CHANGES IN VERSION 1.3.1
--------------------------
USER-VISIBLE CHANGES
o Squashed Bug in philr and philrInv handling of vector input
CHANGES IN VERSION 1.1.0
--------------------------
USER-VISIBLE CHANGES
o Inverse ILR ilrpInv is now implemented as well as the inverse clrp transform
(clrpInv) and the inverse (shiftpInv) function.
o 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.
o Updated documentation
o Various Bugfixes
o Added updated citation information for package
CHANGES IN VERSION 0.99.0
--------------------------
USER-VISIBLE CHANGES
o Removed deprecated functions (c.to.nn and t.to.nn)
o 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).
o Updated introduction to philr-intro vignette.
o Added Install instructions (from source) to readme
o 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
o News file is now parsed by news() function.
CHANGES IN VERSION 0.3.0
--------------------------
INTERNAL CHANGES
o Fixed confusing difference between gp.rowMeans and g.colMeans (now
gp.rowMeans -> g.rowMeans)
o Various other bug fixes
CHANGES IN VERSION 0.1.4
--------------------------
USER-VISIBLE CHANGES
o Introduced new vignette ('philr-intro') based on Global Patterns dataset
from phyloseq
o name.to.nn which (as well as nn.to.name) are now exported!
o Internal plotting functions replaced with annotate_balance and new
geom_balance which was implemented in the package ggtree.
o 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.
INTERNAL
o 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).
CHANGES IN VERSION 0.1.3
--------------------------
USER-VISIBLE CHANGES
o Weighted / Genralized ILR functions now exported (shiftp, clrp, ilrp,
buildilrBasep)
o Renamed function blw.mean.descendants to mean_dist_to_tips
o t.to.nn and c.to.nn replaced by name.to.nn which (as well as nn.to.name)
are now vectorized.
CHANGES IN VERSION 0.1.0
--------------------------
USER-VISIBLE CHANGES
o Basic functions from paper in added
o name.balance can now show vote tallies
o Philr function now warns if zeroes present
o Added convert_to_long function