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 extends the data frame with the
                        graph f_4.
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.
admixture_proportions   Create the list of admixture proportions for an
                        admixture graph.
admixturegraph-package
                        admixturegraph: Visualising and analysing
                        admixture graphs.
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 admix variables have been fixed.
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 simplify them.
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 variables.
extract_admixture_proportion_parameters
                        Extract the admixture proportion parameter from
                        edge specifications.
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.
graph_environment       Build an environment in which f statistics can
                        be evaluated.
graph_to_vector         Graph to vector.
graphs_2_0              Admixture graphs of 2 leaves and 0 admixture
                        events compressed into vectors
graphs_3_0              Admixture graphs of 3 leaves and 0 admixture
                        events compressed into vectors
graphs_3_1              Admixture graphs of 3 leaves and 1 admixture
                        event compressed into vectors
graphs_4_0              Admixture graphs of 4 leaves and 0 admixture
                        events compressed into vectors
graphs_4_1              Admixture graphs of 4 leaves and 1 admixture
                        event compressed into vectors
graphs_4_2              Admixture graphs of 4 leaves and 2 admixture
                        events compressed into vectors
graphs_5_0              Admixture graphs of 5 leaves and 0 admixture
                        events compressed into vectors
graphs_5_1              Admixture graphs of 5 leaves and 1 admixture
                        event compressed into vectors
graphs_5_2              Admixture graphs of 5 leaves and 2 admixture
                        events compressed into vectors
graphs_6_0              Admixture graphs of 6 leaves and 0 admixture
                        events compressed into vectors
graphs_6_1              Admixture graphs of 6 leaves and 1 admixture
                        event compressed into vectors
graphs_6_2              Admixture graphs of 6 leaves and 2 admixture
                        events compressed into vectors
graphs_7_0              Admixture graphs of 7 leaves and 0 admixture
                        events compressed into vectors
graphs_7_1              Admixture graphs of 7 leaves and 1 admixture
                        event compressed into vectors
graphs_8_0              Admixture graphs of 8 leaves and 0 admixture
                        events compressed into vectors
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 contributions.
is_zero                 All overlaps are empty.
log_likelihood          Calculate (essentially) the log likelihood of a
                        graph with parameters, given the observation.
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 to run an MCMC on it.
make_permutations       List of permutations.
model_bayes_factor_n    Computes the Bayes factor between two models
                        from samples from their posterior
                        distributions.
model_likelihood        Computes the likelihood of a model from samples
                        from its posterior distribution.
model_likelihood_n      Computes the likelihood of a model from samples
                        from its posterior distribution.
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 outside of the error bars.
no_poor_fits.agraph_fit
                        Get the number of tests in the fit where the
                        predictions fall outside of the error bars.
no_poor_fits.agraph_fit_list
                        Get the number of tests in the fit where the
                        predictions fall outside of the error bars.
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 of the error bars.
poor_fits.agraph_fit    Get the tests in the fit where the predictions
                        fall outside of the error bars.
poor_fits.agraph_fit_list
                        Get the tests in the fit where the predictions
                        fall outside of the error bars.
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.
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.
summary.agraph_fit      Summary for the fitted graph.
thinning                Thins out an MCMC trace.
vector_to_graph         Vector to graph.
