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Lesson5_rmd.md

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<script type="text/x-mathjax-config"> MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "all"} } }); </script>

Date: 2019-10-28 R version: 3.5.0 *Corresponding author: Your email here

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

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′=γ(t − v**x/c2), to appear within text lines.

Create links to your website.

Make footnotes[1].

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

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

The raw Rmd file also has the code for inserting user comments.

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

Define equations

Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum (π) and energy (Ej) having amplitudes a(π, Ej) (from [1]). $$ \phi n(r,t) = \sum_{i, j} a(p_{i},E_{j}) e^{ \frac{i} {h} (p_{i} \cdot r - E_{j}t) } $$  

Create, alter, and embed plots

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

Show plots with associated code

suppressWarnings(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 the output document from RMarkdown.

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
(unit)
L structural length cm
ee scaled reserve density J (cm3)
D host development ---
RH energy in reproduction buffer J

Use buttons or tabs for sub-chapters

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 ...

More tables

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

Embed code from different languages

This is R code

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

echo "Hello Bash!"
pwd # check working dir
git init # initialise git

Octave (and MATLAB from the RMatlab package).

RMatlab documentation.

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

<!-- 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

# 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

$('.title').css('color', 'red')

Python

x = 'hello, python world!'
print(x.split(' '))

Here's a complete list of available languages

names(knitr::knit_engines$get())
##  [1] "awk"       "bash"      "coffee"    "gawk"      "groovy"   
##  [6] "haskell"   "lein"      "mysql"     "node"      "octave"   
## [11] "perl"      "psql"      "Rscript"   "ruby"      "sas"      
## [16] "scala"     "sed"       "sh"        "stata"     "zsh"      
## [21] "highlight" "Rcpp"      "tikz"      "dot"       "c"        
## [26] "fortran"   "fortran95" "asy"       "cat"       "asis"     
## [31] "stan"      "block"     "block2"    "js"        "css"      
## [36] "sql"       "go"        "python"    "julia"     "sass"     
## [41] "scss"

References

[1] Efthimiades, S., Physical meaning and derivation of Schrodinger and Dirac equations, Department of Natural Sciences, Fordham University, doi: d34464566.

[1] Here is the footnote you created earlier, automatically formatted