distx: Calculate distances with optional grouping and other features
In matR: Metagenomics Analysis Tools

Description Usage Arguments Details Value Author(s) See Also Examples

Calculate several distances and dissimilarities with optional grouping, by default columnwise and pairwise, or from an optionally specified common point.

distx(x, ...)

## S3 method for class 'matrix'
distx(x, method=c("euclidean", "bray-curtis", "jaccard", "mahalanobis",
  "sorensen", "difference", "maximum", "manhattan", "canberra", "binary", "minkowski"), 
  groups=NULL, p=NULL, ..., bycol=TRUE)

## S3 method for class 'biom'
distx(x, method="euclidean", groups=NULL, ..., bycol=TRUE)

`x`	a matrix-like object (`matrix` or `biom`)
`method`	name of distance or dissimilarity measure (`character`)
`groups`	a grouping of columns/rows (`character` or `factor`)
`p`	a single column/row (`numeric`)
`...`	unused
`bycol`	compute columnwise rather than rowwise? (`logical`)

Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.

Daniel T. Braithwaite and Kevin P. Keegan

stats::dist, ecodist::distance

####  Euclidean distance between samples based on raw counts
distx (xx1)

####  alternate dissimilarity measure
distx (xx1, method="bray-curtis")

####  distance in log-transformed data
distx (transform (xx2, t_Log))

####  mean pairwise distance between biomes
distx (xx3, groups="$$biome", method="bray-curtis")