getPhylorareDF: Rarefaction curve of Phylogenetic Diversity
In walterxie/ComMA: Community Matrix Analysis

Description Usage Arguments Details Examples

Use phylorare from David Nipperess's code to build rarefaction curves of phylogenetic diversity of multiple samples. The detail to see http://davidnipperess.blogspot.co.nz.

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getPhylorareDF(t.community.matrix, phylo.tree, min.size = 100,
  sample.sizes = NULL, points.1.min = 6, points.min.max = 9,
  log.fn = "phylo-rare.csv", verbose = T)

`t.community.matrix`	A transposed matrix from community matrix, where rows are samples, columns are OTUs.
`phylo.tree`	A rooted tree of phylo object.
`min.size`	return NULL, if `min(rowSums(t.community.matrix)) < min.size`. Default to 100.
`sample.sizes`	A vector of sample sizes to build phylo rare curve. If NULL, then create automatically from 1 to `max(rowSums(t.community.matrix))`.
`points.1.min, points.min.max`	If `sample.sizes` is NULL, the number of data points is defined between 1 and `min(rowSums(t.community.matrix))` or and `max(rowSums(t.community.matrix))`.
`log.fn`	The CSV file name to store phylo rare data frame. If NULL, then do not log the file.
`verbose`	Default to TRUE

Data input t.community.matrix is a transposed matrix from community matrix we defined in ComMA. phylo.tree is a rooted tree of phylo object, which can get from ape read.tree.