# Admixture Graph Manipulation and Fitting

## Documentation for package ‘admixturegraph’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C E F G I L M N O P R S T V

admixturegraph-package | admixturegraph: Visualising and analysing admixture graphs.

## -- A --

add_an_admixture | Adds a new admixture event to a graph.
add_an_admixture2 | Adds a new admixture event to a graph.
add_a_leaf | Adds a new leaf 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.
admixture_edge | Create an admixture edge from a child to two parents.
admixture_proportions | Create the list of admixture proportions for an admixture graph.
admix_props | Specify the proportions in an admixture event.
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_paths | Compute all paths from one leaf to another.
all_path_overlaps | Get the list of overlaps of all paths.

## -- B --

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.

## -- C --

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.

## -- E --

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

## -- F --

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.
fitted.agraph_fit | Predicted f statistics for the fitted 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.
five_leaves_graphs | Five leaves graphs.
format_path | Create a path data frame from a list of nodes.
four_leaves_graphs | Four leaves graphs.

## -- G --

get_graph_f4_sign | Extracts the sign for the f_4 statistics predicted by the graph.
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
graph_environment | Build an environment in which f statistics can be evaluated.
graph_to_vector | Graph to vector.

## -- I --

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.

## -- L --

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.

## -- M --

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.

## -- N --

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.

## -- O --

overlaps_sign | Get the sign of overlapping paths.

## -- P --

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.

## -- R --

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.

## -- S --

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.

## -- T --

thinning | Thins out an MCMC trace.

## -- V --

vector_to_graph | Vector to graph.