## CRAN

# admixturegraph 1.0.2

Admixture Graph Manipulation and Fitting

Released Dec 13, 2016 by Thomas Mailund

### Dependencies

MASS 7.3-47 neldermead 1.0-10 dplyr 0.7.4 doParallel 1.0.11 ggplot2 2.2.1 pracma 2.1.1 foreach 1.4.4

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-b12</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 0.8.2543 on Dec 17, 2017.

- Graph_construction.we_can_build_a_simple_graph__E1
- Graph_construction.we_can_build_a_simple_graph__E10
- Graph_construction.we_can_build_a_simple_graph__E11
- Graph_construction.we_can_build_a_simple_graph__E12
- Graph_construction.we_can_build_a_simple_graph__E13
- Graph_construction.we_can_build_a_simple_graph__E14
- Graph_construction.we_can_build_a_simple_graph__E15
- Graph_construction.we_can_build_a_simple_graph__E16
- Graph_construction.we_can_build_a_simple_graph__E17
- Graph_construction.we_can_build_a_simple_graph__E18
- Graph_construction.we_can_build_a_simple_graph__E19
- Graph_construction.we_can_build_a_simple_graph__E2
- Graph_construction.we_can_build_a_simple_graph__E3
- Graph_construction.we_can_build_a_simple_graph__E4
- Graph_construction.we_can_build_a_simple_graph__E5
- Graph_construction.we_can_build_a_simple_graph__E6
- Graph_construction.we_can_build_a_simple_graph__E7
- Graph_construction.we_can_build_a_simple_graph__E8
- Graph_construction.we_can_build_a_simple_graph__E9
- Graph_construction.we_can_build_a_simple_tree__E1
- Graph_construction.we_can_build_a_simple_tree__E10
- Graph_construction.we_can_build_a_simple_tree__E11
- Graph_construction.we_can_build_a_simple_tree__E12
- Graph_construction.we_can_build_a_simple_tree__E13
- Graph_construction.we_can_build_a_simple_tree__E2
- Graph_construction.we_can_build_a_simple_tree__E3
- Graph_construction.we_can_build_a_simple_tree__E4
- Graph_construction.we_can_build_a_simple_tree__E5
- Graph_construction.we_can_build_a_simple_tree__E6
- Graph_construction.we_can_build_a_simple_tree__E7
- Graph_construction.we_can_build_a_simple_tree__E8
- Graph_construction.we_can_build_a_simple_tree__E9
- Graph_construction.we_can_build_an_unresolved_simple_tree__E1
- Graph_construction.we_can_build_an_unresolved_simple_tree__E10
- Graph_construction.we_can_build_an_unresolved_simple_tree__E11
- Graph_construction.we_can_build_an_unresolved_simple_tree__E2
- Graph_construction.we_can_build_an_unresolved_simple_tree__E3
- Graph_construction.we_can_build_an_unresolved_simple_tree__E4
- Graph_construction.we_can_build_an_unresolved_simple_tree__E5
- Graph_construction.we_can_build_an_unresolved_simple_tree__E6
- Graph_construction.we_can_build_an_unresolved_simple_tree__E7
- Graph_construction.we_can_build_an_unresolved_simple_tree__E8
- Graph_construction.we_can_build_an_unresolved_simple_tree__E9
- 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__E1
- Path_overlaps.we_can_compute_the_overlap_between_paths__E10
- Path_overlaps.we_can_compute_the_overlap_between_paths__E11
- Path_overlaps.we_can_compute_the_overlap_between_paths__E12
- Path_overlaps.we_can_compute_the_overlap_between_paths__E13
- Path_overlaps.we_can_compute_the_overlap_between_paths__E14
- Path_overlaps.we_can_compute_the_overlap_between_paths__E2
- Path_overlaps.we_can_compute_the_overlap_between_paths__E3
- Path_overlaps.we_can_compute_the_overlap_between_paths__E4
- Path_overlaps.we_can_compute_the_overlap_between_paths__E5
- Path_overlaps.we_can_compute_the_overlap_between_paths__E6
- Path_overlaps.we_can_compute_the_overlap_between_paths__E7
- Path_overlaps.we_can_compute_the_overlap_between_paths__E8
- Path_overlaps.we_can_compute_the_overlap_between_paths__E9
- Paths.we_can_extract_paths_from_a_graph__E1
- Paths.we_can_extract_paths_from_a_graph__E10
- Paths.we_can_extract_paths_from_a_graph__E2
- Paths.we_can_extract_paths_from_a_graph__E3
- Paths.we_can_extract_paths_from_a_graph__E4
- Paths.we_can_extract_paths_from_a_graph__E5
- Paths.we_can_extract_paths_from_a_graph__E6
- Paths.we_can_extract_paths_from_a_graph__E7
- Paths.we_can_extract_paths_from_a_graph__E8
- Paths.we_can_extract_paths_from_a_graph__E9
- Signs.we_extract_the_right_sign_for_f_statistics__E1
- Signs.we_extract_the_right_sign_for_f_statistics__E2
- Signs.we_extract_the_right_sign_for_f_statistics__E3
- Signs.we_extract_the_right_sign_for_f_statistics__E4
- Signs.we_extract_the_right_sign_for_f_statistics__E5
- agraph-examples
- f_statistics.that_the_f_statistics_computes_the_correct_paths_overlaps__E1
- f_statistics.that_the_f_statistics_computes_the_correct_paths_overlaps__E2
- f_statistics.that_the_f_statistics_computes_the_correct_paths_overlaps__E3
- f_statistics.we_get_the_right_symbolic_representation_of_f_statistics__E1
- f_statistics.we_get_the_right_symbolic_representation_of_f_statistics__E2
- f_statistics.we_get_the_right_symbolic_representation_of_f_statistics__E3
- f_statistics.we_get_the_right_symbolic_representation_of_f_statistics__E4
- f_statistics.we_get_the_right_symbolic_representation_of_f_statistics__E5
- f_statistics.we_get_the_right_symbolic_representation_of_f_statistics__E6
- fast_plot-examples
- testthat