r-cran-phangorn 2.4.0-1 / usr / lib / R / site-library / phangorn / NEWS

     CHANGES in PHANGORN VERSION 2.4.0

NEW FEATURES

    o new function add.tips

BUG FIXES

    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     
    


        CHANGES in PHANGORN VERSION 1.1-2

       
NEW FEATURES

    o more generic methods for class splits (print, as.matrix)
    
    o plotBS can plot now cladograms and phylograms
          
BUG FIXES

    o read.phyDat sometimes did not work properly for amino acids 



        CHANGES in PHANGORN VERSION 1.1-1

       
NEW FEATURES

    o optim.pml allows to optimise rooted trees

OTHER CHANGES
 
    o description of getClans improved




        CHANGES in PHANGORN VERSION 1.1-0

       
NEW FEATURES

    o Consistency Index (CI) and and Rentention Index (RI)

    o clanistic tools  

    o new generic function cbind.phyDat

    o optim.parsimony works now also with the fitch algorithm,

      faster than the sankoff version 

BUG FIXES

    o treedist and RF.dist now check whether trees are binary and 
    
      try to handle multifurcations (thanks to Jeremy Beaulieu for bug fixes)  

OTHER CHANGES

    o second vignette describing some special features 
    
    o allTrees is faster 

    o trace and pml.control are now more consistent 

    o optim.pml uses less memory and can be faster 
 
      for data with lots of characters



        CHANGES in PHANGORN VERSION 1.0-2

        
BUG FIXES

    o pml.control did not work properly     

OTHER CHANGES

    o pmlCluster, pmlMix and pmlPart gained an attribute control,

      which controls the outermost loop 
   
    o some more error checking for pml and parsimony classes
    
      (thanks to Emmanuel and Liat)
    
    
    
        CHANGES in PHANGORN VERSION 1.0-1

       
NEW FEATURES

    o ancestral sequence reconstruction 

      (parsimony and likelihood based)

    o a small convenience function acgt2ry for ry-coding

    o as.phylo.splits computes a tree from compatible splits

BUG FIXES

    o a small error in pmlCluster was fixed     
	
OTHER CHANGES
	
    o upgma changed to accommodate change in as.phylo.hclust

    o lento plots are looking nicer

	

	
	CHANGES IN PHANGORN VERSION 1.0-0

        
NEW FEATURES

    o implementation of many nucleotide substitution models 

      (additional general transition models can be defined)

    o new function modelTest, comparison of different phylogenetic model

      with AIC or BIC 

    o Lento plot

    o subset functions for phyDat objects

BUG FIXES

    o an error in pace is fixed 
           
OTHER CHANGES

    o parsimony (fitch and sankoff) can now handle multiPhylo objects

    o splits structure (which is a list of bipartitions), used by lento
    
      and hadamard conjugation  

    o phyDat objects can be more general generated using a contrast
    
      matrix
    


        CHANGES IN PHANGORN VERSION 0.99-6

        
NEW FEATURES

    o pace, extracts the ancestral states of the root of a tree  
  
      using the sankoff algorithm

BUG FIXES

    o fixed a bug in dist.ml (thanks to Emmanuel)

    o fixed a bug introduced to SH.test in 0.99-5
           
OTHER CHANGES

    o fixed several spelling mistakes in the documentation



        CHANGES IN PHANGORN VERSION 0.99-5

        
NEW FEATURES

    o parallel computing via multicore 

      (so far bootstrap.pml, bootstrap.pml profit under linux)

    o compute edge weights for parsimony trees

BUG FIXES

    o optim.pml had problems when 
    
    o as.character converted ?,- wrongly to NA

    o fitch needed binary trees as input, otherwise pscore is

      likely to be wrong (returns now a warning)
      
    o optim.pml had a problem with identical sequences  
           
OTHER CHANGES

    o optim.parsimony returns now a tree with edge weights 
    
    o vignette is enhanced, I fixed some spelling mistakes and added 
  
      some more examples.



        CHANGES IN PHANGORN VERSION 0.99-4

        
NEW FEATURES

    o new generic function unique.phyDat
           
OTHER CHANGES

    o internal data format phyDat changed 
    
      and data are stored more memory efficient
      
      (optim.pml and friends use less memory and may be faster) 
    
        

		CHANGES IN PHANGORN VERSION 0.99-3


BUG FIXES

    o RF.dist sometimes returned wrong distances
    
    o rate parameter is now properly normalized in pml.Part 
    
      and pmlCluster
    
    o simSeq had problems simulating a single character 
        
NEW FEATURES

    o rSPR and rNNI to simulate tree rearrangements

                    
   
		CHANGES IN PHANGORN VERSION 0.99-2


NEW FEATURES

    o bootstrap.pml and bootstrap.phyDat: parametric 
    
      bootstrap methods

    o simSeq: A new function to simulate sequence data 

    o read.phyDat: simplifies reading in alignments
    
    o SH.test: Shimodaira-Hasegawa test
    
    o RF.dist: Robinson-Foulds distance as replacement 
    
      for treedist (uses less memory and is much faster)
          
BUG FIXES

    o dist.ml returned wrong variances.   
    
    o as.character.phyDat, as.data.frame caused an error 
       
      for alignments with only one site.    
          
OTHER CHANGES    
    
    o added vignette describing how to perform some
    
      standard phylogenetic analysis with phangorn.   
      
    o more functions to convert between different data formats.
    
    o NNI tree search is now general possible for 
      
      partition models (pmlPart, pmlCluster)
        
      

		CHANGES IN PHANGORN VERSION 0.0-5


BUG FIXES

    o Solved a namespace problem with ape (>=2.2-3). 



		CHANGES IN PHANGORN VERSION 0.0-4


NEW FEATURES

    o splitsNetwork fits a phylogenetic network using a L1 penalty. 
    
      (High memory consumption)  

    o pmlPen: A new function to estimate penalized likelihood models
    
      for sets of edge weights in mixtures or partition models.

BUG FIXES

    o dist.ml should be more forgiving for different inputs.
    
OTHER CHANGES    
    
    o a new dataset.     
      
      
      

		CHANGES IN PHANGORN VERSION 0.0-3


NEW FEATURES

    o amino acid models 

    o several new maximum likelihood models:
    
      mixture models (pmlMix), and some model for 
      
      phylogenomic data partition models (pmlPart), 
      
      and clustering of partitions / genes (pmlCluster)  
      
      (still experimental, feed back wellcome)
        
    o design matrices for phylogenetic distance methods 
    
    o added some functions useful for simulations
    
      (nni, allTrees) 
    
       
    
OTHER CHANGES    
    
    o the data object phyDat changed slightly internally
    
    o a new dataset 
    
    o read.aa to read amino acid data in phylip format 
      
      based on read.dna from the ape package
       

      
      

		CHANGES IN PHANGORN VERSION 0.0-2


NEW FEATURES

    o more generic functions (plot.pml, update.pml) 
      
            
BUG FIXES

    o the "Fitch" algorithm in parsimony contained a bug 
    
    
OTHER CHANGES    
    
    o pml has a cleaner interface (less parameter)
    
    o new faster parsimony analysis (more compiled C-Code) 
          
    o added NAMESPACE