NEWS

philr 1.20.1

Added user option 'pseudocount' to philr with default value 0 for backwards compatability.

Inverse ILR ilrpInv is now implemented as well as the inverse clrp transform (clrpInv) and the inverse (shiftpInv) function.
In order to untransformed more generally transformed PhILR data (e.g., with branch length weights), a philrInv function has been created, this is likely the most userfriendly way to invert any transformed data.
Updated documentation
Various Bugfixes
Added updated citation information for package

Removed deprecated functions (c.to.nn and t.to.nn)
Removed options for parallel processing in phylo2sbp, with the algorithmic speedups to this function parallel processing is superfluous and not used (even for trees of >45,000 leaves).
Updated introduction to philr-intro vignette.
Added Install instructions (from source) to readme
Added citation info to readme (paper not on bioRxiv) http://biorxiv.org/content/early/2016/08/31/072413 Silverman JS, Washburne A, Mukherjee S, David LA. 2016. A phylogenetic transform enhances analysis of compositional microbiota data. bioRxiv doi: 10.1101/072413
News file is now parsed by news() function.

Fixed confusing difference between gp.rowMeans and g.colMeans (now gp.rowMeans -> g.rowMeans)
Various other bug fixes

Introduced new vignette ('philr-intro') based on Global Patterns dataset from phyloseq
name.to.nn which (as well as nn.to.name) are now exported!
Internal plotting functions replaced with annotate_balance and new geom_balance which was implemented in the package ggtree.
Resolved anorm vs. enorm bug (previously anorm was calculating the euclidean norm due to subsetting behavior in compositions package). With this, also removed dependency on compositions package and reimplemented closure in philr.

gp.rowMeans and g.colMeans now handle calculation of geometric means for rows and columns respectively. Note 'gp' because rowMeans for rows needs to be calculated with weights. (See reference in the documentation for that function).

Weighted / Genralized ILR functions now exported (shiftp, clrp, ilrp, buildilrBasep)
Renamed function blw.mean.descendants to mean_dist_to_tips
t.to.nn and c.to.nn replaced by name.to.nn which (as well as nn.to.name) are now vectorized.