Description Usage Arguments Details Value Author(s) See Also Examples
This is the main function for building the phylogenetic ILR basis, calculating the weightings (of the parts and the ILR coordinates) and then transforming the data.
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df 
matrix of data to be transformed (samples are rows, compositional parts are columns)  zero must be dealt with either with pseudocount, multiplicative replacement, or another method. 
tree 
a 
sbp 
(Optional) give a precomputed sbp matrix 
part.weights 
weightings for parts, can be a named vector with names
corresponding to

ilr.weights 
weightings for the ILR coordiantes can be a named vector with names
corresponding to names of internal nodes of

return.all 
return all computed parts (e.g., computed sign matrix( 
This is a utility function that pulls together a number of other functions
in philr
. The steps that are executed are as follows:
Create sbp (sign matrix) if not given
Create parts weightings if not given
Shift the dataset with respect to the new reference measure (e.g., part weightings)
Create the basis contrast matrix from the sign matrix and the reference measure
Transform the data based on the contrast matrix and the reference measure
Calculate the specified ILR weightings and multiply each balance by the corresponding weighting
Note for both the reference measure (part weightings) and the ILR weightings, specifying 'uniform'
will
give the same results as not weighting at all.
Note that some of the prespecified part.weights assume df
is given as
counts and not as relative abundances. Except in this case counts or relative
abundances can be given.
matrix if return.all=FALSE
, if return.all=TRUE
then a list is returned (see above).
Justin Silverman
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