check_contrasts: function to check if a set of contrasts for a variable are...

In geantonicelli/GLM: set of wrapper and adapter functions for statistical analysis

Description

this function is a wrapper around the functions 'dist.alignment', 'dist.dna', 'nj', 'bionj', 'fastme.bal', 'fastme.ols', 'pml' and 'optim.pml'. it takes a sequences alignment in format 'alignment' of 'DNAbin' matrix and perform all transformations and steps to calculate a phylogenetic distance matrix based on similarity or identity in the case of proteins or based in evolutionary models in the case of DNA or RNA, to perform a likelihood-based phylogenetic clustering and to optimise the phylogeny by a maximum likelihood algorithm

Usage

check_contrasts(variable)

Arguments

variable

Value

the function returns an object of class 'pml' of the 'phangorn' package. Advanced and elaborated plots can be drawn in later steps based on the tree data of the pml class object

Author(s)

gerardo esteban antonicelli

See Also

'omega_factorial' 'es'

Examples

data(fastaRNA)
data(phylipProt)
mytree <- max_likelihood(fastaRNA, type=RNA, clustering=fastme.bal,
                        pml.model=GTR, clean=FALSE)
## Not run: mytree <- max_likelihood(phylipProt, type=protein, pml.model=Blosum62,
                        outgroup=YP_0010399)
## End(Not run)
## Not run: plot.phylo(mytree, type='u')

geantonicelli/GLM documentation built on Dec. 15, 2020, 3:05 p.m.