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_4statistics with the signs predicted by the graph  and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.
Browse man pages Browse package API and functions Browse package files
Author  Thomas Mailund [cre, aut], Kalle Leppala [aut], Svend Nielsen [aut] 
Date of publication  20161213 15:33:28 
Maintainer  Thomas Mailund <mailund@birc.au.dk> 
License  GPL2 
Version  1.0.2 
URL  https://github.com/mailund/admixture_graph 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:

Functions  

add_a_leaf  Man page Source code 
add_an_admixture  Man page Source code 
add_an_admixture2  Man page Source code 
add_graph_f4  Man page Source code 
add_graph_f4_sign  Man page Source code 
admix_props  Man page Source code 
admixture_edge  Man page Source code 
admixture_proportions  Man page Source code 
admixturegraphpackage  Man page 
agraph  Man page Source code 
agraph_children  Man page Source code 
agraph_parents  Man page Source code 
agraph_weights  Man page Source code 
all_graphs  Man page Source code 
all_path_overlaps  Man page Source code 
all_paths  Man page Source code 
all_paths_to_leaves  Source code 
all_paths_to_root  Source code 
arrange_graph  Source code 
bears  Man page 
branch_count  Source code 
break_graph  Source code 
build_edge_optimisation_matrix  Man page Source code 
burn_in  Man page Source code 
calculate_concentration  Man page Source code 
canonise_expression  Man page Source code 
canonise_graph  Man page Source code 
clear_node  Source code 
coef.agraph_fit  Man page Source code 
cost_function  Man page Source code 
drawing_cost  Source code 
edge  Man page Source code 
edge_optimisation_function  Man page Source code 
eight_leaves_trees  Man page 
evaluate_f4  Man page Source code 
examine_edge_optimisation_matrix  Man page Source code 
exceptional_behavior  Source code 
extract_admixture_proportion_parameters  Man page Source code 
extract_graph_parameters  Man page Source code 
extract_trees  Man page Source code 
f2  Man page Source code 
f3  Man page Source code 
f4  Man page Source code 
f4stats  Man page Source code 
fast_fit  Man page Source code 
fast_plot  Man page Source code 
filter_on_leaves  Man page Source code 
first_collision  Source code 
fit_graph  Man page Source code 
fit_graph_list  Man page Source code 
fit_permutations_and_graphs  Man page Source code 
fitted.agraph_fit  Man page Source code 
five_leaves_graphs  Man page 
flow  Source code 
format_edge  Source code 
format_overlaps  Source code 
format_path  Man page Source code 
format_path_overlap  Source code 
four_leaves_graphs  Man page 
get_graph_f4_sign  Man page Source code 
graph_environment  Man page Source code 
graph_to_vector  Man page Source code 
graphs_2_0  Man page 
graphs_3_0  Man page 
graphs_3_1  Man page 
graphs_4_0  Man page 
graphs_4_1  Man page 
graphs_4_2  Man page 
graphs_5_0  Man page 
graphs_5_1  Man page 
graphs_5_2  Man page 
graphs_6_0  Man page 
graphs_6_1  Man page 
graphs_6_2  Man page 
graphs_7_0  Man page 
graphs_7_1  Man page 
graphs_8_0  Man page 
inner_fast_fit  Source code 
inner_fit_graph  Source code 
invent_name  Source code 
is_descendant_of  Man page Source code 
is_negative  Man page Source code 
is_positive  Man page Source code 
is_unknown  Man page Source code 
is_zero  Man page Source code 
leaf_order  Source code 
load_admixture_information  Source code 
log_likelihood  Man page Source code 
log_sum_of_logs  Man page Source code 
make_an_outgroup  Man page Source code 
make_mcmc_model  Man page Source code 
make_permutations  Man page Source code 
make_predict_function  Source code 
model_bayes_factor_n  Man page Source code 
model_likelihood  Man page Source code 
model_likelihood_n  Man page Source code 
mynonneg  Man page Source code 
no_admixture_events  Man page Source code 
no_admixture_events.agraph  Man page Source code 
no_admixture_events.agraph_fit  Man page Source code 
no_admixture_events.agraph_fit_list  Man page Source code 
no_poor_fits  Man page Source code 
no_poor_fits.agraph_fit  Man page Source code 
no_poor_fits.agraph_fit_list  Man page Source code 
overlaps_sign  Man page Source code 
parent_edges  Man page Source code 
path_negative  Source code 
path_non_negative  Source code 
path_non_positive  Source code 
path_overlap  Man page Source code 
path_positive  Source code 
path_probability  Source code 
path_zero  Source code 
plot.agraph  Man page Source code 
plot.agraph_fit  Man page Source code 
plot.f4stats  Man page Source code 
plot_fit_1  Man page Source code 
plot_fit_2  Man page Source code 
poor_fits  Man page Source code 
poor_fits.agraph_fit  Man page Source code 
poor_fits.agraph_fit_list  Man page Source code 
print.agraph_fit  Man page Source code 
project_to_population  Man page Source code 
recognize_forbidden_parellelness  Source code 
refined_graph  Source code 
remove_duplicates  Man page Source code 
remove_eightness  Source code 
remove_false_leaves  Source code 
remove_joints_from_a_tree  Source code 
rename_nodes  Man page Source code 
residuals.agraph_fit  Man page Source code 
root_graph  Source code 
run_metropolis_hasting  Man page Source code 
save_admixture_information  Source code 
seven_leaves_graphs  Man page 
seven_leaves_trees  Man page 
sf2  Man page Source code 
sf3  Man page Source code 
sf4  Man page Source code 
six_leaves_graphs  Man page 
split_first_admixture  Source code 
split_population  Man page Source code 
split_population.agraph_fit  Man page Source code 
split_population.data.frame  Man page Source code 
sum_of_squared_errors  Man page Source code 
sum_of_squared_errors.agraph_fit  Man page Source code 
sum_of_squared_errors.agraph_fit_list  Man page Source code 
summary.agraph_fit  Man page Source code 
symmetry_4_I  Source code 
symmetry_4_II  Source code 
symmetry_4_III  Source code 
symmetry_4_IV  Source code 
symmetry_4_IX  Source code 
symmetry_4_V  Source code 
symmetry_4_VI  Source code 
symmetry_4_VII  Source code 
symmetry_4_VIII  Source code 
symmetry_5_I  Source code 
symmetry_5_II  Source code 
symmetry_5_III  Source code 
symmetry_5_IV  Source code 
symmetry_5_V  Source code 
symmetry_5_VI  Source code 
symmetry_5_VII  Source code 
symmetry_6_I  Source code 
symmetry_6_II  Source code 
symmetry_6_III  Source code 
symmetry_6_IV  Source code 
symmetry_6_IX  Source code 
symmetry_6_V  Source code 
symmetry_6_VI  Source code 
symmetry_6_VII  Source code 
symmetry_6_VIII  Source code 
symmetry_6_X  Source code 
symmetry_6_XI  Source code 
symmetry_6_XII  Source code 
symmetry_6_XIII  Source code 
symmetry_6_XIV  Source code 
symmetry_6_XV  Source code 
symmetry_6_XVI  Source code 
symmetry_6_XVII  Source code 
symmetry_6_XVIII  Source code 
symmetry_7_I  Source code 
symmetry_7_II  Source code 
symmetry_7_III  Source code 
symmetry_7_IV  Source code 
symmetry_7_V  Source code 
symmetry_8_I  Source code 
symmetry_8_II  Source code 
symmetry_8_III  Source code 
symmetry_8_IV  Source code 
thinning  Man page Source code 
try_to_add  Source code 
unpack_environment  Source code 
update_cycle_orientation  Source code 
vector_to_graph  Man page Source code 
Files  

inst
 
inst/doc
 
inst/doc/admixturegraph.html
 
inst/doc/admixturegraph.Rmd  
inst/doc/admixturegraph.R  
tests
 
tests/testthat.R  
tests/testthat
 
tests/testthat/test_path_overlaps.R  
tests/testthat/test_f_statistics.R  
tests/testthat/test_graph_construction.R  
tests/testthat/test_plots.R  
tests/testthat/test_paths.R  
tests/testthat/test_signs.R  
NAMESPACE
 
data
 
data/graphs_5_0.RData
 
data/graphs_7_0.RData
 
data/graphs_8_0.RData
 
data/graphs_5_2.RData
 
data/graphs_3_1.RData
 
data/bears.RData
 
data/graphs_3_0.RData
 
data/graphs_4_1.RData
 
data/graphs_7_1.RData
 
data/graphs_6_2.RData
 
data/datalist
 
data/graphs_4_2.RData
 
data/graphs_5_1.RData
 
data/graphs_2_0.RData
 
data/graphs_6_1.RData
 
data/graphs_4_0.RData
 
data/graphs_6_0.RData
 
R
 
R/symbolicfstatistics.R  
R/evaluatefstatistics.R  
R/signs.R  
R/summarystatistics.R  
R/plot.R  
R/project_and_split.R  
R/filter.R  
R/data.R  
R/f4_plotting.R  
R/fitting.R  
R/paths.R  
R/agraph.R  
R/admixture_graph.R  
R/fitted_plotting.R  
R/overlaps.R  
R/propose.R  
R/mcmc.R  
R/fstatistics.R  
vignettes
 
vignettes/bibliography.bib
 
vignettes/admixturegraph.md  
vignettes/admixturegraph.Rmd  
vignettes/admixturegraph_files
 
vignettes/admixturegraph_files/figurehtml
 
vignettes/admixturegraph_files/figurehtml/new_leaves1.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk11.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk194.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk141.png
 
vignettes/admixturegraph_files/figurehtml/new_admixtures1.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk121.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk41.png
 
vignettes/admixturegraph_files/figurehtml/new_root1.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk91.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk193.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk191.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk101.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk61.png
 
vignettes/admixturegraph_files/figurehtml/bears_graph1.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk182.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk152.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk31.png
 
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vignettes/admixturegraph_files/figurehtml/unnamedchunk81.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk151.png
 
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vignettes/admixturegraph_files/figurehtml/unnamedchunk131.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk192.png
 
vignettes/admixturegraph_files/figurehtml/unnamedchunk51.png
 
vignettes/admixturegraph_files/figurelatex
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk111.pdf
 
vignettes/admixturegraph_files/figurelatex/bears_graph1.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk152.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk191.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk71.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk61.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk181.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk41.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk11.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk121.pdf
 
vignettes/admixturegraph_files/figurelatex/new_admixtures1.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk182.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk31.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk194.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk91.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk51.pdf
 
vignettes/admixturegraph_files/figurelatex/new_root1.pdf
 
vignettes/admixturegraph_files/figurelatex/new_leaves1.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk141.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk192.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk193.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk131.pdf
 
vignettes/admixturegraph_files/figurelatex/unnamedchunk151.pdf
 
README.md  
MD5
 
build
 
build/vignette.rds
 
DESCRIPTION
 
man
 
man/seven_leaves_trees.Rd  
man/path_overlap.Rd  
man/no_admixture_events.agraph_fit_list.Rd  
man/log_likelihood.Rd  
man/agraph_children.Rd  
man/project_to_population.Rd  
man/thinning.Rd  
man/f2.Rd  
man/sum_of_squared_errors.agraph_fit.Rd  
man/add_an_admixture2.Rd  
man/sf2.Rd  
man/plot_fit_2.Rd  
man/log_sum_of_logs.Rd  
man/vector_to_graph.Rd  
man/graphs_3_0.Rd  
man/graphs_6_0.Rd  
man/graphs_6_1.Rd  
man/fast_plot.Rd  
man/graphs_5_2.Rd  
man/graphs_4_0.Rd  
man/poor_fits.agraph_fit.Rd  
man/poor_fits.Rd  
man/coef.agraph_fit.Rd  
man/model_bayes_factor_n.Rd  
man/edge_optimisation_function.Rd  
man/six_leaves_graphs.Rd  
man/graphs_3_1.Rd  
man/f4stats.Rd  
man/plot_fit_1.Rd  
man/graphs_8_0.Rd  
man/graphs_4_1.Rd  
man/remove_duplicates.Rd  
man/split_population.agraph_fit.Rd  
man/is_zero.Rd  
man/plot.f4stats.Rd  
man/no_poor_fits.Rd  
man/sf3.Rd  
man/make_permutations.Rd  
man/all_paths.Rd  
man/agraph_parents.Rd  
man/all_graphs.Rd  
man/bears.Rd  
man/filter_on_leaves.Rd  
man/admixturegraphpackage.Rd  
man/canonise_expression.Rd  
man/agraph.Rd  
man/four_leaves_graphs.Rd  
man/seven_leaves_graphs.Rd  
man/canonise_graph.Rd  
man/get_graph_f4_sign.Rd  
man/examine_edge_optimisation_matrix.Rd  
man/admixture_proportions.Rd  
man/add_graph_f4.Rd  
man/no_admixture_events.agraph.Rd  
man/residuals.agraph_fit.Rd  
man/make_mcmc_model.Rd  
man/edge.Rd  
man/plot.agraph.Rd  
man/cost_function.Rd  
man/graphs_6_2.Rd  
man/poor_fits.agraph_fit_list.Rd  
man/graphs_5_1.Rd  
man/fit_permutations_and_graphs.Rd  
man/sf4.Rd  
man/graphs_7_0.Rd  
man/overlaps_sign.Rd  
man/graphs_5_0.Rd  
man/f4.Rd  
man/add_graph_f4_sign.Rd  
man/model_likelihood.Rd  
man/graphs_2_0.Rd  
man/is_negative.Rd  
man/evaluate_f4.Rd  
man/no_poor_fits.agraph_fit.Rd  
man/sum_of_squared_errors.Rd  
man/mynonneg.Rd  
man/build_edge_optimisation_matrix.Rd  
man/eight_leaves_trees.Rd  
man/graphs_7_1.Rd  
man/rename_nodes.Rd  
man/is_descendant_of.Rd  
man/fast_fit.Rd  
man/no_admixture_events.Rd  
man/sum_of_squared_errors.agraph_fit_list.Rd  
man/run_metropolis_hasting.Rd  
man/no_admixture_events.agraph_fit.Rd  
man/is_positive.Rd  
man/five_leaves_graphs.Rd  
man/agraph_weights.Rd  
man/summary.agraph_fit.Rd  
man/all_path_overlaps.Rd  
man/format_path.Rd  
man/model_likelihood_n.Rd  
man/print.agraph_fit.Rd  
man/is_unknown.Rd  
man/f3.Rd  
man/make_an_outgroup.Rd  
man/graph_to_vector.Rd  
man/calculate_concentration.Rd  
man/graphs_4_2.Rd  
man/extract_admixture_proportion_parameters.Rd  
man/fit_graph_list.Rd  
man/split_population.data.frame.Rd  
man/no_poor_fits.agraph_fit_list.Rd  
man/split_population.Rd  
man/add_a_leaf.Rd  
man/fitted.agraph_fit.Rd  
man/admix_props.Rd  
man/extract_graph_parameters.Rd  
man/add_an_admixture.Rd  
man/burn_in.Rd  
man/graph_environment.Rd  
man/fit_graph.Rd  
man/plot.agraph_fit.Rd  
man/extract_trees.Rd  
man/parent_edges.Rd  
man/admixture_edge.Rd 
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