# Sphinx inventory version 2
# Project: tspaint
# Version: 0.0.9999
# The remainder of this file is compressed using zlib.
tspaint.paint py:function 1 api/paint.html#tspaint.paint -
tspaint.api.paint py:function 1 api/paint.html#tspaint.paint tspaint.paint
tspaint.Painting.introgression_map py:function 1 api/Painting.html#tspaint.Painting.introgression_map -
tspaint.api.Painting.introgression_map py:function 1 api/Painting.html#tspaint.Painting.introgression_map tspaint.Painting.introgression_map
tspaint.Painting.length py:attribute 1 api/Painting.html#tspaint.Painting.length -
tspaint.api.Painting.length py:attribute 1 api/Painting.html#tspaint.Painting.length tspaint.Painting.length
tspaint.Painting.load py:function 1 api/Painting.html#tspaint.Painting.load -
tspaint.api.Painting.load py:function 1 api/Painting.html#tspaint.Painting.load tspaint.Painting.load
tspaint.Painting.plot py:function 1 api/Painting.html#tspaint.Painting.plot -
tspaint.api.Painting.plot py:function 1 api/Painting.html#tspaint.Painting.plot tspaint.Painting.plot
tspaint.Painting.posterior_at py:function 1 api/Painting.html#tspaint.Painting.posterior_at -
tspaint.api.Painting.posterior_at py:function 1 api/Painting.html#tspaint.Painting.posterior_at tspaint.Painting.posterior_at
tspaint.Painting.rate_through_time py:function 1 api/Painting.html#tspaint.Painting.rate_through_time -
tspaint.api.Painting.rate_through_time py:function 1 api/Painting.html#tspaint.Painting.rate_through_time tspaint.Painting.rate_through_time
tspaint.Painting.save py:function 1 api/Painting.html#tspaint.Painting.save -
tspaint.api.Painting.save py:function 1 api/Painting.html#tspaint.Painting.save tspaint.Painting.save
tspaint.Painting.segments py:function 1 api/Painting.html#tspaint.Painting.segments -
tspaint.api.Painting.segments py:function 1 api/Painting.html#tspaint.Painting.segments tspaint.Painting.segments
tspaint.Painting py:class 1 api/Painting.html#tspaint.Painting -
tspaint.api.Painting py:class 1 api/Painting.html#tspaint.Painting tspaint.Painting
tspaint.fit py:function 1 api/fit.html#tspaint.fit -
tspaint.em.fit py:function 1 api/fit.html#tspaint.fit tspaint.fit
tspaint.FitResult py:class 1 api/FitResult.html#tspaint.FitResult -
tspaint.em.FitResult py:class 1 api/FitResult.html#tspaint.FitResult tspaint.FitResult
tspaint.output.posterior_table py:function 1 api/output.posterior_table.html#tspaint.output.posterior_table -
tspaint.output.hard_segments py:function 1 api/output.hard_segments.html#tspaint.output.hard_segments -
tspaint.output.Segment py:class 1 api/output.Segment.html#tspaint.output.Segment -
tspaint.output.missing_info_mask py:function 1 api/output.missing_info_mask.html#tspaint.output.missing_info_mask -
tspaint.output.posterior_at py:function 1 api/output.posterior_at.html#tspaint.output.posterior_at -
tspaint.reference_qc py:function 1 api/reference_qc.html#tspaint.reference_qc -
tspaint.introgression.reference_qc py:function 1 api/reference_qc.html#tspaint.reference_qc tspaint.reference_qc
tspaint.foreign_tracts py:function 1 api/foreign_tracts.html#tspaint.foreign_tracts -
tspaint.introgression.foreign_tracts py:function 1 api/foreign_tracts.html#tspaint.foreign_tracts tspaint.foreign_tracts
tspaint.detect_ghost py:function 1 api/detect_ghost.html#tspaint.detect_ghost -
tspaint.introgression.detect_ghost py:function 1 api/detect_ghost.html#tspaint.detect_ghost tspaint.detect_ghost
tspaint.detect_archaic py:function 1 api/detect_archaic.html#tspaint.detect_archaic -
tspaint.archaic.detect_archaic py:function 1 api/detect_archaic.html#tspaint.detect_archaic tspaint.detect_archaic
tspaint.output.loo_posterior_table py:function 1 api/output.loo_posterior_table.html#tspaint.output.loo_posterior_table -
tspaint.introgression.ReferenceQC.flagged_tracts py:function 1 api/introgression.ReferenceQC.html#tspaint.introgression.ReferenceQC.flagged_tracts -
tspaint.introgression.ReferenceQC.foreign_fraction py:function 1 api/introgression.ReferenceQC.html#tspaint.introgression.ReferenceQC.foreign_fraction -
tspaint.introgression.ReferenceQC.introgression_map py:function 1 api/introgression.ReferenceQC.html#tspaint.introgression.ReferenceQC.introgression_map -
tspaint.introgression.ReferenceQC.summary py:function 1 api/introgression.ReferenceQC.html#tspaint.introgression.ReferenceQC.summary -
tspaint.introgression.ReferenceQC py:class 1 api/introgression.ReferenceQC.html#tspaint.introgression.ReferenceQC -
tspaint.introgression.GhostResult.tracts py:function 1 api/introgression.GhostResult.html#tspaint.introgression.GhostResult.tracts -
tspaint.introgression.GhostResult py:class 1 api/introgression.GhostResult.html#tspaint.introgression.GhostResult -
tspaint.introgression.foreignness_track py:function 1 api/introgression.foreignness_track.html#tspaint.introgression.foreignness_track -
tspaint.archaic.ArchaicResult.tracts py:function 1 api/archaic.ArchaicResult.html#tspaint.archaic.ArchaicResult.tracts -
tspaint.archaic.ArchaicResult py:class 1 api/archaic.ArchaicResult.html#tspaint.archaic.ArchaicResult -
tspaint.validate.balanced_accuracy py:function 1 api/validate.balanced_accuracy.html#tspaint.validate.balanced_accuracy -
tspaint.validate.per_base_accuracy py:function 1 api/validate.per_base_accuracy.html#tspaint.validate.per_base_accuracy -
tspaint.validate.mean_confidence py:function 1 api/validate.mean_confidence.html#tspaint.validate.mean_confidence -
tspaint.validate.reliability_curve py:function 1 api/validate.reliability_curve.html#tspaint.validate.reliability_curve -
tspaint.validate.breakpoint_precision_recall py:function 1 api/validate.breakpoint_precision_recall.html#tspaint.validate.breakpoint_precision_recall -
tspaint.validate.switch_density py:function 1 api/validate.switch_density.html#tspaint.validate.switch_density -
tspaint.validate.tract_boundary_error py:function 1 api/validate.tract_boundary_error.html#tspaint.validate.tract_boundary_error -
tspaint.validate.breakpoint_flicker py:function 1 api/validate.breakpoint_flicker.html#tspaint.validate.breakpoint_flicker -
tspaint.validate.map_truth py:function 1 api/validate.map_truth.html#tspaint.validate.map_truth -
tspaint.compare.tspaint_paint py:function 1 api/compare.tspaint_paint.html#tspaint.compare.tspaint_paint -
tspaint.compare.nearest_reference_paint py:function 1 api/compare.nearest_reference_paint.html#tspaint.compare.nearest_reference_paint -
tspaint.compare.rfmix_paint py:function 1 api/compare.rfmix_paint.html#tspaint.compare.rfmix_paint -
tspaint.io_rfmix.rfmix_paint py:function 1 api/compare.rfmix_paint.html#tspaint.compare.rfmix_paint tspaint.compare.rfmix_paint
tspaint.compare.head_to_head py:function 1 api/compare.head_to_head.html#tspaint.compare.head_to_head -
tspaint.compare.score_painter py:function 1 api/compare.score_painter.html#tspaint.compare.score_painter -
tspaint.io.tsinfer py:function 1 api/io.tsinfer.html#tspaint.io.tsinfer -
tspaint.io_tsinfer.tsinfer py:function 1 api/io.tsinfer.html#tspaint.io.tsinfer tspaint.io.tsinfer
tspaint.io.relate py:function 1 api/io.relate.html#tspaint.io.relate -
tspaint.io_relate.relate py:function 1 api/io.relate.html#tspaint.io.relate tspaint.io.relate
tspaint.io.singer py:function 1 api/io.singer.html#tspaint.io.singer -
tspaint.io_singer.singer py:function 1 api/io.singer.html#tspaint.io.singer tspaint.io.singer
tspaint.io.add_mutations py:function 1 api/io.add_mutations.html#tspaint.io.add_mutations -
tspaint.io_tsinfer.add_mutations py:function 1 api/io.add_mutations.html#tspaint.io.add_mutations tspaint.io.add_mutations
tspaint.io.write_haploid_vcf py:function 1 api/io.write_haploid_vcf.html#tspaint.io.write_haploid_vcf -
tspaint.io_singer.write_haploid_vcf py:function 1 api/io.write_haploid_vcf.html#tspaint.io.write_haploid_vcf tspaint.io.write_haploid_vcf
tspaint.io.check_persistence py:function 1 api/io.check_persistence.html#tspaint.io.check_persistence -
tspaint.io_relate.check_persistence py:function 1 api/io.check_persistence.html#tspaint.io.check_persistence tspaint.io.check_persistence
tspaint.io_genotypes.Variants py:class 1 api/io_genotypes.Variants.html#tspaint.io_genotypes.Variants -
tspaint.bp.bp_paint py:function 1 api/bp.bp_paint.html#tspaint.bp.bp_paint -
tspaint.bp.horizontal.bp_paint py:function 1 api/bp.bp_paint.html#tspaint.bp.bp_paint tspaint.bp.bp_paint
tspaint.bp.bp_smooth py:function 1 api/bp.bp_smooth.html#tspaint.bp.bp_smooth -
tspaint.bp.horizontal.bp_smooth py:function 1 api/bp.bp_smooth.html#tspaint.bp.bp_smooth tspaint.bp.bp_smooth
tspaint.bp.bp_smooth_track py:function 1 api/bp.bp_smooth_track.html#tspaint.bp.bp_smooth_track -
tspaint.bp.horizontal.bp_smooth_track py:function 1 api/bp.bp_smooth_track.html#tspaint.bp.bp_smooth_track tspaint.bp.bp_smooth_track
tspaint.bp.bp_vs_deadband_experiment py:function 1 api/bp.bp_vs_deadband_experiment.html#tspaint.bp.bp_vs_deadband_experiment -
tspaint.bp.experiments.bp_vs_deadband_experiment py:function 1 api/bp.bp_vs_deadband_experiment.html#tspaint.bp.bp_vs_deadband_experiment tspaint.bp.bp_vs_deadband_experiment
tspaint.fit_rate_through_time py:function 1 api/fit_rate_through_time.html#tspaint.fit_rate_through_time -
tspaint.dating.em.fit_rate_through_time py:function 1 api/fit_rate_through_time.html#tspaint.fit_rate_through_time tspaint.fit_rate_through_time
tspaint.RateThroughTime.plot py:function 1 api/RateThroughTime.html#tspaint.RateThroughTime.plot -
tspaint.dating.em.RateThroughTime.plot py:function 1 api/RateThroughTime.html#tspaint.RateThroughTime.plot tspaint.RateThroughTime.plot
tspaint.RateThroughTime py:class 1 api/RateThroughTime.html#tspaint.RateThroughTime -
tspaint.dating.em.RateThroughTime py:class 1 api/RateThroughTime.html#tspaint.RateThroughTime tspaint.RateThroughTime
tspaint.dating.paint_qt py:function 1 api/dating.paint_qt.html#tspaint.dating.paint_qt -
tspaint.dating.estep.paint_qt py:function 1 api/dating.paint_qt.html#tspaint.dating.paint_qt tspaint.dating.paint_qt
tspaint.dating.rate_through_time_binned py:function 1 api/dating.rate_through_time_binned.html#tspaint.dating.rate_through_time_binned -
tspaint.dating.estep.rate_through_time_binned py:function 1 api/dating.rate_through_time_binned.html#tspaint.dating.rate_through_time_binned tspaint.dating.rate_through_time_binned
tspaint.dating.make_Q_of_cell py:function 1 api/dating.make_Q_of_cell.html#tspaint.dating.make_Q_of_cell -
tspaint.dating.em.make_Q_of_cell py:function 1 api/dating.make_Q_of_cell.html#tspaint.dating.make_Q_of_cell tspaint.dating.make_Q_of_cell
tspaint.dating.directional_rate_splines py:function 1 api/dating.directional_rate_splines.html#tspaint.dating.directional_rate_splines -
tspaint.dating.mstep.directional_rate_splines py:function 1 api/dating.directional_rate_splines.html#tspaint.dating.directional_rate_splines tspaint.dating.directional_rate_splines
tspaint.dating.fit_poisson_spline py:function 1 api/dating.fit_poisson_spline.html#tspaint.dating.fit_poisson_spline -
tspaint.dating.mstep.fit_poisson_spline py:function 1 api/dating.fit_poisson_spline.html#tspaint.dating.fit_poisson_spline tspaint.dating.fit_poisson_spline
tspaint.dating.select_lambda_gcv py:function 1 api/dating.select_lambda_gcv.html#tspaint.dating.select_lambda_gcv -
tspaint.dating.mstep.select_lambda_gcv py:function 1 api/dating.select_lambda_gcv.html#tspaint.dating.select_lambda_gcv tspaint.dating.select_lambda_gcv
tspaint.dating.log_time_grid py:function 1 api/dating.log_time_grid.html#tspaint.dating.log_time_grid -
tspaint.dating.grid.log_time_grid py:function 1 api/dating.log_time_grid.html#tspaint.dating.log_time_grid tspaint.dating.log_time_grid
tspaint.dating.split_branch py:function 1 api/dating.split_branch.html#tspaint.dating.split_branch -
tspaint.dating.grid.split_branch py:function 1 api/dating.split_branch.html#tspaint.dating.split_branch tspaint.dating.split_branch
tspaint.dating.branch_cell_stats py:function 1 api/dating.branch_cell_stats.html#tspaint.dating.branch_cell_stats -
tspaint.dating.estep.branch_cell_stats py:function 1 api/dating.branch_cell_stats.html#tspaint.dating.branch_cell_stats tspaint.dating.branch_cell_stats
tspaint.dating.composite_transition py:function 1 api/dating.composite_transition.html#tspaint.dating.composite_transition -
tspaint.dating.estep.composite_transition py:function 1 api/dating.composite_transition.html#tspaint.dating.composite_transition tspaint.dating.composite_transition
tspaint.simulate_admixture py:function 1 api/simulate_admixture.html#tspaint.simulate_admixture -
tspaint.sim.simulate_admixture py:function 1 api/simulate_admixture.html#tspaint.simulate_admixture tspaint.simulate_admixture
tspaint.local_ancestry_truth py:function 1 api/local_ancestry_truth.html#tspaint.local_ancestry_truth -
tspaint.sim.local_ancestry_truth py:function 1 api/local_ancestry_truth.html#tspaint.local_ancestry_truth tspaint.local_ancestry_truth
tspaint.sim.admixture_demography py:function 1 api/sim.admixture_demography.html#tspaint.sim.admixture_demography -
tspaint.sim.simulate_admixture_impure_refs py:function 1 api/sim.simulate_admixture_impure_refs.html#tspaint.sim.simulate_admixture_impure_refs -
tspaint.sim.simulate_admixture_with_ghost py:function 1 api/sim.simulate_admixture_with_ghost.html#tspaint.sim.simulate_admixture_with_ghost -
tspaint.sim.admixture_demography_with_ghost py:function 1 api/sim.admixture_demography_with_ghost.html#tspaint.sim.admixture_demography_with_ghost -
tspaint.make_generator_2state py:function 1 api/make_generator_2state.html#tspaint.make_generator_2state -
tspaint.model.make_generator_2state py:function 1 api/make_generator_2state.html#tspaint.make_generator_2state tspaint.make_generator_2state
tspaint.model.transition_matrix py:function 1 api/model.transition_matrix.html#tspaint.model.transition_matrix -
tspaint.model.stationary_distribution py:function 1 api/model.stationary_distribution.html#tspaint.model.stationary_distribution -
tspaint.model.tip_emission py:function 1 api/model.tip_emission.html#tspaint.model.tip_emission -
tspaint.model.query_emission py:function 1 api/model.query_emission.html#tspaint.model.query_emission -
tspaint.model.validate_generator py:function 1 api/model.validate_generator.html#tspaint.model.validate_generator -
tspaint.experiments.admixture_experiment py:function 1 api/experiments.admixture_experiment.html#tspaint.experiments.admixture_experiment -
tspaint.experiments.age_sweep py:function 1 api/experiments.age_sweep.html#tspaint.experiments.age_sweep -
tspaint.experiments.scaling_sweep py:function 1 api/experiments.scaling_sweep.html#tspaint.experiments.scaling_sweep -
tspaint.experiments.fragmentation_experiment py:function 1 api/experiments.fragmentation_experiment.html#tspaint.experiments.fragmentation_experiment -
tspaint.experiments.arg_ensemble_experiment py:function 1 api/experiments.arg_ensemble_experiment.html#tspaint.experiments.arg_ensemble_experiment -
tspaint.experiments.singer_ensemble_experiment py:function 1 api/experiments.singer_ensemble_experiment.html#tspaint.experiments.singer_ensemble_experiment -
tspaint.experiments.impure_reference_experiment py:function 1 api/experiments.impure_reference_experiment.html#tspaint.experiments.impure_reference_experiment -
tspaint.experiments.impure_reference_sweep py:function 1 api/experiments.impure_reference_sweep.html#tspaint.experiments.impure_reference_sweep -
tspaint.experiments.flicker_vs_true_boundaries py:function 1 api/experiments.flicker_vs_true_boundaries.html#tspaint.experiments.flicker_vs_true_boundaries -
tspaint.ensemble.merge_posterior_tables py:function 1 api/ensemble.merge_posterior_tables.html#tspaint.ensemble.merge_posterior_tables -
tspaint.ensemble.MergedSegment py:class 1 api/ensemble.MergedSegment.html#tspaint.ensemble.MergedSegment -
tspaint.pruning.prune_tree py:function 1 api/pruning.prune_tree.html#tspaint.pruning.prune_tree -
tspaint.pruning.prune_root py:function 1 api/pruning.prune_root.html#tspaint.pruning.prune_root -
tspaint.accumulate.accumulate_sufficient_statistics py:function 1 api/accumulate.accumulate_sufficient_statistics.html#tspaint.accumulate.accumulate_sufficient_statistics -
tspaint.branch_stats.branch_expected_stats py:function 1 api/branch_stats.branch_expected_stats.html#tspaint.branch_stats.branch_expected_stats -
tspaint.em.build_emissions py:function 1 api/em.build_emissions.html#tspaint.em.build_emissions -
tspaint.em.m_step_Q py:function 1 api/em.m_step_Q.html#tspaint.em.m_step_Q -
tspaint.em.m_step_pi py:function 1 api/em.m_step_pi.html#tspaint.em.m_step_pi -
tspaint.em.m_step_w py:function 1 api/em.m_step_w.html#tspaint.em.m_step_w -
tspaint.ranked.ranked_tree_sequence py:function 1 api/ranked.ranked_tree_sequence.html#tspaint.ranked.ranked_tree_sequence -
tspaint.diagnostics.persistence_summary py:function 1 api/diagnostics.persistence_summary.html#tspaint.diagnostics.persistence_summary -
tspaint.diagnostics.node_persistence py:function 1 api/diagnostics.node_persistence.html#tspaint.diagnostics.node_persistence -
tspaint.diagnostics.edge_span_summary py:function 1 api/diagnostics.edge_span_summary.html#tspaint.diagnostics.edge_span_summary -
