Lesson5_rmd.Rmd

---
title: "Using RMarkdown for reproducible and neat documents"
author: |
  | Your name here
  | Your affiliation here
params:
  date: !r Sys.Date()
  email: Your email here
  version: !r getRversion()
output:
  pdf_document:
    toc: yes
    toc_depth: '4'
    includes:
      in_header:  # add .tex file with header content
    highlight: tango
    template: null
    number_sections: false
    fig_width: 4
    fig_height: 5
    fig_caption: true
    df_print: tibble 
    # citation_package: biblatex # natbib
    latex_engine: pdflatex #lualatex #xelatex #pdflatex
    keep_tex: false # keep .tex file in dir 
  html_document:
    code_folding: show
    highlight: tango
    number_sections: no
    toc: yes
    toc_depth: 4
    toc_float: yes
tags:
  classoption: article
  linkcolor: blue
  urlcolor: blue
---

<!-- 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=25,tinytex.verbose = TRUE, width.cutoff=25)
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,
 tidy.opts=list(width.cutoff=25) # set width of code chunks in output
)

### run this once  
# tinytex::install_tinytex()
# require(tinytex)
# install.packages("pacman")
# require(pacman)

suppressWarnings(pacman::p_load(dplyr,ggplot2,plotly,DT,htmlwidgets,viridis,reticulate))
# update.packages("htmlwidgets")


### updating latex pcks (june 2020)  
# update.packages(ask = FALSE, checkBuilt = TRUE) 
# tinytex::tlmgr_update()  # update LaTeX packages
# tinytex::reinstall_tinytex() # if lazy load corrupt error, restart r and try again
# 'Lesson5_rmd.md' file overrides PDF rendering, so check this file for possible typos/errors  

# render by command line
# for word
# rmarkdown::render("Lesson5_rmd.Rmd", output_format = "word_document")
# for pdf after setting eval=T in Embed imgs/pdf code chunk 
# rmarkdown::render("Lesson5_rmd.Rmd", output_format = "pdf_document")

# ------ potential solution for text wrapping in code chunks for PDF
# set text/limits (N) within code chunks using str_wrap(width=N)
# rep("String with trailing,
# middle, and leading white space\t String with trailing,
#     middle, and leading white space\t ",10) %>%  
# stringr::str_wrap(width=10)

```

\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 easily create headings. This is a first order heading.

## Then move down in heading order size

### Like this subheading

#### And this fourth order heading

<!-- To create a new line of text, insert two spaces after every line in the `Rmd` file, then hit _ENTER_. -->

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].

Insert line breaks <br>  between text like this, which works best in large <br> slabs of text

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

<!-- horizontal line  -->  
<!-- *****    -->
  
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' -->

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

<!-- page break  -->
\newpage

## Define equations

Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum ($\pi$) and energy ($E_{j}$) having amplitudes $a(\pi,E_{j})$ (from [[1]](https://www.academia.edu/33763545/Concise_derivation_of_the_Schr%C3%B6dinger_equation)).

$$
\phi n(r,t) =
  \sum_{i, j} a(p_{i},E_{j})
  e^{
    \frac{i}
    {h}
    (p_{i} \cdot r - E_{j}t)
}
$$
\  
<!-- !!! uncheck the below to include images in HTML and word renders -->
<!-- !!! pdf render code is found in the below commmit -->
<!-- ## Embed images/gifs: -->

<!-- ![Great power is pretty boring](https://raw.githubusercontent.com/darwinanddavis/EmoRyCodingClub/master/img/opm.jpg). -->
<!-- code for img in pdf: commit L5 rmd external test final - cmd line pdf/word knit -->

\newpage    

## Create, alter, and embed plots
```{r,echo=F,eval=T}
par(mar=rep(1,4))
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,message=F,width.cutoff=25}
suppressWarnings(require(viridis))
bm <- 1
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 the output document 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}
suppressWarnings(pacman::p_load(plotly,ggplot2))
set.seed(12) # set a number seed for reproducible number results
nn <- 100

random_data <- data.frame("X" = rnorm(nn),
           "Y" = sample(nn/2,nn,replace=T),
           "NN" = nn)

p <- ggplot() +
  geom_point(data=random_data,aes(X,Y,
                 colour=rainbow(nn),
                 size=sample(Y)/5),
                 alpha=abs(rnorm(nn))) +
  labs(x = "Random normally distributed data",
       y = "Sampled integers") +
  theme_minimal() +
  theme(legend.position='none')
ggplotly(p,tooltip=c("X","Y"))

```

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

```{r,cache=T,warning=F, echo=F}
suppressWarnings(pacman::p_load(DT,htmlwidgets))
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}
pck <- 0
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())
```

# References

[1] Efthimiades, S., Physical meaning and derivation of Schrodinger and Dirac equations, Department of Natural Sciences, Fordham University, [doi: d34464566](https://www.academia.edu/33763545/Concise_derivation_of_the_Schr%C3%B6dinger_equation).