CRAN
apTreeshape 1.5-0
Analyses of Phylogenetic Treeshape
Released Apr 4, 2018 by Michael Blum
Dependencies
quantreg 5.36 pbapply 1.3-4 cubature 1.3-11 ape 5.1 coda 0.19-1
Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005)
Installation
Maven
This package can be included as a dependency from a Java or Scala project by including
the following your project's pom.xml
file.
Read more
about embedding Renjin in JVM-based projects.
<dependencies> <dependency> <groupId>org.renjin.cran</groupId> <artifactId>apTreeshape</artifactId> <version>1.5-0-b6</version> </dependency> </dependencies> <repositories> <repository> <id>bedatadriven</id> <name>bedatadriven public repo</name> <url>https://nexus.bedatadriven.com/content/groups/public/</url> </repository> </repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:apTreeshape')
Test Results
This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.
- aldous.test-examples
- all.equal.treeshape-examples
- as.phylo.treeshape-examples
- as.treeshape-examples
- cladesize-examples
- colless-examples
- cutreeshape-examples
- get_PD_sample-examples
- get_tree_beta-examples
- hivtree.treeshape-examples
- index.test-examples
- likelihood.test-examples
- maxlik.betasplit-examples
- mcmc_alpha-examples
- mcmc_eta-examples
- plot.treeshape-examples
- rtreeshape-examples
- sackin-examples
- shape.statistic-examples
- shift.test-examples
- simulate_kingman-examples
- simulate_tree-examples
- simulate_yule-examples
- smaller.clade.spectrum-examples
- spectrum.treeshape-examples
- subtree.test-examples
- summary.treeshape-examples
- tipsubtree-examples
- treeshape-examples
- universal.treeshape-examples