Intro R

icebreakeR: An Introduction to R
Andrew Robinson
Department of Mathematics & Statistics University of Melbourne
Andrew Robinson (University of Melbourne)
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Outline
1 2 3 4 5 6 7 8 9 10 11 12
Introduction Infrastructure Showcase Interface Conclusion Classes and Objects Object Types Programming Descriptions Graphics Linear Models Mixed-Effects Models
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Introduction
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What is R?
R is a programming language that has been optimized for data analysis and modeling. R can be used as an object-oriented programming language, or as a statistical environment within which sets of instructions can be performed automatically.
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Why use R?
1 2
R runs on Windows, Mac-OS, and Unix variants; R provides a vast number of useful statistical tools;
1
many of which have been painstakingly tested;
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R produces publication-quality graphics in a variety of formats;

A R plays well with L TEX via the Sweave package; R plays well with FORTRAN, C, and shell scripts;
R scales, making it useful for small and large projects; R is object-oriented; R eschews the GUI.
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Why avoid R?
Frustration!
1 2 3 4 5
R cannot do everything; R will not hold your hand; The documentation can be opaque; R can drive you crazy, or age you prematurely; The contributed packages have been exposed to varying degrees of testing and analysis; R stores objects in RAM; R eschews the GUI.
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A contrast
1 2
R is object-oriented; SAS is PROCedure-oriented;
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Infrastructure
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Organization
File structure: project

data, documents, graphics, images, notes, scripts.
Exercise 1
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Getting going and stopping

Getting Going
Starting R Adding Packages
Exercise 2
Stopping
Cancelling operations Quitting
Exercise 3
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Working Directory
Where it all begins.
Relevant commands
getwd() setwd("new working directory ")
Exercise 4
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Showcase
Work through the exercise in the Showcase chapter. Reect on the commonalities between the exercise and what you need from R.
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Getting Local Help
R comes with internal help. Use the examples.
Relevant commands
help(object ) ?object help.search("phrase ") help.start()
Exercise 5
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Remote Help
The Internet is a vast repository of advice. Most of it is good.
Relevant commands
RSiteSearch() Google
R-help . . .
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Responsive Help
A list-server exists. Information is available at: https://stat.ethz.ch/mailman/listinfo/r-help
Relevant issues
Post questions as a last resort. http://www.r-project.org/posting-guide.html
Exercise 6
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Writing Scripts
Why write scripts?
Relevant issues
source("script-name.R ", echo=TRUE) Comments: #
Exercise 7
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Work Spaces
The workspace is the container of all your objects.
Relevant commands
ls() rm(object ) rm(list=ls()) save.image() save(object ) load()
Exercise 8
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History
The past.
Relevant commands
savehistory() loadhistory()
Exercise 9
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Extensibility
R starts speedily.
Relevant commands
require(package ) installed.packages() available.packages() install.packages(package )
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Interface
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Import and Export
Import
read.xxx ()
Exercise 10
Export
write.xxx () pdf("pdf-name.pdf ") . . . dev.off()
Exercise 11
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R is hard work
Work hard!
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R is hard work
Work hard!
That means:
Read widely. Use the resources available. Experiment patiently and exibly. Keep scripts. Comment generously.
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What is an Object?
Characteristics Everything. Objects are realizations of a class. All objects have attributes.
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Why use Objects?
Using objects simplies many complicated problems.

1 2 3
Communication. Comparison. Coercion.
But you have to put them somewhere!
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Assignment
Relevant commands
name <- definition class(object ) Every object that is followed by () is a function, being called. Every object that is followed by [] is being sub- or super-setted.
Exercise 12
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Object Types
Atomistic
Numeric. String. Factor. Integer. Logical. Missing.
Exercise 13
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Object Types
Containers
Vector
Vectorization
Exercise 14
Dataframe.
Exercise 15
Matrix. Array. List.
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Messing with Data
merge() reshape() order()
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Programming
Write your own functions. Flow control Scoping Class control
Exercise 16
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Data Descriptions
Simple data descriptions are readily available. Univariate

Numerical Categorical
Multivariate
Numerical/Numerical Numerical/Categorical Categorical/Categorical
Exercise 17
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Graphics
All the little pieces . . .

plot(x, y, . . .) xlim=, ylim= xlab=, ylab= main= col= pch=, lty=, . . .
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Graphics: Organization
par(. . .) las=1 mfrow=c(2,2) mar=c(4,4,3,2) new=TRUE
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Graphics: Augmentation
plot(x, y, . . .) points() axis() mtext() box() legend()
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Graphics: Permanance
Right-click the graphic, copy as windows metale, and paste to a document. Or . . . pdf("pdf-name.pdf ") plot(x, y, . . .) dev.off()
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Graphics: Challenges
Error Bars Colour by groups
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Graphics: Contributions
trellis (lattice package) grammar of graphics (ggplot, ggplot2 packages)
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Graphics: Exercises
Exercise 18 Exercise 19
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Linear Models
name <- lm(y x )
Useful Options
data = dataframe na.action = na.exclude
Occasional Options
subset = logical or index weights = weights formula = terms(y x, keep.order = TRUE)
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Diagnostics Code
plot(model )
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Diagnostics Interpretation
10 0 10 20 30
Residuals
q 117 q q qq qq qqq q q q q qq q q q q q q q q q q q q qq q q q q q q q qq qq q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q qq q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq qqq q q q q q q q q qq q q q q q q q q q q q q qq q q q q q q q q q q qq q qq q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q
Standardized residuals
Residuals vs Fitted
Normal QQ
2 0 2 4 6
qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q
117 q
376 q 415 q
q 376 q 415
15 Standardized residuals
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ScaleLocation Fitted values

2.5 2.0 1.5 1.0 0.5 0.0
415 q 376 q
q q 117 q q q qq q q q q q q q q q qq q q q q q qq qq q q q q q q q q q q q qq q q q q q qq q q q q q q q q qq qq q q q q qq q q q q q qq q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q qq q q q q q q qq q q qq q q q q q qq q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q qq q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q qq q q q q q qq q q q q q qq q q q q q q q q q q q q q qq q q q qq q qq q q q q qq q q qq q q q q q q q qq qq qq q q qq q qq q q q
Residuals vs Leverage Theoretical Quantiles

2 0 2 4 6 8
q q q q q q q q qq q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q qq q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q 376 q 415 q q q q
245 q 0.5
Cook's distance 0.02 0.03 0.04
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Estimation 1
> summary(hd.lm) Call: lm(formula = height.m ~ dbh.cm, data = ufc) Residuals: Min 1Q -33.5257 -2.8619
Median 0.1320
3Q 2.8512
Max 13.3206
Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 12.67570 0.56406 22.47 <2e-16 *** dbh.cm 0.31259 0.01388 22.52 <2e-16 *** --Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
' '
Residual standard error: 4.941 on 389 degrees of freedom Multiple R-Squared: 0.566, Adjusted R-squared: 0.5649 F-statistic: 507.4 on 1 and 389 DF, p-value: < 2.2e-16
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Prediction
predict(model, newdata=new-dataframe, . . .)
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Inference
> anova(hd.lm) Analysis of Variance Table Response: height.m Df Sum Sq Mean Sq F value Pr(>F) dbh.cm 1 12388.1 12388.1 507.38 < 2.2e-16 *** Residuals 389 9497.7 24.4 --Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
' '
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Exercise
Exercise 20
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Characteristics
Mixed-eects models incorporate two kinds of predictor variables. Fixed eects - speak for themselves. Random eects - represent a population.
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Necessity
Natural resources data commonly have hierarchical structure. Trees within plots within stands within forests. Times within trees . . . Mixed-eects models enable the modeling of correlated data without violation of important regression assumptions.
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Necessity
Natural resources data commonly have hierarchical structure. Trees within plots within stands within forests. Times within trees . . . Mixed-eects models enable the modeling of correlated data without violation of important regression assumptions.
Regression assumptions.
True relationship is linear. Residuals are normally distributed. Residuals have identical distribution (variance). Residuals are independent.
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Utility
Mixed eects models allow the estimation of useful quantities. Variance components. Intra-class correlation.
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Yet another perspective
Construct a height-diameter relationship using two randomly selected plots in a forest, and that we have measured three trees on each. Growing conditions are quite dierent on the plots, leading to a systematic dierence between the height-diameter relationship on each. If we t a simple regression to the trees then we obtain a residual/tted value plot. If we t a simple regression to the trees with an intercept for each plot then we obtain a residual/tted value plot.
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50
0.5
q q
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q q
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Height (m)
Residuals
Residuals
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Diameter (cm)
Fitted Values
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Decomposition 1
Note that the model specication implies that: yij y ij = ij and The true relationship is linear.
i
(1)
N (0, 2 )
i
The
are independent.
Clearly not true.
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Decomposition 2
What if we could make: i + ij yij y ij = b Then we merely need to assume that: The true relationship is linear.
2) bi N (0, b ij
(2)
N (0, 2 )
ij
The
are independent.
Much more tenable!
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Decomposition 3
The assumptions are satised because the systematic dierences between the plots, which previously produced correlation, are now accounted for by the new random eects. However, when the time comes to use the model for prediction, we do not need to know the plot identity, as the xed eects do not require it.
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Data - Height/Diameter from Stage (1963)
A brief synopsis: a sample of 66 trees was selected in national forests around northern and central Idaho. According to Stage (pers. comm. 2003), the trees were selected purposively. The habitat type and diameter at 46 were also recorded for each tree, as was the national forest from which it came. Each tree was then split, and decadal measures were made of height and diameter inside bark at 46 .
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Scatterplot
60 50 Height (m) 40 30 20 10 0
q q q q
q q q q q q q qq q q q q q qq q q qq q q q q q q qqqq q q qq q q q q q q q qq q q qq q q q q q q q q q q qq q qq q qq q qq qq q q q q q q q q q q q q qq q q q q q qq q q q qq q q q q qq qq q q qq q q qq qq qqq qq q q q q q q q q qq q q q q q q qq q q q q q q q q q q q q q q q q qq q q q q q q qq q q q q q q q qq q q q q q q q q q q q q q q qq q q q q q q q q q q q q q qqq q q q q q q q q q qq q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q qq q qq q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q qq q q q qq q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q
20
40 Dbhib (cm)
60
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Figure: Al Stages Grand Fir stem analysis data: height (m) against diameter (cm). These were dominant and co-dominant trees.
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Another look
Kaniksu
60 60 Ts/Pac Ts/Op
Coeur d'Alene
AG/Pach Ts/Pac PA/Pach 60
St. Joe
Ts/Pac PA/Pach Th/Pach
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Clearwater
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Th/Pach AG/Pach PA/Pach 60
Clark Fork
PA/Pach Ts/Pac
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Figure: Al Stages Grand Fir Stem Analysis Data: height (ft, vertical axes) against diameter (inches, horizontal axes) by National Forest. These were dominant and co-dominant trees.
Model for getting it wrong in R
hi = 0 + 1 di +
(3)
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Model for getting it wrong in R
hi = 0 + 1 di +
(3)
True relationship is linear.
i
N (0, 2 )
Cov ( i , j ) = 0 for i = j
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Diagnostics for getting it wrong in R

Standardized residuals
Residuals vs Fitted
155 q 156 q 157 q q q q q q qq q q q q qqq q q q qqq q q q q q qqq q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q qq q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q qq q q q qq q q q q qq qq q q q q q q qq qq q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q qqq q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q qq q q q q q q q q q q q q q q q q q q q q qq q q q q q qq q qq q q q q qq q q q qq q q q q q q q q q q q qq q q q q q q q q q q q q q qq q qq qq q q qq q qq q q q q q q q qq q q q q q q q q q qqq q q q qqq q qqq qq q q q qq
Normal QQ
4 2 0 2
155 q 156 157 qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq
Residuals
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155 q 156 q 157 q q q q q qq q qq qq q qq q q q q q q q q q q q q q qqq qqq q qqq q q qqq q q q qq q q q q q q qq q qq q q q q q qq q q q q q q qq q q q qq q q q q q q q q qq q q q q q q q qq qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q qq q q q qq q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q qq q q q q q q qq qq q q q q qq q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q qq q q q q qq qq q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q qq q q q q q qq q q qq q qq q qq q qq q q q q q qq q q q q q q q q q q q q q q q q q q q qq q q q q q q qq q qq q q q qq q q q q qq q qq q q q q q q q q q qq q q q qq q q q
ScaleLocation Fitted values
Residuals vs Leverage Theoretical Quantiles

4
q q q q q q q q q q qq qq q q q q q qq q q q q q q q q q q q q qq q q q q q q q q q q q q q q qq q q q qq q q q q q q q q q q q q q qq q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q qq q q q q q q qq q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq qq qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q qq q q q q qq q q q q q qq qq q q q q q 468 245 469 q q
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Figure: Popular regression diagnostics from R.
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Model for getting it less wrong in R
hit = 0 + (1 + b1i ) dit +
it
(4)
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Model for getting it less wrong in R
hit = 0 + (1 + b1i ) dit +
it
(4)
True relationship is linear.
2 ) b1i N (0, b 1 it
N (0, 2 )
jt ) ig )
Cov ( it , Cov ( it ,
= 0 for i = j = 0 for t = g
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Assumptions for getting it less wrong in R
Now, the key assumptions that were making are that:

1 2 3
the model structure is correctly specied the tree and forest random eects are normally distributed, the tree random eects are homoscedastic within the forest random eects. the inner-most residuals are normally distributed, the inner-most residuals are homoscedastic within and across the tree random eects. the innermost residuals are independent within the groups.
4 5
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Diagnostics for getting it less wrong in R
Model Structure (I)

Innermost Residuals
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q q qq q q qq q q q q qq q qq q qq q q qq q q q q q q q q q q qq q q q q q q q q q qq q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q qq qqq q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q
Model Structure (II)

4 2 0 2
q q q q
Observed Values
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q q q q q q q q q q q q q qq q q q q q q q q qq q q q q q qq q qq q q q q q q q q q q q q q q q q qq q qq q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q qq q q q q q q q q q q qq q q q qq q q q q
10 20 30 40 50 60
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Fitted Values
Fitted Values
Figure: Useful regression diagnostics from R.
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QQ plot: Tree
q
QQ plot: Residuals
q
Sample Quantiles
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q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq
Sample Quantiles
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q
q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q
Theoretical Quantiles
Theoretical Quantiles
Figure: More useful regression diagnostics from R.
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2.1291 0.5629 0.1856 1.2749
Variance of withinTree Residuals
Innermost Residuals
q q q q
4
q q q
0
q q
0 2
q q q q q qq q q q q qq q q q q q qq q q q q qqqq q q q qq q q qq q q q q q q q q q qqq q q qq q q q
71 12 65 70 36 18 15
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Autocorrelation
1.0 0.5 0.0
q q q q q
Correlation
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q q q q q q
10
Lag
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The roles differ
For the design,

xed eects represent themselves; random eects represent a population.
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The roles differ
Within the model,

xed eects explain variation; random eects organize unexplained variation.
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Another perspective
Random eects are eects that common sense says will explain variation, but you dont want to have to know them in order to be able to apply the model.
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Modelling is much more involved
Add a new dimension to your ow chart!
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A Modelling Strategy
The modeling strategy depends on the modelers intention.

1
Fit baseline model.

1 2
Include the meaningful xed eects. Include the design random eects.
2 3
Check the assumption diagnostics. Add or modify random components until diagnostics are satised.
1 2 3
a heteroskedastic variance structure (several candidates) a correlation structure (several candidates) extra random eects (e.g. random slopes)
4 5
Consider adding more xed eects. Re-examine the diagnostics, add/modify random eects, etc.
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Basic Model Statement

Y = X + Zb +
b N (0, D) N (0, R)
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Y = X + Zb +
b N (0, D) N (0, R)
Design Matrices
X allocates the xed eects. Z allocates the random eects.
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Y = X + Zb +
b N (0, D) N (0, R)
Design Matrices
X allocates the xed eects. Z allocates the random eects.
Covariance Matrices
D describes the random eects covariance. R allocates the residuals covariance.
Y = X + Zb +
Var (Y | X, Z, , b) = R
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Y = X + Zb +
Var (Y | X, Z, , b) = R Var (Y | X, ) = ZDZ + R = V
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Log Likelihood
1 n 1 L (, V | Y, X) = ln (|V|) ln (2 ) (Y X ) V1 (Y X ) 2 2 2
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Profile out
= (X V1 X)1 X V1 Y
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is gone!
L (, V | Y, X) = f (V, Y, X, Z, D, R)
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is gone!
by substitution. by maximization and then Estimate V
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ReML
Maximum likelihood estimators of covariance parameters are usually negatively biased.
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ReML
Briey, ReML involves applying ML, but replacing Y with KY; X with 0; Z with K Z; and V with K VK where K is such that K X = 0.
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Intro R

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icebreakeR: An Introduction to R

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

many of which have been painstakingly tested;

R produces publication-quality graphics in a variety of formats;

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

R is object-oriented; SAS is PROCedure-oriented;

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

File structure: project

Andrew Robinson (University of Melbourne)

Getting going and stopping

Andrew Robinson (University of Melbourne)

Where it all begins.

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Getting Local Help

R comes with internal help. Use the examples.

Andrew Robinson (University of Melbourne)

The Internet is a vast repository of advice. Most of it is good.

Andrew Robinson (University of Melbourne)

A list-server exists. Information is available at: https://stat.ethz.ch/mailman/listinfo/r-help

Andrew Robinson (University of Melbourne)

Why write scripts?

Andrew Robinson (University of Melbourne)

The workspace is the container of all your objects.

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Import and Export

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Why use Objects?

Using objects simplies many complicated problems.

Communication. Comparison. Coercion.

But you have to put them somewhere!

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Messing with Data

merge() reshape() order()

Andrew Robinson (University of Melbourne)

Write your own functions. Flow control Scoping Class control

Andrew Robinson (University of Melbourne)

Simple data descriptions are readily available. Univariate

Andrew Robinson (University of Melbourne)

All the little pieces . . .

Andrew Robinson (University of Melbourne)

par(. . .) las=1 mfrow=c(2,2) mar=c(4,4,3,2) new=TRUE

Andrew Robinson (University of Melbourne)

plot(x, y, . . .) points() axis() mtext() box() legend()

Andrew Robinson (University of Melbourne)

Andrew Robinson (University of Melbourne)

Error Bars Colour by groups

Andrew Robinson (University of Melbourne)