richness.yule.test

a matrix or a data frame with at least two columns: the first
    one gives the number of species in clades with a trait supposed to
    increase or decrease diversification rate, and the second one the number of
    species in the sister-clades without the trait. Each
    row represents a pair of sister-clades.

a numeric vector giving the divergence times of each pair of
    clades in <code>x</code>.


  This function performs a test of shift in diversification rate using
  probabilities from the Yule process.


htest

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.

richness.yule.test: Test of Diversification-Shift With the Yule Process

Description

Usage

Arguments

Value

References

See Also

Examples