CRAN

TESS 2.1.0

Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events

Released Oct 28, 2015 by Sebastian Hoehna

This package can be loaded by Renjin but 8 out 19 tests failed.

Dependencies

ape 5.1 coda 0.19-1 Rcpp deSolve 1.21

Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.

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>TESS</artifactId>
    <version>2.1.0-b99</version>
  </dependency>
</dependencies>
<repositories>
  <repository>
    <id>bedatadriven</id>
    <name>bedatadriven public repo</name>
    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
  </repository>
</repositories>

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Renjin CLI

If you're using Renjin from the command line, you load this library by invoking:

library('org.renjin.cran:TESS')

Test Results

This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.

Source

C++

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