BritishBirds            Conservation status of British birds (Thomas
                        2008)
IsaacEtAl               Example dataset for the caper package
VCV.array               Create a 2D or 3D variance-covariance matrix
                        from a phylogeny
anova.caic              Anova and model checking methods for
                        independent contrast models.
anova.pgls              Anova and AIC tables for 'pgls' models.
brunch                  Comparative analysis using the brunch
                        algorithm.
caic-class              The 'caic' S3 object class and methods
caic.diagnostics        Diagnostic tools for independent contrasts
                        models
caper-benchmarks        Datasets used for benchmarking caper
caper-package           Comparative analysis of phylogenetics and
                        evolution in R (caper)
clade.matrix            Create a clade matrix from a phylogeny
clade.members           Identify tips descended from a node
coef.pgls               Generic model methods for 'pgls' models.
comparative.data        Comparative dataset creation
crunch                  Comparative analysis using the crunch
                        algorithm.
fusco.test              Imbalance statistics using Fusco and Cronk's
                        method.
fuscoBirdData           Example dataset for Fusco imbalance
                        calculations
growTree                Tree simulation with traits.
macrocaic               Comparative analysis using independent
                        contrasts on species richness data.
pd.calc                 Calculate and bootstrap phylogenetic diversity
                        measurements.
perissodactyla          Example dataset for the CAIC package
pgls                    Phylogenetic generalized linear models
pgls.profile            Likelihood profiles and confidence intervals
                        for 'pgls' models.
phylo.d                 Calculates the phylogenetic D statistic
phylo.d.subset          Calculates the phylogenetic D statistic across
                        clades within a phylogeny
plot.pgls               Diagnostic plots for 'pgls' models.
shorebird               Example dataset for the caper package
summary.caic            Summarize a crunch, brunch or macrocaic
                        analysis
syrphidae               The syrphidae dataset of Katzourakis et al.
                        2001
