sitesMinEntropy {sitePath} | R Documentation

## Fixation sites prediction

### Description

After finding the `lineagePath` of a phylogenetic tree, `sitesMinEntropy` perform entropy minimization on every site of the sequence to group the tips according to amino acid/nucleotide.

### Usage

    sitesMinEntropy(x, ...)

    ## S3 method for class 'lineagePath'
    sitesMinEntropy(
      x,
      minEffectiveSize = NULL,
      searchDepth = 1,
      method = c("compare", "insert", "delete"),
      ...
    )

### Arguments

`x` | A `lineagePath` object returned from `lineagePath` function.
`...` | further arguments passed to or from other methods.
`minEffectiveSize` | The minimum number of tips in a group.
`searchDepth` | The function uses heuristic search but the termination of the search cannot be intrinsically decided. `searchDepth` is needed to tell the search when to stop.
`method` | The strategy for predicting the fixation. The basic approach is entropy minimization and can be achieved by adding or removing fixation point, or by comparing the two.

### Value

A `sitesMinEntropy` object.

### Examples

    data(zikv_tree_reduced)
    data(zikv_align_reduced)
    tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
    sitesMinEntropy(lineagePath(tree))

[Package sitePath version 1.6.6 Index]