distance: Calculate various multivariate distance metrics

In walterxie/ComMA: Community Matrix Analysis

Description

Data input cm is community matrix defined in ComMA. Rows are OTUs or individual species, and columns are sites or samples. It is a transposed matrix of vegdist input.

Usage

getDissimilarity(cm, tree = NA, is.transposed = FALSE, progressBar = TRUE,
  method = c("beta1-1", "jaccard", "horn.morisita", "bray.curtis",
  "unwt.unif", "wt.unif"))

beta1minus1(cm, is.transposed = FALSE, progressBar = TRUE,
  return.dist = TRUE)

TurnoverDist(t.community.matrix)

Arguments

cm	The community matrix.
tree	The ape tree object required to caculate UniFrac. It cannot be NA, as default, for method="unwt.unif" or "wt.unif".
is.transposed	If TRUE, then the community matrix is already transposed to be the valid input of vegdist. Default to FASLE.
progressBar	Whether to print progress bar only when method="beta1-1" calculated by beta1minus1, default to TRUE.
method	The method to calculate similarity/dissimilarity distance. The options are jaccard, horn.morisita, bray.curtis, beta1-1, and unwt.unif, wt.unif. The last two are unweighted or weighted UniFrac from phyloseq. Default to beta1-1, but it is slow.
return.dist	If TRUE, as default, return a dist object, otherwise return a matrix.

Details

getDissimilarity calculates various multivariate distance metrics among samples.

beta1minus1 calculates beta1-1.

TurnoverDist returns a dist composed of pair-wise turnovers.

Value

getDissimilarity returns a dist object of similarity/dissimilarity, whose rows and columns are sample names from the community matrix.

Examples

dist.jaccard <- getDissimilarity(cm, method="jaccard")

turnover.dist <- beta1minus1(cm)

turnover.dist <- TurnoverDist(t.community.matrix)

walterxie/ComMA documentation built on May 3, 2019, 11:51 p.m.