250)[sc]);sc <- sc+100}
}else{par(mfrow=c(1,1))
  plot(rr,las=1,bty="n",col=adjustcolor(viridis(N),0.5),pch=20,cex=runif(10,1,5),
       main=main,xlab=xlab)}
```

Figure 2. Example of a plot with improved graphics and its associated code embedded into a PDF from RMarkdown. 

\newpage  

## And tables  

Table 1. Definitions of model parameters for individual hosts and **parasites**. Dimensions and units: -, dimensionless; cm, centimetres; J, Joules; L, length.    

| Parameter | Definition | Dimension<br/>(unit) | 
| :---: | :--- | ---: |    
| _L_ | structural length | cm |
| _ee_ | scaled reserve density | J (cm^3^) |
| _D_ | host development | --- |
| _RH_ | energy in reproduction buffer| J |

\newpage  



## Use buttons or tabs for sub-chapters {.tabset .tabset-fade .tabset-pills}  

### Chapter 1  
*Then you can add whatever you want here* like you would normally write in the `Rmd` file.  
\  

### Chapter 2 (with new code)  
Here's an Easter egg for you ...  

```{r,echo=F,message=F}
lapply(list(require(plotly),require(ggplot2)),suppressWarnings)
nn <- 100
p <- ggplot() +
  geom_point(aes(rnorm(nn),sample(nn/2,nn,replace=T)),colour = rainbow(nn),size=sample(nn/2,nn,replace=T)/5,alpha=abs(rnorm(nn))) +
  labs(x = "Random normally distributed data",
       y = "Sampled integers") +
  theme_minimal()
ggplotly(p)
```

### More tables   
Here's a new way of creating tables using the `DT` package  

```{r,cache=T,warning=F, echo=F}
lapply(list(require(DT),require(htmlwidgets)),suppressWarnings)
caption <- "Table 1. The 'mtcars' dataset presented in a datatable. Try editing the columns and cells." 
datatable(mtcars, 
          rownames = T, 
          filter="top", 
          options = list(pageLength = 5, scrollX=T),
          class = "cell-border stripe",
          editable = "cell",
          caption = caption 
          )
```


***      

## Embed code from different languages  

### This is `R` code  
```{r, eval=F}
if(pck==1){
  p<-c("rJava", "RNetLogo"); remove.packages(p)
  # then install rJava and RNetLogo from source
  install.packages("rJava", repos = "https://cran.r-project.org/")
  install.packages("RNetLogo", repos = "https://cran.r-project.org/")
}
```

### `shell/bash`  
```{bash, eval=F}
echo "Hello Bash!"  
pwd # check working dir
git init # initialise git
```

### Octave (and MATLAB from the `RMatlab` package).  
[`RMatlab documentation`](https://cran.r-project.org/web/packages/R.matlab/index.html).  
```{octave, eval=F}
b = [4; 9; 2] # Column vector
A = [ 3 4 5;
      1 3 1;
      3 5 9 ]
x = A \ b     # Solve the system Ax = b
```

### HTML    
```{html, eval=F}
<!-- links-->
		<div class="footer">
			<a href="dd_feed.html" 
			class="transition fade_in">
				Latest post
			</a>
			&nbsp; &nbsp; &nbsp;
			<a href="dd_contact.html" 
			class="transition fade_in">
				Contact
			</a>
			&nbsp; &nbsp; &nbsp;
			<a href="dd_subscribe.html"
			class="transition fade_in">
				Subscribe
			</a>
		</div>
```

### CSS
```{css, eval=F}
# custom code for the tabs in this file
.btn {
    border-width: 0 0px 0px 0px;
    font-weight: normal;
    text-transform: ;
}
.btn-default {
    color: #f08080;
    background-color: #ffffff;
    border-color: #ffffff;
}
```

### Javascript to access `html` and `css`  
```{js, eval=F}
$('.title').css('color', 'red')
```

### Python  
```{python, eval=F}
x = 'hello, python world!'
print(x.split(' '))
```

### Here's a complete list of available languages  
```{r eval=T}
names(knitr::knit_engines$get())
```