Admixture Graph Manipulation and Fitting

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. |

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