Wrapper function for finding fixation and parallel sites
Core number set to 1 will disable multiprocessing
sitePath 1.9.4
Fix: special case when tree root has more than one lineage path
sitePath 1.9.3
Fix: invalid parallel mutations at divergent node.
Update DESCRIPTION, README and vignettes.
sitePath 1.9.2
Allow partially plot 'lineagePath'.
Improved 'plotMutSites' function for 'lineagePath'.
sitePath 1.9.1
Add 'useSites' argument to 'setSiteNumbering' function.
First 'stable' path as default 'lineagePath'.
Enable plot functions for 'parallelSites'.
sitePath 1.7.8
Change default 'minSNP' value for 'parallelSites' function.
sitePath 1.7.7
Fix: Add 'rmarkdown' in 'Suggests'.
Only plot paths with duplication in number for 'sneakPeek' function.
sitePath 1.7.6
Bug fix: empty groups produced by 'groupTips' function.
Create 'paraFixSites' and 'fixationIndel' functions.
sitePath 1.7.5
Treat 'phyMSAmatched' object as 'lineagePath' class for simplicity.
Improved multiprocessing.
Fix: repeated cluster name by '.assignClusterNames' internal function.
Rename 'allSitesPos' to 'allSitesName'.
Add 'plotMutSites' support for 'lineagePath' and 'fixationSites' objects.
sitePath 1.7.4
'cl.cores' option for turning multiprocessing on and off.
sitePath 1.7.3
Fix: inability to get position of all the sites.
sitePath 1.7.2
Fix: missing export for 'plot.phyMSAmatched' function.
Fix: 'addMSA' function unable to handle 'treedata' object.
Multiprocess for 'addMSA' and 'sitesMinEntropy' function.
sitePath 1.7.1
Guess sequence type based on ATCG proportion for 'addMSA'.
sitePath 1.6.2
Fix: Wrong ancestral node at divergent point (labeling issue).
Fix: Better strategy for conflicting 'AA' at divergent point.
sitePath 1.6.1
Fix: Super slow 'lineagePath' computation improved and traded to 'addMSA'.
Fix: 'lumpyCluster' applies median to avoid outlier.
Bug fix: catch missing fixed mutation by going trough all paths.
sitePath 1.5.25
Bug fix: use 'geom_point2' instead of 'geom_tippoint' to avoid error.
sitePath 1.5.24
Add sequence type option for for DNA and amino acid.
Deprecate 'multiFixationSites' function.
Use 'y' argument as mutation label option in 'plot.sitePath' function.
Finer lineage resolving method used in 'lineagePath' function.
sitePath 1.5.23
Create 'groupTips' functions to replace 'as.list' functions for
'fixationSites' and 'fixationPath' object.
Create 'sitesMinEntropy' function to output raw result of entropy
minimization.
Create 'parallelSites' function and other functions for its return object
such as 'plotSingleSite' and 'as.data.frame'
sitePath 1.5.22
Fix missing newline when printing 'phyMSAmatched' object.
Create 'as.list.fixationSites' for retrieving grouped tips.
Remove 'tipname' option in 'as.data.frame.fixationSites'.
sitePath 1.5.21
Fix wrong group name in some corner cases.
Use 'ggtree' for 'plotSingleSite'.
sitePath 1.5.20
Further fix the merging issue in 'fixationSites'.
sitePath 1.5.19
Speed up 'SNPsites'.
sitePath 1.5.18
Bifurcation check for the phylogenetic tree and force bifurcation.
Fix path merging issue in 'fixationSites'.
sitePath 1.5.17
Import 'aes' and 'theme' from 'ggplot2'.
sitePath 1.5.16
Allow turning off mutation label for 'plot.fixationSites' while
legend of cluster name becomes compulsory.
Import 'scale_color_manual' from 'ggplot2'.
Update vignette.
sitePath 1.5.15
Bug fix: NA in cluster name.
sitePath 1.5.14
Add 'as.treedata' function for 'fixationSites'.
sitePath 1.5.13
Hierarchical naming of the clusters.
sitePath 1.5.12
Establish 'phyMSAmatched' S3 class for better encapsulation.
sitePath 1.5.11
Deprecate 'multiFixationSites' function.
sitePath 1.5.8
Wrap mutations text in 'plot.fixationSites'.
Remove 'color' argument for 'plot.fixationSites' as the number of groups
is usually unknown.
sitePath 1.5.7
Left padding with 0 for the cluster name.
Add mutation label when plot 'fixationSites'.
Add 'as.data.frame' function for 'fixationSites'.
sitePath 1.5.6
Add 'sitewiseClusters' function and plot function for its visualization.
sitePath 1.5.5
Add 'plotMutSites' function to visualize mutations of each tree tip.
sitePath 1.5.4
Use 'ggtree' for 'plot.lineagePath'.
More informative plot for 'sneakPeek' and add 'lineagePath' function
for its return.
sitePath 1.5.3
Add 'as.phylo.fixationSites' function that represent site fixations
as simplified phylgenetic tree.
sitePath 1.5.2
Add 'minEffectiveSize' in 'plot.fixationSites' for filtering
small sized tip clusters.
sitePath 1.5.1
Add 'plot.fixationSites' function.
sitePath 1.4.1
Fix: broken link in the DESCRIPTION.
sitePath 1.3.1
Bug fix: using sequence similarity failed to find 'lineagePath'.
sitePath 1.2.2
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.
Bug fix: malfunctional 'setSiteNumbering'.
sitePath 1.2.1
Bug fix: plot warning caused by 'tab' character
Bug fix: bad design causing 'multiFixationSites' extremely slow
Bug fix: 'fixationSites' gives replicated tips when combined
sitePath 1.1.10
Allow user to choose whether to show tip labels in the plot functions
sitePath 1.1.9
Add progress bar for the resampling and summarizing step of the function
'multiFixationSites'
sitePath 1.1.8
Add 'plot' function for directly plotting the return of 'extractSite'
Apply resampling method for 'multiFixationSites'
The function 'fixationSites' applys the old 'multiFixationSites'
sitePath 1.1.7
Add functionality 'extractSite' to allow accessing a single site from
the result of 'fixationSites' and 'multiFixationSites'
sitePath 1.1.6
Add functionality 'setSiteNumbering' to allow manipulating the
reference of site numbering
sitePath 1.1.5
Move similarity calculation to 'addMSA'. This will slow the function
sitePath 1.1.4
Use total number of tips divided by number of nodes as 'minEffectiveSize'
Ignore invariant sites when search for fixation sites
sitePath 1.1.3
Expose 'searchDepath' for 'multiFixationSites'
sitePath 1.1.2
Use 'multiFixationSites' for both single and multiple fixation sites
sitePath 1.1.1
Bug fix: Error when adding new result in 'fixationSites'
sitePath 0.99.28
Bug fix: Internal indexing error in 'multiFixationSites'
The default for 'makePlot' in 'sneakPeak' changed to False
The default 'tolerance' in 'fixationSite' changed to 0.01
Improve visualization of 'fixationSites' return
sitePath 0.99.27
Improve 'multiFixationSite' with a two-way greedy algorithm
Use dash line for excluded 'lineagePath' in 'plotSingleSite'
sitePath 0.99.26
Bug fix: 'nodeAAsum' subscript out of bound in 'multiFixationSite'
sitePath 0.99.25
Use amino acid color for 'plotSingleSite.fixationSite'
Add 'excluded' legend to 'plotSingleSite'
Update DESCRIPTION and NEWS
Use BiocStyle for vignettes
sitePath 0.99.6
New functionality 'multiFixationSites'
Rewrite pruner functions
Add 'minPath' argument for 'sneakPeek'
'sitePath' function's name changed to 'lineagePath'