Man pages for mailund/admixture_graph
Admixture Graph Manipulation and Fitting

add_a_leafAdds a new leaf to a graph.
add_an_admixtureAdds a new admixture event to a graph.
add_an_admixture2Adds a new admixture event to a graph.
add_graph_f4Evalutes the f_4 statistics for all rows in a data frame and...
add_graph_f4_signExtend a data frame with f_4 statistics predicted by a graph.
admix_propsSpecify the proportions in an admixture event.
admixture_edgeCreate an admixture edge from a child to two parents.
admixturegraph-packageadmixturegraph: Visualising and analysing admixture graphs.
admixture_proportionsCreate the list of admixture proportions for an admixture...
agraphCreate an admixture graph object.
agraph_childrenBuild the child incidene matrix from an parent edge list.
agraph_parentsBuild the parent incidence matrix from an edge list.
agraph_weightsBuild the matrix of admixture proportions from an edge list.
all_graphsAll graphs.
all_path_overlapsGet the list of overlaps of all paths.
all_pathsCompute all paths from one leaf to another.
bearsStatistics for populations of bears
build_edge_optimisation_matrixBuild a matrix coding the linear system of edges once the...
burn_inRemoves the first k rows from a trace.
calculate_concentrationBuilding a proxy concentration matrix.
canonise_expressionUsed to recognize similar expressions and to possibly...
canonise_graphCanonise graph.
coef.agraph_fitParameters for the fitted graph.
cost_functionThe cost function fed to Nelder-Mead.
edgeCreate an edge from a child to a parent.
edge_optimisation_functionMore detailed edge fitting than mere cost_function.
eight_leaves_treesEight leaves trees.
evaluate_f4Evaluates an f_4 statistics in a given environment.
examine_edge_optimisation_matrixExamine the edge optimisation matrix to detect unfitted admix...
export_to_qpGraphExport to Patterson's qpGraph format.
extract_admixture_proportion_parametersExtract the admixture proportion parameter from edge...
extract_graph_parametersExtract all the parameters a graph contains.
extract_treesExtract trees
f2Calculate the f_2(A, B) statistics.
f3Calculate the f_3(A; B, C) statistics.
f4Calculate the f_4(W, X; Y, Z) statistics.
f4statsMake a data frame an f_4 statistics object.
fast_fitA fast version of graph fitting.
fast_plotFast version of graph plotting.
filter_on_leavesFilter data so all W, X, Y and Z are leaves in the graph.
fit_graphFit the graph parameters to a data set.
fit_graph_listFit lots of graphs to data.
fit_permutations_and_graphsFit lots of graphs to data.
fitted.agraph_fitPredicted f statistics for the fitted graph.
five_leaves_graphsFive leaves graphs.
format_pathCreate a path data frame from a list of nodes.
four_leaves_graphsFour leaves graphs.
get_graph_f4_signExtracts the sign for the f_4 statistics predicted by the...
graph_environmentBuild an environment in which f statistics can be evaluated.
graphs_2_0Admixture graphs of 2 leaves and 0 admixture events...
graphs_3_0Admixture graphs of 3 leaves and 0 admixture events...
graphs_3_1Admixture graphs of 3 leaves and 1 admixture event compressed...
graphs_4_0Admixture graphs of 4 leaves and 0 admixture events...
graphs_4_1Admixture graphs of 4 leaves and 1 admixture event compressed...
graphs_4_2Admixture graphs of 4 leaves and 2 admixture events...
graphs_5_0Admixture graphs of 5 leaves and 0 admixture events...
graphs_5_1Admixture graphs of 5 leaves and 1 admixture event compressed...
graphs_5_2Admixture graphs of 5 leaves and 2 admixture events...
graphs_6_0Admixture graphs of 6 leaves and 0 admixture events...
graphs_6_1Admixture graphs of 6 leaves and 1 admixture event compressed...
graphs_6_2Admixture graphs of 6 leaves and 2 admixture events...
graphs_7_0Admixture graphs of 7 leaves and 0 admixture events...
graphs_7_1Admixture graphs of 7 leaves and 1 admixture event compressed...
graphs_8_0Admixture graphs of 8 leaves and 0 admixture events...
graph_to_vectorGraph to vector.
is_descendant_ofIs descendant of.
is_negativeAll overlaps are either empty or have a negative weight.
is_positiveAll overlaps are either empty or have a positive weight.
is_unknownOverlapping edges have both positive and negative...
is_zeroAll overlaps are empty.
log_likelihoodCalculate (essentially) the log likelihood of a graph with...
log_sum_of_logsComputes the log of a sum of numbers all given in log-space.
make_an_outgroupMake an outgroup.
make_mcmc_modelCollect the information about a graph and a data set needed...
make_permutationsList of permutations.
model_bayes_factor_nComputes the Bayes factor between two models from samples...
model_likelihoodComputes the likelihood of a model from samples from its...
model_likelihood_nComputes the likelihood of a model from samples from its...
mynonnegNon negative least square solution.
no_admixture_eventsGet the number of admixture events in a graph.
no_admixture_events.agraphGet the number of admixture events in a graph.
no_admixture_events.agraph_fitGet the number of admixture events in a fitted graph.
no_admixture_events.agraph_fit_listGet the number of admixture events in a list of fitted graph.
no_poor_fitsGet the number of tests in the fit where the predictions fall...
no_poor_fits.agraph_fitGet the number of tests in the fit where the predictions fall...
no_poor_fits.agraph_fit_listGet the number of tests in the fit where the predictions fall...
overlaps_signGet the sign of overlapping paths.
parent_edgesCreate the list of edges for an admixture graph.
path_overlapCollect the postive and negative overlap between two paths.
plot.agraphPlot an admixture graph.
plot.agraph_fitPlot the fit of a graph to data.
plot.f4statsPlot the fit of a graph to data.
plot_fit_1A plot of the cost function or number of fitted statistics.
plot_fit_2A contour plot of the cost function.
poor_fitsGet the tests in the fit where the predictions fall outside...
poor_fits.agraph_fitGet the tests in the fit where the predictions fall outside...
poor_fits.agraph_fit_listGet the tests in the fit where the predictions fall outside...
print.agraph_fitPrint function for the fitted graph.
project_to_populationMap sample names to population names.
remove_duplicatesRemove duplicate graphs from a list.
rename_nodesRename nodes.
residuals.agraph_fitErrors of prediction in the fitted graph
run_metropolis_hastingRun a Metropolis-Hasting MCMC to sample graph parameters.
seven_leaves_graphsSeven leaves graphs.
seven_leaves_treesSeven leaves trees.
sf2Calculate the f_2(A, B) statistics.
sf3Calculate the f_3(A; B, C) statistics.
sf4Calculate the f_4(W, X; Y, Z) statistics.
six_leaves_graphsSix leaves graphs.
split_populationReverse a projection of samples to populations.
split_population.agraph_fitReverse a projection of samples to populations.
split_population.data.frameReverse a projection of samples to populations.
summary.agraph_fitSummary for the fitted graph.
sum_of_squared_errorsGet the sum of squared errors for a fitted graph.
sum_of_squared_errors.agraph_fitGet the sum of squared errors for a fitted graph.
sum_of_squared_errors.agraph_fit_listGet the sum of squared errors for a list of fitted graph.
thinningThins out an MCMC trace.
vector_to_graphVector to graph.
mailund/admixture_graph documentation built on May 21, 2017, 5:41 p.m.