| 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. |
