Admixture Graph Manipulation and Fitting


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Documentation for package ‘admixturegraph’ version 1.0.2

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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.