## CRAN

# admixturegraph 1.0.2

Admixture Graph Manipulation and Fitting

Released Dec 13, 2016 by Thomas Mailund [cre, aut], Kalle Leppala [aut], Svend Nielsen [aut]

### Dependencies

MASS 7.3-45 neldermead 1.0-10 ggplot2 2.2.0 dplyr 0.5.0 foreach 1.4.3 pracma 1.9.5 doParallel 1.0.10

Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data -- for example by comparing the sign of f_4-statistics with the signs predicted by the graph -- and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.

## 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>admixturegraph</artifactId> <version>1.0.2-b8</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:admixturegraph')

## Test Results

This package was last tested against Renjin 0.8.2442 on Sep 25, 2017.

- Graph_construction.we_can_build_a_simple_graph_
- Graph_construction.we_can_build_a_simple_tree_
- Graph_construction.we_can_build_an_unresolved_simple_tree_
- Graph_construction.we_get_errors_when_specifying_admixture_proportions_for_non-existing_edges_
- Graph_construction.we_get_errors_when_specifying_an_edge_between_non-existing_nodes_
- Graph_plotting.complex_non-planar_grahs_plot_fine_
- Graph_plotting.trees_plot_fine_
- Path_overlaps.we_can_compute_the_overlap_between_paths_
- Paths.we_can_extract_paths_from_a_graph_
- Signs.we_extract_the_right_sign_for_f_statistics_
- agraph-examples
- f_statistics.that_the_f_statistics_computes_the_correct_paths_overlaps_
- fast_plot-examples
- testthat