admixturegraph: Admixture Graph Manipulation and Fitting

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.

Author
Thomas Mailund [cre, aut], Kalle Leppala [aut], Svend Nielsen [aut]
Date of publication
2016-08-16 19:47:25
Maintainer
Thomas Mailund <mailund@birc.au.dk>
License
GPL-2
Version
1.0.1
URLs

View on CRAN

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_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...
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_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.
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.
residuals.agraph_fit
Errors of prediction in the fitted graph
run_metropolis_hasting
Run a Metropolis-Hasting MCMC to sample graph parameters.
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.

Files in this package

admixturegraph
admixturegraph/inst
admixturegraph/inst/doc
admixturegraph/inst/doc/admixturegraph.html
admixturegraph/inst/doc/admixturegraph.Rmd
admixturegraph/inst/doc/admixturegraph.R
admixturegraph/tests
admixturegraph/tests/testthat.R
admixturegraph/tests/testthat
admixturegraph/tests/testthat/test_path_overlaps.R
admixturegraph/tests/testthat/test_f_statistics.R
admixturegraph/tests/testthat/test_graph_construction.R
admixturegraph/tests/testthat/test_plots.R
admixturegraph/tests/testthat/test_paths.R
admixturegraph/tests/testthat/test_signs.R
admixturegraph/NAMESPACE
admixturegraph/data
admixturegraph/data/bears.RData
admixturegraph/R
admixturegraph/R/symbolic-f-statistics.R
admixturegraph/R/evaluate-f-statistics.R
admixturegraph/R/signs.R
admixturegraph/R/summary-statistics.R
admixturegraph/R/plot.R
admixturegraph/R/project_and_split.R
admixturegraph/R/filter.R
admixturegraph/R/data.R
admixturegraph/R/f4_plotting.R
admixturegraph/R/fitting.R
admixturegraph/R/paths.R
admixturegraph/R/agraph.R
admixturegraph/R/admixture_graph.R
admixturegraph/R/fitted_plotting.R
admixturegraph/R/overlaps.R
admixturegraph/R/propose.R
admixturegraph/R/mcmc.R
admixturegraph/R/f-statistics.R
admixturegraph/vignettes
admixturegraph/vignettes/bibliography.bib
admixturegraph/vignettes/admixturegraph.md
admixturegraph/vignettes/admixturegraph.Rmd
admixturegraph/vignettes/admixturegraph_files
admixturegraph/vignettes/admixturegraph_files/figure-html
admixturegraph/vignettes/admixturegraph_files/figure-html/new_leaves-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-1-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/new_admixtures-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-12-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-4-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/new_root-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-9-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-10-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-6-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/bears_graph-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-3-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-7-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-11-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-8-1.png
admixturegraph/vignettes/admixturegraph_files/figure-html/unnamed-chunk-5-1.png
admixturegraph/README.md
admixturegraph/MD5
admixturegraph/build
admixturegraph/build/vignette.rds
admixturegraph/DESCRIPTION
admixturegraph/man
admixturegraph/man/seven_leaves_trees.Rd
admixturegraph/man/path_overlap.Rd
admixturegraph/man/no_admixture_events.agraph_fit_list.Rd
admixturegraph/man/log_likelihood.Rd
admixturegraph/man/agraph_children.Rd
admixturegraph/man/project_to_population.Rd
admixturegraph/man/thinning.Rd
admixturegraph/man/f2.Rd
admixturegraph/man/sum_of_squared_errors.agraph_fit.Rd
admixturegraph/man/add_an_admixture2.Rd
admixturegraph/man/sf2.Rd
admixturegraph/man/plot_fit_2.Rd
admixturegraph/man/log_sum_of_logs.Rd
admixturegraph/man/fast_plot.Rd
admixturegraph/man/poor_fits.agraph_fit.Rd
admixturegraph/man/poor_fits.Rd
admixturegraph/man/coef.agraph_fit.Rd
admixturegraph/man/model_bayes_factor_n.Rd
admixturegraph/man/edge_optimisation_function.Rd
admixturegraph/man/six_leaves_graphs.Rd
admixturegraph/man/f4stats.Rd
admixturegraph/man/plot_fit_1.Rd
admixturegraph/man/split_population.agraph_fit.Rd
admixturegraph/man/is_zero.Rd
admixturegraph/man/plot.f4stats.Rd
admixturegraph/man/no_poor_fits.Rd
admixturegraph/man/sf3.Rd
admixturegraph/man/make_permutations.Rd
admixturegraph/man/all_paths.Rd
admixturegraph/man/agraph_parents.Rd
admixturegraph/man/bears.Rd
admixturegraph/man/filter_on_leaves.Rd
admixturegraph/man/admixturegraph-package.Rd
admixturegraph/man/canonise_expression.Rd
admixturegraph/man/agraph.Rd
admixturegraph/man/four_leaves_graphs.Rd
admixturegraph/man/get_graph_f4_sign.Rd
admixturegraph/man/examine_edge_optimisation_matrix.Rd
admixturegraph/man/admixture_proportions.Rd
admixturegraph/man/add_graph_f4.Rd
admixturegraph/man/no_admixture_events.agraph.Rd
admixturegraph/man/residuals.agraph_fit.Rd
admixturegraph/man/make_mcmc_model.Rd
admixturegraph/man/edge.Rd
admixturegraph/man/plot.agraph.Rd
admixturegraph/man/cost_function.Rd
admixturegraph/man/poor_fits.agraph_fit_list.Rd
admixturegraph/man/fit_permutations_and_graphs.Rd
admixturegraph/man/sf4.Rd
admixturegraph/man/overlaps_sign.Rd
admixturegraph/man/f4.Rd
admixturegraph/man/add_graph_f4_sign.Rd
admixturegraph/man/model_likelihood.Rd
admixturegraph/man/is_negative.Rd
admixturegraph/man/evaluate_f4.Rd
admixturegraph/man/no_poor_fits.agraph_fit.Rd
admixturegraph/man/sum_of_squared_errors.Rd
admixturegraph/man/mynonneg.Rd
admixturegraph/man/build_edge_optimisation_matrix.Rd
admixturegraph/man/eight_leaves_trees.Rd
admixturegraph/man/fast_fit.Rd
admixturegraph/man/no_admixture_events.Rd
admixturegraph/man/sum_of_squared_errors.agraph_fit_list.Rd
admixturegraph/man/run_metropolis_hasting.Rd
admixturegraph/man/no_admixture_events.agraph_fit.Rd
admixturegraph/man/is_positive.Rd
admixturegraph/man/five_leaves_graphs.Rd
admixturegraph/man/agraph_weights.Rd
admixturegraph/man/summary.agraph_fit.Rd
admixturegraph/man/all_path_overlaps.Rd
admixturegraph/man/format_path.Rd
admixturegraph/man/model_likelihood_n.Rd
admixturegraph/man/print.agraph_fit.Rd
admixturegraph/man/is_unknown.Rd
admixturegraph/man/f3.Rd
admixturegraph/man/make_an_outgroup.Rd
admixturegraph/man/calculate_concentration.Rd
admixturegraph/man/extract_admixture_proportion_parameters.Rd
admixturegraph/man/split_population.data.frame.Rd
admixturegraph/man/no_poor_fits.agraph_fit_list.Rd
admixturegraph/man/split_population.Rd
admixturegraph/man/add_a_leaf.Rd
admixturegraph/man/fitted.agraph_fit.Rd
admixturegraph/man/admix_props.Rd
admixturegraph/man/extract_graph_parameters.Rd
admixturegraph/man/add_an_admixture.Rd
admixturegraph/man/burn_in.Rd
admixturegraph/man/graph_environment.Rd
admixturegraph/man/fit_graph.Rd
admixturegraph/man/plot.agraph_fit.Rd
admixturegraph/man/extract_trees.Rd
admixturegraph/man/parent_edges.Rd
admixturegraph/man/admixture_edge.Rd