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Basic Usability
Getting R
1.1 What Is R
1.2 Where Do I Get It?
Language & Grammar
2.1 Overview
2.2 Function Quickie
2.3 Variables
2.4 Data Types
Table 2.1: Common constants you will run across in R
2.5 Operators
2.6 Useful Functions
2.7 Exercises
Biologically Motivated Topics
Data Frames
3.1 Data Input/Output
3.2 Slicing
3.3 Complex Selections
3.4 Useful Functions
3.5 Exercises
Summary Statistics
4.1 Distributions
4.2 Random Number Generation
Figure 4.8: Histogram with labels and main title changed
4.3 Descriptive Statistics
4.4. RELATIONSHIPS BETWEEN PAIRS OF VARIABLES 63
4.4 Relationships Between Pairs of Variables
Figure 4.15: Scatter plot of some semi-random points
Figure 4.16: Example plot of two variables used to test correlations
4.5 Useful Functions
4.6 Exercises
Contingency Tables
5.1 One Random Sample
5.2 Paired Observations
5.3 Several Random Samples
5.4. THE FORMULA NOTATION & BOX PLOTS 83
5.4 The Formula Notation & Box Plots
5.5 Useful Functions
5.6 Exercises
Linear Models
6.1 The t-test
6.2. REGRESSION WITH A SINGLE VARIABLE 91
6.2 Regression With A Single Variable
Figure 6.1: Plot of single variable regression values
Figure 6.2: Regression model added to plot of points using abline function
Figure 6.3: Regression model with ﬁtted line and formula
6.3 Multiple Regression
6.4 Analysis of Variance
6.5 Useful Functions
6.6 Exercises
Working With Images
7.1 Image Data
7.3 Components of A Pixmap
7.4 Image Operations
7.5. CREATING IMAGES PROGRAMATICALLY 117
7.5 Creating Images Programatically
7.6 Useful Functions
7.7 Exercises
Matrix Analysis
8.1 Matrices In R
8.2 Stage-Classiﬁed Matrix Models
Figure 8.6: Size of the four stage classes through time
8.3 Useful Functions
8.4 Exercises
Working With Strings
9.1 Parsing Text Data
9.2 Producing Formatted Output
Table 9.1: Caption For Table
9.3. PLOTTING SPECIAL CHARACTERS 159
9.3 Plotting Special Characters
Figure 9.4: Example of using the expression function to annotate a graphic
9.4 Useful Functions
9.5 Exercises
Basic Scripts
10.1 Writing Scripts
10.2 Evaluating Scripts
10.4 Useful Functions
10.5 Exercises
Programming
11.2 Conditional Statements
11.3 Outlining A Program
11.4 Creating A Program
11.5 Synopsis
11.6 Useful Functions
11.7 Exercises
12.1 Function Syntax
12.3 Useful Functions
12.4 Exercises
B.1 Library Availability
B.2 Installing Libraries
Figure B.1: Example of CRAN mirror window as viewed on Linux
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Biological Data Analysis Using R

# Biological Data Analysis Using R

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01/06/2013

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