groupTips {sitePath} | R Documentation

## The grouping of tree tips

### Description

The tips between divergent nodes or fixation mutations on the lineages are each gathered as group.

### Usage

    groupTips(tree, ...)

    ## S3 method for class 'phyMSAmatched'
    groupTips(
      tree,
      similarity = NULL,
      simMatrix = NULL,
      forbidTrivial = TRUE,
      tipnames = TRUE,
      ...
    )

    ## S3 method for class 'lineagePath'
    groupTips(tree, tipnames = TRUE, ...)

    ## S3 method for class 'sitesMinEntropy'
    groupTips(tree, tipnames = TRUE, ...)

    ## S3 method for class 'fixationSites'
    groupTips(tree, tipnames = TRUE, ...)

    ## S3 method for class 'fixationPath'
    groupTips(tree, tipnames = TRUE, ...)

### Arguments

`tree` | The return from `addMSA`, `lineagePath`, `sitesMinEntropy` or other functions.
`...` | Other arguments.
`similarity` | This decides how minor SNPs are to remove. If provided as fraction between 0 and 1, then the minimum number of SNP will be total tips times `similariy`. If provided as integer greater than 1, the minimum number will be `similariy`. The default `similariy` is 0.05 for `lineagePath`.
`simMatrix` | Deprecated and will not have effect.
`forbidTrivial` | Does not allow trivial trimming.
`tipnames` | If return tips as integer or tip names.

### Value

`groupTips` returns grouping of tips.

### Examples

    data(zikv_tree)
    data(zikv_align)
    tree <- addMSA(zikv_tree, alignment = zikv_align)
    groupTips(tree)

[Package sitePath version 1.6.6 Index]