Intro to R for Biologists

log(2)

## [1] 0.6931

log(10)

## [1] 2.303

Fails:

2 + 2*w

Need to define 'w'

w <- 10
2 + 2 * w

## [1] 22

library(lattice)
dat <- read.table('data/ISIT.txt',header=TRUE,sep='\t')
xyplot(Sources~SampleDepth|factor(Station),data=dat,
xlab='Sample Depth',ylab='Sources',
strip=function(bg='white', ...)
strip.default(bg='white',...),
panel=function(x,y){
panel.grid(h=-1,v=2)
I1=order(x)
llines(x[I1],y[I1],col=1)})

It is impossible to remember all the commands and programs!

Therefore, VERY important to:

1. Write SIMPLE code
2. Write many comments describing what the code does:

# a comment

# load libraries/packages
library(lattice)
# read in data
dat <- read.table('data/ISIT.txt',header=TRUE,sep='\t')

# Start plotting:
#   - plot Sources as a function of SampleDepth,
#   - use a panel for each Station
#   - use colour black (col = 1), and 
#   - specify x and y labels (xlab and ylab).
#   - use white background in the boxes that contain station labels

xyplot(Sources~SampleDepth|factor(Station),data=dat,
xlab='Sample Depth',ylab='Sources',
strip=function(bg='white', ...)
strip.default(bg='white',...),
panel=function(x,y){
  # avoid grid lines
  # avoid spaghetti plots
  # plot data as lines (in black)
panel.grid(h=-1,v=2)
I1=order(x)
llines(x[I1],y[I1],col=1)})

• Use spaces to indicate groups of commands
• Use spaces around text

# load libraries/packages
library(lattice)
# read in data
dat <- read.table('data/ISIT.txt', header = TRUE, sep = '\t')

# Start plotting:
#   - plot Sources as a function of SampleDepth,
#   - use a panel for each Station
#   - use colour black (col = 1), and 
#   - specify x and y labels (xlab and ylab).
#   - use white background in the boxes that contain station labels

xyplot(Sources ~ SampleDepth | factor(Station), data = dat,
      xlab = 'Sample Depth', ylab = 'Sources',
      strip = function(bg = 'white', ...)
      strip.default(bg = 'white', ...),
      panel = function(x, y){
        # avoid grid lines
        # avoid spaghetti plots
        # plot data as lines (in black)
        panel.grid(h = -1, v = 2)
        I1 = order(x)
        llines(x[I1], y[I1], col = 1)
      } # close panel()
) # close xyplot

Good style is important because while your code only has one author, it will usually have multiple readers

Hadley Wickham

• an overview
  • Google
  • Hadley Wickham's guide

Text editors use unformatted plain text with no hidden characters or code. Thus, what you paste in to R is what runs. Most text editors also have nice syntax highlighting. Word processors such as MS-Word contain formatted text.

Common ones:

• Notepad
• TINN-R
• WinEdt

Hard-core

• emacs
• vi(m)

NEVER, NEVER M$-Word/equivalent!

It is possible to do graphics that would maybe be faster in Excel ...

• if you only have to do them once, and
• if they are not too complex.

• ~ ‘library’
• A collection of previously programmed functions
• Equivalent to many commercial software: e.g. Multivariate stats: vegan = PCORD, CANOCO etc.
• Need to download from CRAN:

install.packages("foo")
library(foo) # or
require(foo)

q()

Save workspace? Usually not.

Better to save commands as text files

rm(list = ls(all = TRUE))