weight.taxo

weight.taxo2

x, y

<code>weight.taxo</code> computes a matrix whose entries [i, j] are set to 1
 if x[i] == x[j], 0 otherwise. <code>weight.taxo2</code> computes a matrix whose entries [i, j] are set to 1
 if x[i] == x[j] AND y[i] != y[j], 0 otherwise. The diagonal [i, i] is always set to 0. The returned matrix can be used as a weight matrix in
 <code><a rd-options="" href="/link/Moran.I?package=ape&version=4.0" data-mini-rdoc="ape::Moran.I">Moran.I</a></code>. <code>x</code> and <code>y</code> may be vectors of
 factors. See further details in <code>vignette("MoranI")</code>.

manip

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.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

weight.taxo function

<code>weight.taxo</code> computes a matrix whose entries [i, j] are set to 1
 if x[i] == x[j], 0 otherwise.

 <code>weight.taxo2</code> computes a matrix whose entries [i, j] are set to 1
 if x[i] == x[j] AND y[i] != y[j], 0 otherwise.

 The diagonal [i, i] is always set to 0.

 The returned matrix can be used as a weight matrix in
 <code><a rd-options='' href='Moran.I'>Moran.I</a></code>. <code>x</code> and <code>y</code> may be vectors of
 factors.

 See further details in <code>vignette("MoranI")</code>.

weight.taxo: Define Similarity Matrix

Description

Usage

Arguments

Value

See Also