This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
Author(s): Emmanuel Paradis
Edition: 1
Year: 2006
Language: English
Pages: 221
Tags: Биологические дисциплины;Матметоды и моделирование в биологии;
0387329145......Page 1
Contents......Page 9
1.1 Strategic Considerations......Page 13
1.2 Notations......Page 16
1.3.1 Installations......Page 17
1.3.2 Configurations......Page 19
2.1 The Command Line Interface......Page 21
2.2.1 Vector......Page 23
2.2.2 Factor......Page 26
2.2.3 Matrix......Page 27
2.2.4 Data Frame......Page 28
2.2.5 List......Page 29
2.3 The Help System......Page 30
2.4 Creating Graphics......Page 31
2.6 Using R Functions......Page 32
2.7.1 Loops......Page 33
2.7.2 Apply-Like Functions......Page 34
2.8 Exercises......Page 35
3.1 Phylogenetic Data as R Objects......Page 37
3.1.1 The Class "phylo" (ape)......Page 38
3.1.3 The Class "matching" (ape)......Page 39
3.2.1 Phylogenies......Page 40
3.2.3 Molecular Sequences......Page 42
3.3 Writing Data......Page 45
3.4.1 Basic Tree Manipulation......Page 47
3.4.2 Rooted Versus Unrooted Trees......Page 48
3.4.3 Dichotomous Versus Multichotomous Trees......Page 49
3.4.4 Summarizing and Comparing Trees......Page 50
3.4.5 Converting Objects......Page 51
3.4.6 Manipulating DNA Data......Page 52
3.5 Generating Random Trees......Page 56
3.6.1 Sylvia Warblers......Page 58
3.6.2 Phylogeny of the Felidae......Page 62
3.6.3 Snake Venom Proteome......Page 64
3.6.4 Mammalian Mitochondrial Genomes......Page 67
3.6.5 Butterfly DNA Barcodes......Page 74
3.7 Exercises......Page 76
4.1 Simple Tree Drawing......Page 77
4.1.1 Annotating Trees......Page 83
4.1.2 Showing Clades......Page 92
4.2 Combining Plots......Page 95
4.3 Large Phylogenies......Page 101
4.4 Perspectives......Page 104
4.5 Exercises......Page 106
5 Phylogeny Estimation......Page 107
5.1.1 Calculating Distances......Page 108
5.1.2 Simple Clustering and UPGMA......Page 111
5.2 Maximum Likelihood Methods......Page 112
5.2.1 Substitution Models: A Primer......Page 113
5.2.2 Estimation with Molecular Sequences......Page 118
5.2.3 Finding the Maximum Likelihood Tree......Page 122
5.2.4 DNA Mining with PHYML......Page 123
5.3 Bootstrap Methods and Distances Between Trees......Page 124
5.3.1 Resampling Phylogenetic Data......Page 125
5.3.2 Bipartitions and Computing Bootstrap Values......Page 127
5.3.4 Consensus Trees......Page 130
5.4 Molecular Dating......Page 131
5.5.1 Sylvia Warblers......Page 133
5.5.2 Phylogeny of the Felidae......Page 137
5.5.3 Butterfly DNA Barcodes......Page 141
5.7 Exercises......Page 143
6.1 Phylogenetic Comparative Methods......Page 145
6.1.1 Phylogenetically Independent Contrasts......Page 147
6.1.2 Phylogenetic Autoregression......Page 150
6.1.3 Autocorrelative Models......Page 151
6.1.4 Multivariate Decomposition......Page 154
6.1.5 Generalized Least Squares......Page 156
6.1.6 Generalized Estimating Equations......Page 159
6.1.7 Mixed Models and Variance Partitioning......Page 161
6.1.8 The Ornstein–Uhlenbeck Model......Page 163
6.1.9 Perspectives......Page 165
6.2 Estimating Ancestral Characters......Page 166
6.2.1 Continuous Characters......Page 167
6.2.2 Discrete Characters......Page 168
6.3 Analysis of Diversification......Page 172
6.3.1 Graphical Methods......Page 173
6.3.2 Birth–Death Models......Page 175
6.3.3 Survival Models......Page 179
6.3.4 Goodness-of-Fit Tests......Page 181
6.3.5 Tree Shape and Indices of Diversification......Page 182
6.4 Perspectives......Page 184
6.5.1 Sylvia Warblers......Page 185
6.5.2 Phylogeny of the Felidae......Page 188
6.6 Exercises......Page 192
7.1.1 Object-Orientation......Page 194
7.1.2 Variable Definition and Scope......Page 196
7.1.3 How R Works......Page 197
7.2 Writing Functions in R......Page 198
7.3.1 Simple Interfaces......Page 200
7.3.2 Complex Interfaces......Page 201
7.4.1 A Minimalist Package......Page 203
7.5 Performance Issues and Strategies......Page 204
References......Page 209
D......Page 219
P......Page 220
Z......Page 221
