CHANGES IN VERSION 1.8.4 ------------------------- o Fix: special case when tree root has more than one lineage path CHANGES IN VERSION 1.8.3 ------------------------- o Fix: invalid parallel mutations at divergent node. o Update DESCRIPTION, README and vignettes. CHANGES IN VERSION 1.8.2 ------------------------- o Bug fix: 'allSitesName' returns NULL for 'paraFixSites'. o Fix: reduced plot legend label for ggplot2 version 3.3.4. CHANGES IN VERSION 1.8.1 ------------------------- o Fix: missing 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