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NEWS
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CHANGES in PHANGORN VERSION 2.11.0
OTHER CHANGES
o Vignettes have been reorganised, rewritten and vastly improved thanks to
Iris.
o small improvements to plot.codonTest, plot.networx
o rell bootstrap values are now computed by default in optim.pml / pml_bb
BUG FIXES
o fixed bug which caused warning on CRAN
o densiTree does not draw an empty plot any more
o Replace rgl.texts with texts3d, oull reqiest by Duncan Murdoch (thanks)
o changes in read.nexus.splits and read.nexus.networx to work with the
moving targets SplitsTree6/SplitsTreeCE
CHANGES in PHANGORN VERSION 2.10.0
NEW FEATURES
o several improvements to simplify workflow and flatten learning curve.
o new function pml_bb, combining generation of starting trees, pml and
optim.pml and allowing modelTest object as input.
o tipdated phylogenies estimation (was with limitations possible before,
but not documented).
o Mkv model, edge length and rearrangements only work for ultrametric and
tiplabeled phylogenies so far.
o Added experimental version of RELL bootstrap (Minh et al. 2013 Ultrafast
Approximation for Phylogenetic Bootstrap).
o modelTest now tests several models for USER defined data.
OTHER CHANGES
o some default values of of pratchet changed
o updated, improved and reorganized several vignettes.
o function allSitePattern got an argument additional type.
CHANGES in PHANGORN VERSION 2.9.0
BUG FIXES
o modelTest did not work if no tree was supplied
NEW FEATURES
o some tidy functions: glance.phyDat, tidy.modelTest
OTHER CHANGES
o dist.ml is a lot faster for the JC69 and F81 models if there are no
ambiguous sites present.
o added a few helper function to simplifiy some workflows (e.g. modelTest)
CHANGES in PHANGORN VERSION 2.8.0
BUG FIXES
o Use USE_FC_LEN_T in the C prototypes of LAPACK functions to correspond to
code produced by gfortran >= 7. The mechanism was introduced in R 3.6.2
and is planned to make its use obligatory in R 4.2.0.
o bug in dna2codon fixed.
o codon models (codonTest) most likely did not work properly for models
other than the standard code.
NEW FEATURES
o free rate model
o Mkv model (so far only for rooted trees)
o better support for ultrametric and time trees
OTHER CHANGES
o optim.pml has internally been reorganized to be easier to maintain and
extend.
o pml.control got an additional argument tau which controls the minimal edge
length during optimisation.
o trees constructed with allCompat, maxCladeCred now have support values
stored in the node.labels
o switched from magrittr %>% to the native pipe |>
dropped dependency on magrittr
CHANGES in PHANGORN VERSION 2.7.1
BUG FIXES
o several bug fixes in parsimony code
CHANGES in PHANGORN VERSION 2.7.0
BUG FIXES
o several bug fixes, e.g. which called bootstrap.pml and pratchet to crash
OTHER CHANGES
o internal functions for handling bipartitions have been harmonized with ape
and some functions like maxCladeCred are faster
CHANGES in PHANGORN VERSION 2.6.0
NEW FEATURES
o transfer bootstrap (Lemoine et al. 2018)
o pratchet saves trees visited during search, which can be used as
(approximate) bootstrap values
CHANGES in PHANGORN VERSION 2.6.0
NEW FEATURES
o rewritten fitch algorithm to be more memory efficient, often faster
and without limitation on the number of states
o dist.hamming may handle larger datasets and can be faster
o add Laguerre quadrature as option for discrete rate classes (experimental)
o additional genetic codes for codon models.
OTHER CHANGES
o conversion between alignment formats is faster and more memory efficient,
allowing the handling of larger datasets
o changed R dependencies to 3.6.0 mainly to supply nicer palettes via
hcl.colors()
o lots of small improvements to especially for codon models
o tests are now done by tinytest, dropped dependencies on testthat, vdiffr
o all vignettes are now based on Rmarkdown
o pmlPart and pmlMix are a bit more robust
CHANGES in PHANGORN VERSION 2.5.4
NEW FEATURES
o dist.ml, dist.hamming, dist.logDet and dist.p also take DNAbin or
AAbin objects as input
BUG FIXES
o bootstrap.pml returned an error with argument optNni=T
Best practise is to always use TRUE and not T as shortcut
OTHER CHANGES
o several more unit tests
CHANGES in PHANGORN VERSION 2.5.2
NEW FEATURES
o pratchet, optim.parsimony, optim.pml all may now return trees with
multifurcations in case duplicated sequences are discovered. This may
lead to speeding up computations and improved tree topology search.
o function codonTest which adds codon models to detect positive selection
(M1a, M2a) and several options to estimate codon frequencies
(F3x4, F1x4). Can be pretty slow and still experimental.
o broom type tidy function for several objects to easier compare models
o new "equal_angle" layout for 2D-networks (now the default), gives usually
nicer layout of phylogenetic networks
o tiplabels, nodelabels, edgelabels from ape work for plot.networx if
plotted with base R
OTHER CHANGES
o several small improvements to more intuitively use pml and phyDat
objects, like subsetting phyDat objects with "[i, j]".
o several more unit tests
o two new contributors, Keren and Richel
o optim.parsimony, pratchet, pmlMix and pmlPart may return the current best
tree or object when interrupted.
o roxygen2 is used to generate NAMESPACE file
CHANGES in PHANGORN VERSION 2.4.0
NEW FEATURES
o new function add.tips
BUG FIXES
o midpoint works now for trees with only 2 tips
o densiTree, bug report by Richel Bilderbeek
o tree rearrangement in optim.pml return tree with double edge matrix
o phyDat should work now for named vectors
OTHER CHANGES
o many more unit tests
o more consistent coding style
o flashClust and seqLogo are not suggested packages any more
CHANGES in PHANGORN VERSION 2.3.0
NEW FEATURES
o new function mast to compute the maximum agreement subtree
o identify.networx to identify splits in a network
o densiTree got more attributes
o unique.dist, to filter duplicate distances
o ancestral.pml and ancestral.pars are now may return proper phyDat objects
and in for DNA may return ambiguous states
BUG FIXES
o densiTree may if the consensus tree had different ordering of labels
OTHER CHANGES
o acctran allows multiPhylo objects as input
o rNNI has been completely rewritten and is faster
CHANGES in PHANGORN VERSION 2.2.0
NEW FEATURES
o midpoint in now generic and works for multiPhylo objects
o as.bitsplits.splits to better interact with ape
BUG FIXES
o bug fix in RI and CI for ambiguous data
OTHER CHANGES
o added roxygen2 documentation, so R code is now much better documented,
reorganisation of some documentation
o many more unit tests
CHANGES in PHANGORN VERSION 2.1.0
NEW FEATURES
o new functions to compute the (approximate) SPR distance (sprdist, SPR.dist)
contributed by Leonardo de Oliveira Martins.
o super tree methods based on NNI and SPR distances
BUG FIXES
o fixed bug in KF.dist
OTHER CHANGES
o improvements to as.networx. It often now produces networks with less edges
resulting in much nicer plots
o plot.networx does take a different layout algorithm
o as.data.frame.phyDat and as.character.phyDat return amino acids
now in upper cases
o more unit tests
o improved cbind.phyDat, faster and more flexible
o phangorn now requires ape 4.0
o phangorn now imports Rcpp, but not nnls any more
CHANGES in PHANGORN VERSION 2.0.4
NEW FEATURES
o new weighted Robinson-Foulds (1979) distance wRF, suggested by Michelle Kendall
and normalized Robinson-Foulds suggested by Sereina Rutschmann
o codon model "YN98" can be called directly, improved documentation
o bootstrap.phyDat got an new argument jumble,
which randomizes input order of sequences
OTHER CHANGES
o more unit tests
CHANGES in PHANGORN VERSION 2.0.3
NEW FEATURES
o new function maxCladeCred computing the maximum clade credibility tree
from a sample of trees
o function read.nexus.networx and write.nexus.networx to import / export
phylogenetic networx to SplitsTree
o function as.AAbin.phyDat to exchange data with the new AAbin class from ape
o likelihood ratchet (Vos 2003) topology optimisation in optim.pml
o with KF.dist (Kuhner & Felsenstein) and path.dist can be used like RF.dist
BUG FIXES
o improvements to optim.pml to avoid numerical problems,
can now handle much more taxa (still experimantal)
OTHER CHANGES
o mrca.phylo can be used like mrca from ape (faster for large trees)
o individual splits can be colored in lento plots (suggested by France Thouzé)
o plot.networx now (silently) returns a networx object with some of the graphics
parameters, more plot options
o lots of small changes to make handling and identifying splits, edges in
trees and networks easier
o plotBS has a new argument frame and arguments BStrees can be empty
o new vignette IntertwiningTreesAndNetworks
CHANGES in PHANGORN VERSION 2.0.2
OTHER CHANGES
o phangorn now suggests only the Biostrings and not depends on it
o some improvements to bab (branch and bound), may be faster
CHANGES in PHANGORN VERSION 2.0.0
NEW FEATURES
o as.phyDat.MultipleAlignment to excange data with Biostrings
o dist.ml can now compute distances using a discrete gamma model
and the "F81" model.
o optim.pml got a new rearrangement argument and can now
use a stochastic rearrangements similar to Nguyen et al. (2015)
BUG FIXES
o plotBS may double counted edges when rooted trees were in the sample
OTHER CHANGES
o optim.pml uses more C code and should be more robust
o more unit tests
o baseFreq got additional parameter 'all' similar to base.freq in ape
o lots of little improvements in the manual and help files
o modelTest now also shows AIC weights and model="all" will test
all available models
CHANGES in PHANGORN VERSION 1.99.14
NEW FEATURES
o phyDat2alignment to exports files to seqinr
o readDist, writeDist to import / export distance matrices
o cophenetic distance function for splits and networx
o added unit tests
BUG FIXES
o as.splits.networx did not work properly for 4 taxa
(reported by Laurélène Faye)
o RF.dist returned sometimes wrong values
(reported by Andres Dajles)
o plotBS did sometimes not work if the tree had no edge lengths
o plotBS did not work propoerly if input trees were rooted
(reported by Quynh Quach)
o plot.networx ignored cex argument in "2D" plots
o Siblings ignored include.self argument if node is a vector
OTHER CHANGES
o plotBS got an additional argument p to plot only support values
greater than p
o pml and optim.pml now uses more C-code (and is a bit faster)
o defaults in modelTest changed
o discrete.gamma is now exported in the NAMESPACE
CHANGES in PHANGORN VERSION 1.99-13
OTHER CHANGES
o improved importing and conversion of data
o improved stability of pml and optim.pml
CHANGES in PHANGORN VERSION 1.99-12
NEW FEATURES
o added neighborNet algorithm (Bryant and Moulton 2004)
very experimental at the moment
BUG FIXES
o plotBS was not working correctly if bootstraped trees are in
compressed form (bug report by Tobias Müller)
OTHER CHANGES
o many splits and networx methods have been improved
and a vignette was added
o phangorn now suggests only the rgl and not depends on it
to avoid problems on different platforms (suggestion by Matt Pennell)
o new package dependencies knitr for html vignettes and nnls
CHANGES in PHANGORN VERSION 1.99-10
BUG FIXES
o reorder.networx may not work as expected
o Gamma model was not working properly in simSeq.pml
CHANGES in PHANGORN VERSION 1.99-9
BUG FIXES
o bug fixes for clang environment
o midpoint takes care of node labels
CHANGES in PHANGORN VERSION 1.99-8
NEW FEATURES
o pmlPart got an argument rooted to handle rooted trees
o simSeq is now a generic function. This simplifies the
construcion of parametric bootstrap test
o SOWH.test (very experimental)
o as.networx and plot.networx improved considerably
(often generate networks less edges)
and planar graphs are now plotted nicely
BUG FIXES
o fixed some bugs in ancestral.pars
o amino acid model "Blosum62" was not working
OTHER CHANGES
o improvements to read.nexus.splits, write.nexus.splits to
be more consistant with SplitsTree
o splitsNetwork got an additional argument splits
o help for consensusNet, as.splits, as.networx have been reorganised
and improved
o treedist is much faster for larger trees
o several changes to keep R CMD check happy
o a development version phangorn is now available on github
https://github.com/KlausVigo/phangorn.git
CHANGES in PHANGORN VERSION 1.99-6
NEW FEATURES
o cladePar helps coloring trees
o treedist is faster for larger trees, better documentation and examples
BUG FIXES
o the plot of consensusNet shows now the proper bootstrap values
OTHER CHANGES
o phangorn does not depend only suggest rgl
(should build on OS X now)
o default rearrangement for parsimony is now "SPR"
CHANGES in PHANGORN VERSION 1.99-5
NEW FEATURES
o RF.dist works also on "multiPhylo" objects and is quite fast
o optim.pml can now handle NNI tree arrangements for rooted trees,
still experimental but useful for dating etc.
BUG FIXES
o rNNI did return sometimes trees without tip labels
o SH.test did not work for pmlCluster objects
o df for rooted rooted/ultrametric trees are correctly computed
OTHER CHANGES
o lots of internal code C-code changed
o exports of some of the internal ML function, this should speed up in
future other packages e.g. the colescentMCMC package, which use them
considerably (interface may changes in the future)
o registered C routines
CHANGES in PHANGORN VERSION 1.99-0
NEW FEATURES
o new function dist.p to estimate pairwise polymorphism
p-distances from DNA sequences
BUG FIXES
o as.data.frame.phyDat returned only site patterns and so did
write.phyDat for nexus files
o some of the recently introduced (1.7-4) amino acid models were not known
by all functions and contained NAs
OTHER CHANGES
o changed package imports and depends structure to aviod error messages,
thanks to Brian Ripley
o a lot of the internal C-code has changed
CHANGES in PHANGORN VERSION 1.7-4
NEW FEATURES
o densiTree plots are available now
o new species tree and super tree methods
o more amino acid models
BUG FIXES
o phangorn now depends on rgl instead of suggests rgl,
rgl wants to be loaded before igraph, otherwise a compiling error
on some platforms occured!
o fixed a bug that sometimes caused in pratched to crash
o fixed a bug when using negative indices in subset.phyDat
o the search heuristic SPR in optim.parsimony evaluates now more trees
and is more likely to find better ones
OTHER CHANGES
o underlying C-code for several functions has changed.
less memory reallocations and potentially time savings
hopefully I included not too many bugs
o optimising edge length changed from Jacobi to Gauss-Seidel method
and will hopefully be more robust in the long term!
o Descendants is much faster for option type="all"
o plotAnc gives user more control and produces nicer plots
CHANGES in PHANGORN VERSION 1.7-1
NEW FEATURES
o pmlPart got additional argument model
(request from Santiago Claramunt)
BUG FIXES
o pmlPart should be more robust
OTHER CHANGES
o started reorganising the code
o underlying code of several parsimony functions has changed and
these are now considerably faster
o some examples are changed to allow faster checking on CRAN
CHANGES in PHANGORN VERSION 1.6-5
NEW FEATURES
o dist.hamming handles ambigious states now as dist.ml
(request from Arne Mooers)
BUG FIXES
o phangorn links properly to ape
CHANGES in PHANGORN VERSION 1.6-3
NEW FEATURES
o optim.parsimony has a new search heuristic (SPR)
BUG FIXES
o changed package to work with igraph >= 0.6
OTHER CHANGES
o arguments of pratchet changed
CHANGES in PHANGORN VERSION 1.6-0
NEW FEATURES
o dist.ml has more options and is faster (ca. 5 times for nucleotides and 20 times for amino acids)
BUG FIXES
o plotBS did not work properly with ape version 3.0
OTHER CHANGES
o vignettes changed for a faster compilation of the package
o Ancestors allows a vector of nodes as input
o midpoint uses less memory and works for larger trees (10000 of tips)
o ancestral.pars gives better formated output
CHANGES in PHANGORN VERSION 1.5-1
OTHER CHANGES
o several examples changed for a faster compilation of the package
CHANGES in PHANGORN VERSION 1.5-0
NEW FEATURES
o codon models can be used directly
(dn/ds ratio can be computed)
o modelTest works now also for amino acids
BUG FIXES
o the code to compute RI and CI changed and should be more robust
OTHER CHANGES
o package parallel is used instead of multicore
o vignettes, examples, help improved
o ChangeLog is called NEWS
CHANGES in PHANGORN VERSION 1.4-1
NEW FEATURES
o parsimony branch-and-bould algorithms bab (so far pretty slow and memory intensive)
o more amino acid models
o function nnls.tree to compute non-negative edge weights for
a given tree and a distance matrix
BUG FIXES
o allTrees returns now an integer edge matrix,
this could have caused some problems previously
o CI and RI now take better care of ambiguous states
o dist.ml has default value for amino acids
o as.splits.multiPhylo produces more sensible bipartitions
and so lento and consensusNet produce more useful plots
(thanks to Emmanuel Paradis)
OTHER CHANGES
o several changes to the networx classes and methods
o modelTest now also returns the function calls of the estimated models,
which can be used in downstream analyses
o vignette "Trees" has a few more examples
o dist.ml is more general (base frequencies and rate matrix can be supplied)
o pml objects are more compact, thanks to the Matrix package
o xtable is now a suggested package (needed for vignettes)
CHANGES in PHANGORN VERSION 1.4-0
NEW FEATURES
o plot.network to plot split networks in 3D (requires rgl) and 2D
(still very experimantal)
o consensusNet computes consensus networks
o Lento plot allows to take multiPhylo objects as input
BUG FIXES
o CI and RI did not work with only one site pattern present
o pratchet returned only one, not all of the best trees found
OTHER CHANGES
o phangorn now requires the Matrix, igraph and rgl packages
o designTree returns a sparse Matrix and this can save a lot of memory
o internal code for computing bipartitions is much faster for large trees,
and so are several functions depending on it, e.g. RF.dist, treedist, Descendants
CHANGES in PHANGORN VERSION 1.3-1
BUG FIXES
o the multicore package may failed, if executed in a GUI environment,
more error checks included
o optim.pml, in rare cases may failed to optimize edge length
(should be more robust now)
OTHER CHANGES
o some changes to keep R CMD check happy
o modelTest, pratchet, bootstrap.pml, bootstrap.phyDat
got an additional argument multicore option to switch
between serial and parallel execution
CHANGES in PHANGORN VERSION 1.3-0
NEW FEATURES
o acctran to assign edge length to parsimony trees
OTHER CHANGES
o phangorn can now be cited
o additional and improved ancestral reconstructions methods
(ACCTRAN, MPR)
o new vignette describing ancestral sequence reconstruction
CHANGES in PHANGORN VERSION 1.2-0
NEW FEATURES
o new function pratchet (parsimony ratchet)
o new function midpoint for rooting trees
o new function pruneTree to build concensus trees from node labels
(e.g. bootstrap values)
o multicore support for modelTest
BUG FIXES
o ancestral.pars sometimes did not show all possible states
o the call-attributes did not get proper changed in update.pml and
optim.pml
OTHER CHANGES
o there is now a general help page displayed with '?phangorn'
o dist.hamming is faster
o getClans, getSlices and getDiverstity can now
handle multifurcating trees