pre-assessment {sitePath} | R Documentation

## Things can be done before the analysis

### Description

`similarityMatrix` calculates similarity between aligned sequences The similarity matrix can be used in `groupTips` or `lineagePath`

`sneakPeek` is intended to plot 'similarity' (actually the least percentage of 'major SNP') as a threshold against number of output lineagePath. This plot is intended to give user a rought view about how many lineages they could expect from the 'similarity' threshold in the function `lineagePath`. The number of lineagePath is preferably not be too many or too few. The result excludes where the number of lineagePath is greater than number of tips divided by 20 or user-defined maxPath. The zero lineagePath result will also be excluded.

### Usage

    similarityMatrix(tree)

    sneakPeek(tree, step = 10, maxPath = NULL, minPath = 1, makePlot = FALSE)

### Arguments

`tree` | The return from `addMSA` function
`step` | the 'similarity' window for calculating and ploting. To better see the impact of threshold on path number. The default is 10.
`maxPath` | maximum number of path to return show in the plot. The number of path in the raw tree can be far greater than trimmed tree. To better see the impact of threshold on path number. This is preferably specified. The default is one 20th of tree tip number.
`minPath` | minimum number of path to return show in the plot. To better see the impact of threshold on path number. The default is 1.
`makePlot` | whether make a dot plot when return

### Value

`similarityMatrix` returns a diagonal matrix of similarity between sequences

`sneakPeek` return the similarity threhold against number of lineagePath. There will be a simple dot plot between threshold and path number if `makePlot` is TRUE.

### Examples

    data('zikv_tree')
    data('zikv_align')
    tree <- addMSA(zikv_tree, alignment = zikv_align)
    simMatrix <- similarityMatrix(tree)
    sneakPeek(tree)

[Package sitePath version 1.3.1 Index]