CHANGES IN VERSION 1.11.2
-------------------------
o More function availability for objects
CHANGES IN VERSION 1.11.1
-------------------------
o Wrapper function for finding fixation and parallel sites
o Core number set to 1 will disable multiprocessing
CHANGES IN VERSION 1.9.4
-------------------------
o Fix: special case when tree root has more than one lineage path
CHANGES IN VERSION 1.9.3
-------------------------
o Fix: invalid parallel mutations at divergent node.
o Update DESCRIPTION, README and vignettes.
CHANGES IN VERSION 1.9.2
-------------------------
o Allow partially plot 'lineagePath'.
o Improved 'plotMutSites' function for 'lineagePath'.
CHANGES IN VERSION 1.9.1
-------------------------
o Add 'useSites' argument to 'setSiteNumbering' function.
o First 'stable' path as default 'lineagePath'.
o Enable plot functions for 'parallelSites'.
CHANGES IN VERSION 1.7.8
-------------------------
o Change default 'minSNP' value for 'parallelSites' function.
CHANGES IN VERSION 1.7.7
-------------------------
o Fix: Add 'rmarkdown' in 'Suggests'.
o Only plot paths with duplication in number for 'sneakPeek' function.
CHANGES IN VERSION 1.7.6
-------------------------
o Bug fix: empty groups produced by 'groupTips' function.
o Create 'paraFixSites' and 'fixationIndel' functions.
CHANGES IN VERSION 1.7.5
-------------------------
o Treat 'phyMSAmatched' object as 'lineagePath' class for simplicity.
o Improved multiprocessing.
o Fix: repeated cluster name by '.assignClusterNames' internal function.
o Rename 'allSitesPos' to 'allSitesName'.
o Add 'plotMutSites' support for 'lineagePath' and 'fixationSites' objects.
CHANGES IN VERSION 1.7.4
-------------------------
o 'cl.cores' option for turning multiprocessing on and off.
CHANGES IN VERSION 1.7.3
-------------------------
o Fix: inability to get position of all the sites.
CHANGES IN VERSION 1.7.2
-------------------------
o Fix: missing export for 'plot.phyMSAmatched' function.
o Fix: 'addMSA' function unable to handle 'treedata' object.
o Multiprocess for 'addMSA' and 'sitesMinEntropy' function.
CHANGES IN VERSION 1.7.1
-------------------------
o Guess sequence type based on ATCG proportion for 'addMSA'.
CHANGES IN VERSION 1.6.2
-------------------------
o Fix: Wrong ancestral node at divergent point (labeling issue).
o Fix: Better strategy for conflicting 'AA' at divergent point.
CHANGES IN VERSION 1.6.1
-------------------------
o Fix: Super slow 'lineagePath' computation improved and traded to 'addMSA'.
o Fix: 'lumpyCluster' applies median to avoid outlier.
o Bug fix: catch missing fixed mutation by going trough all paths.
CHANGES IN VERSION 1.5.25
-------------------------
o Bug fix: use 'geom_point2' instead of 'geom_tippoint' to avoid error.
CHANGES IN VERSION 1.5.24
-------------------------
o Add sequence type option for for DNA and amino acid.
o Deprecate 'multiFixationSites' function.
o Use 'y' argument as mutation label option in 'plot.sitePath' function.
o Finer lineage resolving method used in 'lineagePath' function.
CHANGES IN VERSION 1.5.23
-------------------------
o Create 'groupTips' functions to replace 'as.list' functions for
'fixationSites' and 'fixationPath' object.
o Create 'sitesMinEntropy' function to output raw result of entropy
minimization.
o Create 'parallelSites' function and other functions for its return object
such as 'plotSingleSite' and 'as.data.frame'
CHANGES IN VERSION 1.5.22
-------------------------
o Fix missing newline when printing 'phyMSAmatched' object.
o Create 'as.list.fixationSites' for retrieving grouped tips.
o Remove 'tipname' option in 'as.data.frame.fixationSites'.
CHANGES IN VERSION 1.5.21
-------------------------
o Fix wrong group name in some corner cases.
o Use 'ggtree' for 'plotSingleSite'.
CHANGES IN VERSION 1.5.20
-------------------------
o Further fix the merging issue in 'fixationSites'.
CHANGES IN VERSION 1.5.19
-------------------------
o Speed up 'SNPsites'.
CHANGES IN VERSION 1.5.18
-------------------------
o Bifurcation check for the phylogenetic tree and force bifurcation.
o Fix path merging issue in 'fixationSites'.
CHANGES IN VERSION 1.5.17
-------------------------
o Import 'aes' and 'theme' from 'ggplot2'.
CHANGES IN VERSION 1.5.16
-------------------------
o Allow turning off mutation label for 'plot.fixationSites' while
legend of cluster name becomes compulsory.
o Import 'scale_color_manual' from 'ggplot2'.
o Update vignette.
CHANGES IN VERSION 1.5.15
-------------------------
o Bug fix: NA in cluster name.
CHANGES IN VERSION 1.5.14
-------------------------
o Add 'as.treedata' function for 'fixationSites'.
CHANGES IN VERSION 1.5.13
-------------------------
o Hierarchical naming of the clusters.
CHANGES IN VERSION 1.5.12
-------------------------
o Establish 'phyMSAmatched' S3 class for better encapsulation.
CHANGES IN VERSION 1.5.11
-------------------------
o Deprecate 'multiFixationSites' function.
CHANGES IN VERSION 1.5.8
-------------------------
o Wrap mutations text in 'plot.fixationSites'.
o Remove 'color' argument for 'plot.fixationSites' as the number of groups
is usually unknown.
CHANGES IN VERSION 1.5.7
-------------------------
o Left padding with 0 for the cluster name.
o Add mutation label when plot 'fixationSites'.
o Add 'as.data.frame' function for 'fixationSites'.
CHANGES IN VERSION 1.5.6
-------------------------
o Add 'sitewiseClusters' function and plot function for its visualization.
CHANGES IN VERSION 1.5.5
-------------------------
o Add 'plotMutSites' function to visualize mutations of each tree tip.
CHANGES IN VERSION 1.5.4
-------------------------
o Use 'ggtree' for 'plot.lineagePath'.
o More informative plot for 'sneakPeek' and add 'lineagePath' function
for its return.
CHANGES IN VERSION 1.5.3
-------------------------
o Add 'as.phylo.fixationSites' function that represent site fixations
as simplified phylgenetic tree.
CHANGES IN VERSION 1.5.2
-------------------------
o Add 'minEffectiveSize' in 'plot.fixationSites' for filtering
small sized tip clusters.
CHANGES IN VERSION 1.5.1
-------------------------
o Add 'plot.fixationSites' function.
CHANGES IN VERSION 1.4.1
-------------------------
o Fix: broken link in the DESCRIPTION.
CHANGES IN VERSION 1.3.1
-------------------------
o Bug fix: using sequence similarity failed to find 'lineagePath'.
CHANGES IN VERSION 1.2.2
-------------------------
o Bug fix: infinity loop might occur when using 'fixationSites' or
'multiFixatoinSites' caused by internal function. There's no solution
for version 1.2.x, so choices are given to possibly avoid it.
o Bug fix: malfunctional 'setSiteNumbering'.
CHANGES IN VERSION 1.2.1
-------------------------
o Bug fix: plot warning caused by 'tab' character
o Bug fix: bad design causing 'multiFixationSites' extremely slow
o Bug fix: 'fixationSites' gives replicated tips when combined
CHANGES IN VERSION 1.1.10
-------------------------
o Allow user to choose whether to show tip labels in the plot functions
CHANGES IN VERSION 1.1.9
-------------------------
o Add progress bar for the resampling and summarizing step of the function
'multiFixationSites'
CHANGES IN VERSION 1.1.8
-------------------------
o Add 'plot' function for directly plotting the return of 'extractSite'
o Apply resampling method for 'multiFixationSites'
o The function 'fixationSites' applys the old 'multiFixationSites'
CHANGES IN VERSION 1.1.7
-------------------------
o Add functionality 'extractSite' to allow accessing a single site from
the result of 'fixationSites' and 'multiFixationSites'
CHANGES IN VERSION 1.1.6
-------------------------
o Add functionality 'setSiteNumbering' to allow manipulating the
reference of site numbering
CHANGES IN VERSION 1.1.5
-------------------------
o Move similarity calculation to 'addMSA'. This will slow the function
CHANGES IN VERSION 1.1.4
-------------------------
o Use total number of tips divided by number of nodes as 'minEffectiveSize'
o Ignore invariant sites when search for fixation sites
CHANGES IN VERSION 1.1.3
-------------------------
o Expose 'searchDepath' for 'multiFixationSites'
CHANGES IN VERSION 1.1.2
-------------------------
o Use 'multiFixationSites' for both single and multiple fixation sites
CHANGES IN VERSION 1.1.1
-------------------------
o Bug fix: Error when adding new result in 'fixationSites'
CHANGES IN VERSION 0.99.28
-------------------------
o Bug fix: Internal indexing error in 'multiFixationSites'
o The default for 'makePlot' in 'sneakPeak' changed to False
o The default 'tolerance' in 'fixationSite' changed to 0.01
o Improve visualization of 'fixationSites' return
CHANGES IN VERSION 0.99.27
-------------------------
o Improve 'multiFixationSite' with a two-way greedy algorithm
o Use dash line for excluded 'lineagePath' in 'plotSingleSite'
CHANGES IN VERSION 0.99.26
-------------------------
o Bug fix: 'nodeAAsum' subscript out of bound in 'multiFixationSite'
CHANGES IN VERSION 0.99.25
-------------------------
o Use amino acid color for 'plotSingleSite.fixationSite'
o Add 'excluded' legend to 'plotSingleSite'
o Update DESCRIPTION and NEWS
o Use BiocStyle for vignettes
CHANGES IN VERSION 0.99.6
-------------------------
o New functionality 'multiFixationSites'
o Rewrite pruner functions
o Add 'minPath' argument for 'sneakPeek'
o 'sitePath' function's name changed to 'lineagePath'
o Minimum entropy
o The underlying data structure
CHANGES IN VERSION 0.99.5
-------------------------
o Add new functionality 'addMSA'
o Avoid 'root.phylo' function