admixturegraph: Admixture Graph Manipulation and Fitting
Version 1.0.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorThomas Mailund [cre, aut], Kalle Leppala [aut], Svend Nielsen [aut]
Date of publication2016-12-13 15:33:28
MaintainerThomas Mailund <mailund@birc.au.dk>
LicenseGPL-2
Version1.0.2
URL https://github.com/mailund/admixture_graph
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("admixturegraph")

Man pages

add_a_leaf: Adds a new leaf to a graph.
add_an_admixture: Adds a new admixture event to a graph.
add_an_admixture2: Adds a new admixture event to a graph.
add_graph_f4: Evalutes the f_4 statistics for all rows in a data frame and...
add_graph_f4_sign: Extend a data frame with f_4 statistics predicted by a graph.
admix_props: Specify the proportions in an admixture event.
admixture_edge: Create an admixture edge from a child to two parents.
admixturegraph-package: admixturegraph: Visualising and analysing admixture graphs.
admixture_proportions: Create the list of admixture proportions for an admixture...
agraph: Create an admixture graph object.
agraph_children: Build the child incidene matrix from an parent edge list.
agraph_parents: Build the parent incidence matrix from an edge list.
agraph_weights: Build the matrix of admixture proportions from an edge list.
all_graphs: All graphs.
all_path_overlaps: Get the list of overlaps of all paths.
all_paths: Compute all paths from one leaf to another.
bears: Statistics for populations of bears
build_edge_optimisation_matrix: Build a matrix coding the linear system of edges once the...
burn_in: Removes the first k rows from a trace.
calculate_concentration: Building a proxy concentration matrix.
canonise_expression: Used to recognize similar expressions and to possibly...
canonise_graph: Canonise graph.
coef.agraph_fit: Parameters for the fitted graph.
cost_function: The cost function fed to Nelder-Mead.
edge: Create an edge from a child to a parent.
edge_optimisation_function: More detailed edge fitting than mere cost_function.
eight_leaves_trees: Eight leaves trees.
evaluate_f4: Evaluates an f_4 statistics in a given environment.
examine_edge_optimisation_matrix: Examine the edge optimisation matrix to detect unfitted admix...
extract_admixture_proportion_parameters: Extract the admixture proportion parameter from edge...
extract_graph_parameters: Extract all the parameters a graph contains.
extract_trees: Extract trees
f2: Calculate the f_2(A, B) statistics.
f3: Calculate the f_3(A; B, C) statistics.
f4: Calculate the f_4(W, X; Y, Z) statistics.
f4stats: Make a data frame an f_4 statistics object.
fast_fit: A fast version of graph fitting.
fast_plot: Fast version of graph plotting.
filter_on_leaves: Filter data so all W, X, Y and Z are leaves in the graph.
fit_graph: Fit the graph parameters to a data set.
fit_graph_list: Fit lots of graphs to data.
fit_permutations_and_graphs: Fit lots of graphs to data.
fitted.agraph_fit: Predicted f statistics for the fitted graph.
five_leaves_graphs: Five leaves graphs.
format_path: Create a path data frame from a list of nodes.
four_leaves_graphs: Four leaves graphs.
get_graph_f4_sign: Extracts the sign for the f_4 statistics predicted by the...
graph_environment: Build an environment in which f statistics can be evaluated.
graphs_2_0: Admixture graphs of 2 leaves and 0 admixture events...
graphs_3_0: Admixture graphs of 3 leaves and 0 admixture events...
graphs_3_1: Admixture graphs of 3 leaves and 1 admixture event compressed...
graphs_4_0: Admixture graphs of 4 leaves and 0 admixture events...
graphs_4_1: Admixture graphs of 4 leaves and 1 admixture event compressed...
graphs_4_2: Admixture graphs of 4 leaves and 2 admixture events...
graphs_5_0: Admixture graphs of 5 leaves and 0 admixture events...
graphs_5_1: Admixture graphs of 5 leaves and 1 admixture event compressed...
graphs_5_2: Admixture graphs of 5 leaves and 2 admixture events...
graphs_6_0: Admixture graphs of 6 leaves and 0 admixture events...
graphs_6_1: Admixture graphs of 6 leaves and 1 admixture event compressed...
graphs_6_2: Admixture graphs of 6 leaves and 2 admixture events...
graphs_7_0: Admixture graphs of 7 leaves and 0 admixture events...
graphs_7_1: Admixture graphs of 7 leaves and 1 admixture event compressed...
graphs_8_0: Admixture graphs of 8 leaves and 0 admixture events...
graph_to_vector: Graph to vector.
is_descendant_of: Is descendant of.
is_negative: All overlaps are either empty or have a negative weight.
is_positive: All overlaps are either empty or have a positive weight.
is_unknown: Overlapping edges have both positive and negative...
is_zero: All overlaps are empty.
log_likelihood: Calculate (essentially) the log likelihood of a graph with...
log_sum_of_logs: Computes the log of a sum of numbers all given in log-space.
make_an_outgroup: Make an outgroup.
make_mcmc_model: Collect the information about a graph and a data set needed...
make_permutations: List of permutations.
model_bayes_factor_n: Computes the Bayes factor between two models from samples...
model_likelihood: Computes the likelihood of a model from samples from its...
model_likelihood_n: Computes the likelihood of a model from samples from its...
mynonneg: Non negative least square solution.
no_admixture_events: Get the number of admixture events in a graph.
no_admixture_events.agraph: Get the number of admixture events in a graph.
no_admixture_events.agraph_fit: Get the number of admixture events in a fitted graph.
no_admixture_events.agraph_fit_list: Get the number of admixture events in a list of fitted graph.
no_poor_fits: Get the number of tests in the fit where the predictions fall...
no_poor_fits.agraph_fit: Get the number of tests in the fit where the predictions fall...
no_poor_fits.agraph_fit_list: Get the number of tests in the fit where the predictions fall...
overlaps_sign: Get the sign of overlapping paths.
parent_edges: Create the list of edges for an admixture graph.
path_overlap: Collect the postive and negative overlap between two paths.
plot.agraph: Plot an admixture graph.
plot.agraph_fit: Plot the fit of a graph to data.
plot.f4stats: Plot the fit of a graph to data.
plot_fit_1: A plot of the cost function or number of fitted statistics.
plot_fit_2: A contour plot of the cost function.
poor_fits: Get the tests in the fit where the predictions fall outside...
poor_fits.agraph_fit: Get the tests in the fit where the predictions fall outside...
poor_fits.agraph_fit_list: Get the tests in the fit where the predictions fall outside...
print.agraph_fit: Print function for the fitted graph.
project_to_population: Map sample names to population names.
remove_duplicates: Remove duplicate graphs from a list.
rename_nodes: Rename nodes.
residuals.agraph_fit: Errors of prediction in the fitted graph
run_metropolis_hasting: Run a Metropolis-Hasting MCMC to sample graph parameters.
seven_leaves_graphs: Seven leaves graphs.
seven_leaves_trees: Seven leaves trees.
sf2: Calculate the f_2(A, B) statistics.
sf3: Calculate the f_3(A; B, C) statistics.
sf4: Calculate the f_4(W, X; Y, Z) statistics.
six_leaves_graphs: Six leaves graphs.
split_population: Reverse a projection of samples to populations.
split_population.agraph_fit: Reverse a projection of samples to populations.
split_population.data.frame: Reverse a projection of samples to populations.
summary.agraph_fit: Summary for the fitted graph.
sum_of_squared_errors: Get the sum of squared errors for a fitted graph.
sum_of_squared_errors.agraph_fit: Get the sum of squared errors for a fitted graph.
sum_of_squared_errors.agraph_fit_list: Get the sum of squared errors for a list of fitted graph.
thinning: Thins out an MCMC trace.
vector_to_graph: Vector to graph.

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
admixturegraph-package 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/symbolic-f-statistics.R
R/evaluate-f-statistics.R
R/signs.R
R/summary-statistics.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/f-statistics.R
vignettes
vignettes/bibliography.bib
vignettes/admixturegraph.md
vignettes/admixturegraph.Rmd
vignettes/admixturegraph_files
vignettes/admixturegraph_files/figure-html
vignettes/admixturegraph_files/figure-html/new_leaves-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-1-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-4.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-14-1.png
vignettes/admixturegraph_files/figure-html/new_admixtures-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-12-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-4-1.png
vignettes/admixturegraph_files/figure-html/new_root-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-9-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-3.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-10-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-6-1.png
vignettes/admixturegraph_files/figure-html/bears_graph-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-3-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-7-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-11-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-8-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-13-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-5-1.png
vignettes/admixturegraph_files/figure-latex
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-11-1.pdf
vignettes/admixturegraph_files/figure-latex/bears_graph-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-2.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-7-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-6-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-4-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-1-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-12-1.pdf
vignettes/admixturegraph_files/figure-latex/new_admixtures-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-2.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-3-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-4.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-9-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-5-1.pdf
vignettes/admixturegraph_files/figure-latex/new_root-1.pdf
vignettes/admixturegraph_files/figure-latex/new_leaves-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-14-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-2.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-3.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-13-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-1.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/admixturegraph-package.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
admixturegraph documentation built on May 19, 2017, 5:14 p.m.