makeLabel
(Package: ape) :
Label Management
This is a generic function with methods for character vectors, trees of class "phylo", lists of trees of class "multiPhylo", and DNA sequences of class "DNAbin". All options for the class character may be used in the other methods.
● Data Source:
CranContrib
● Keywords: manip
● Alias: makeLabel, makeLabel.DNAbin, makeLabel.character, makeLabel.multiPhylo, makeLabel.phylo
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bd.ext
(Package: ape) :
Extended Version of the Birth-Death Models to Estimate Speciation
This function fits by maximum likelihood a birth-death model to the combined phylogenetic and taxonomic data of a given clade. The phylogenetic data are given by a tree, and the taxonomic data by the number of species for the its tips.
● Data Source:
CranContrib
● Keywords: models
● Alias: bd.ext
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This function makes node labels in a tree in a flexible way.
● Data Source:
CranContrib
● Keywords: manip
● Alias: makeNodeLabel
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read.dna
(Package: ape) :
Read DNA Sequences in a File
These functions read DNA sequences in a file, and returns a matrix or a list of DNA sequences with the names of the taxa read in the file as rownames or names, respectively. By default, the sequences are stored in binary format, otherwise (if as.character = "TRUE") in lower case.
● Data Source:
CranContrib
● Keywords: IO
● Alias: read.FASTA, read.dna
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mcconwaysims.test
(Package: ape) :
McConway-Sims Test of Homogeneous Diversification
This function performs the McConway–Sims test that a trait or variable does not affect diversification rate.
● Data Source:
CranContrib
● Keywords: htest
● Alias: mcconwaysims.test
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binaryPGLMM
(Package: ape) :
Phylogenetic Generalized Linear Mixed Model for Binary Data
binaryPGLMM performs linear regression for binary phylogenetic data, estimating regression coefficients with approximate standard errors. It simultaneously estimates the strength of phylogenetic signal in the residuals and gives an approximate conditional likelihood ratio test for the hypothesis that there is no signal. Therefore, when applied without predictor (independent) variables, it gives a test for phylogenetic signal for binary data. The method uses a GLMM approach, alternating between penalized quasi-likelihood (PQL) to estimate the "mean components" and restricted maximum likelihood (REML) to estimate the "variance components" of the model.
● Data Source:
CranContrib
● Keywords: regression
● Alias: binaryPGLMM, binaryPGLMM.sim, print.binaryPGLMM
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compute.brlen
(Package: ape) :
Branch Lengths Computation
This function computes branch lengths of a tree using different methods.
● Data Source:
CranContrib
● Keywords: manip
● Alias: compute.brlen
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This function implements a method for checking whether an incomplete set of distances satisfy certain conditions that might make it uniquely determine the edge weights of a given topology, T. It prints information about whether the graph with vertex set the set of leaves, denoted by X, and edge set the set of non-missing distance pairs, denoted by L, is connected or strongly non-bipartite. It then also checks whether L is a triplet cover for T.
● Data Source:
CranContrib
● Keywords: multivariate
● Alias: ewLasso
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pic.ortho
(Package: ape) :
Phylogenetically Independent Orthonormal Contrasts
This function computes the orthonormal contrasts using the method described by Felsenstein (2008). Only a single trait can be analyzed; there can be several observations per species.
● Data Source:
CranContrib
● Keywords: regression
● Alias: pic.ortho
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These functions plot correlagrams previously computed with correlogram.formula.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: plot.correlogram, plot.correlogramList
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