TreeTools v0.1.3
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Create, Modify and Analyse Phylogenetic Trees
Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include: generation of trees with specified shapes;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
calculation of ancestor-descendant relationships;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and
analysis of partitions and partition information.
Functions in TreeTools
| Name | Description | |
| Lobo.data | Raw data from Zhang et al. 2016 | |
| AllAncestors | List all ancestral nodes | |
| Cladewise | Reorder trees | |
| Lobo.phy | Data from Zhang et al. 2016 in phyDat format | |
| CharacterInformation | Character information content | |
| AncestorEdge | Ancestral edge | |
| ConsensusWithout | Consensus without taxa | |
| BalancedTree | Generate a Balanced Tree | |
| .DecodeRaw | Decode Splits objects | |
| NewickTree | Newick Tree | |
| DescendantEdges | Descendant Edges | |
| Neworder | Reorder edges of a phylogenetic tree | |
| CompatibleSplits | Which splits are compatible? | |
| DoubleFactorial | Double Factorial | |
| N1Spr | Number of trees one SPR step away | |
| EdgeAncestry | Edge ancestry | |
| NSplits | Number of distinct partitions | |
| NTip | Number of tips in a phylogenetic tree | |
| EdgeDistances | Distance between edges | |
| SplitMatchProbability | Probability of matching this well | |
| NonDuplicateRoot | Non-duplicate root | |
| PectinateTree | Generate a Pectinate Tree | |
| ReadCharacters | Read characters from Nexus file | |
| ReadTntTree | Parse TNT Tree | |
| NJTree | Neighbour Joining Tree | |
| ApeTime | Ape Time | |
| StringToPhyDat | String to phyDat | |
| RightmostCharacter | Rightmost character of string | |
| RenumberTree | Renumber a tree in preorder | |
| Subsplit | Subset of a split on fewer taxa | |
| UnrootedTreesMatchingSplit | Number of trees consistent with split | |
| TrivialSplits | Are splits trivial? | |
| MRCA | Most Recent Common Ancestor | |
| ExtractTaxa | Extract taxa from a matrix block | |
| SplitFrequency | Frequency of splits | |
| EnforceOutgroup | Force taxa to form an outgroup | |
| MatrixToPhyDat | Matrix to phyDat | |
| RenumberTips | Renumber a tree's tips | |
| SortTree | Sort tree | |
| NPartitionPairs | Distributions of tips consistent with a partition pair | |
| TipsInSplits | Tips contained within splits | |
| Renumber | Renumber a tree's nodes and tips | |
| SingleTaxonTree | SingleTaxonTree | |
| as.Splits | As splits | |
| TreeNumber | Unique integer indices for bifurcating tree topologies | |
| SplitInformation | Information content of a split | |
| TreeShape | Integer representing shape of a tree | |
| TreeIsRooted | Is tree rooted? | |
| logDoubleFactorials | Natural logarithms of double factorials | |
| match.Splits | Match splits | |
| doubleFactorials | Double factorials | |
| in.Splits | Splits in Splits object | |
| Subtree | Extract subtree | |
| brewer | Brewer palettes | |
| TreesMatchingSplit | Number of trees matching a bipartition split | |
| as.Newick | Write a phylogenetic tree in Newick format | |
| TreeTools-package | TreeTools: Create, Modify and Analyse Phylogenetic Trees | |
| PhyToString | phyDat to String | |
| UnshiftTree | Add Tree to Start of List | |
| NRooted | Number of rooted/unrooted trees | |
| RandomTree | Generate a random tree topology | |
| SupportColour | Support colour | |
| TipLabels | Extract tip labels | |
| print.TreeNumber | Print TreeNumber object | |
| RootTree | Root a phylogenetic tree | |
| SampleOne | Quick sample | |
| AddTip | Add a tip to a phylogenetic tree | |
| CladeSizes | Clade sizes | |
| CollapseNode | Collapse nodes on a phylogenetic tree | |
| No Results! | ||
Vignettes of TreeTools
| Name | ||
| filesystem-navigation.Rmd | ||
| load-data.Rmd | ||
| load-trees.Rmd | ||
| No Results! | ||
Last month downloads
Details
| License | GPL (>= 3) |
| Copyright | Incorporates C/C++ code from: ape by Emmanuel Paradis;
phangorn by Klaus Scheip |
| URL | https://ms609.github.io/TreeTools, https://github.com/ms609/TreeTools |
| BugReports | https://github.com/ms609/TreeTools/issues |
| SystemRequirements | C++11 |
| RdMacros | Rdpack |
| LazyData | true |
| ByteCompile | true |
| Encoding | UTF-8 |
| Language | en-GB |
| LinkingTo | Rcpp |
| VignetteBuilder | knitr |
| RoxygenNote | 6.1.1 |
| NeedsCompilation | yes |
| Packaged | 2019-12-19 17:20:16 UTC; ms609 |
| Repository | CRAN |
| Date/Publication | 2019-12-19 18:20:07 UTC |
| depends | ape (>= 5.0) , R (>= 3.4.0) |
| imports | colorspace , phangorn (>= 2.2.1) , R.cache |
| suggests | knitr , Rcpp , Rdpack , rmarkdown , shiny , testthat |
| Contributors | Emmanuel Paradis, Klaus Schliep |
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