Function reference • admixtools

ADMIXTOOLS programs
`qp3pop()`	Estimate f3 statistics
`qpdstat()`	Estimate f4 statistics
`qpf4ratio()`	Estimate admixture proportions via f4 ratios
`qpwave()`	Estimate admixture waves
`qpadm()`	Estimate admixture weights
`qpgraph()`	Compute the fit of an admixture graph
Wrapper functions
`qp3pop_wrapper()`	Wrapper function around the original qp3Pop program
`qpadm_wrapper()`	Wrapper function around the original qpAdm program
`qpdstat_wrapper()`	Wrapper function around the original qpDstat program
`qpf4ratio_wrapper()`	Wrapper function around the original qpF4ratio program
`qpgraph_wrapper()`	Wrapper function around the original qpGraph program
`qpwave_wrapper()`	Wrapper function around the original qpWave program
Parsing functions
`parse_dot()`	Read graph in dot format
`parse_qp3pop_output()`	Read qp3Pop output file
`parse_qpadm_output()`	Read qpAdm output file
`parse_qpdstat_output()`	Read qpDstat output file
`parse_qpf4ratio_output()`	Read qpF4ratio output file
`parse_qpgraph_graphfile()`	Read qpGraph graph file
`parse_qpgraph_output()`	Read qpGraph output file
Plotting functions
`plot_comparison()`	Compare two models
`plot_graph()`	Plot an admixture graph
`plot_graph_map()`	Plot an admixture graph on a map
`plot_map()`	Plot samples on a map
`plotly_comparison()`	Compare two models
`plotly_graph()`	Plot an admixture graph using plotly
Resampling functions
`qp3pop_resample_inds()` `qpdstat_resample_inds()` `qpwave_resample_inds()` `qpadm_resample_inds()` `qpgraph_resample_inds()`	Run models while leaving out individuals
`qp3pop_resample_snps()` `qpdstat_resample_snps()` `qpwave_resample_snps()` `qpadm_resample_snps()` `qpgraph_resample_snps()`	Run models while leaving out SNP blocks
Reading and writing
`extract_f2()`	Compute and store blocked f2 statistics
`extract_counts()`	Extract and store data needed to compute blocked f2
`f2_from_precomp()`	Read blocked f2 statistics from disk
`read_packedancestrymap()`	Read genotype data from packedancestrymap files
`read_plink()`	Read genotype data from `PLINK` files
`packedancestrymap_to_afs()`	Read allele frequencies from packedancestrymap files
`plink_to_afs()`	Read allele frequencies from `PLINK` files
`packedancestrymap_to_plink()`	Convert EIGENSTRAT or PACKEDANCESTRYMAP to PLINK
Model exploration
`find_graphs()`	Find well fitting admixture graphs
`qpwave_pairs()`	Compute all pairwise qpwave p-values
`qpadm_rotate()`	Compute p-values for many qpadm models
Everything
`admixtools`	Tools for inferring demographic history from genetic data
`afs_to_counts()`	Compute count blocks and write them to disk
`afs_to_f2()`	Compute f2 blocks and write them to disk
`afs_to_f2_blocks()`	Compute all pairwise f2 statistics
`agraph_to_igraph()`	Convert agraph to igraph
`boo_list()`	Generate a list of bootstrap resampled arrays
`compare_fits()`	Compare the fit of two qpgraph models
`compare_fits2()`	Compare the fit of two qpgraph models
`compare_fits4()`	Compare the fit of two qpgraph models
`count_snps()`	Count SNPs in an f2-statistics array
`count_zero_edges()`	Count zero-length edges
`decomposed_tree_neighbors()`	Find all trees within SPR distance of 1 of all graph component trees
`delete_admix()`	Delete an admixture edge
`delete_groups()`	Delete groups
`delete_leaf()`	Remove population from graph
`desimplify_graph()`	Add two nodes before each admixture node
`edges_to_igraph()`	Convert data frame graph to igraph
`eigenstrat_to_afs()`	Read allele frequencies from EIGENSTRAT files
`est_to_boo()`	Turn per-block estimates into bootstrap estimates
`est_to_loo()`	Turn per-block estimates into leave-one-out estimates
`example_anno`	Data frame with sample annotations
`example_f2_blocks`	Blocked f2-statistics for 7 populations
`example_graph`	Admixture graph for 7 populations
`example_igraph`	Admixture graph for 7 populations
`example_opt`	Data frame with one fitted admixture graph
`example_qpgraph_ref_results`	example_graph fitted using qpGraph
`example_triples`	Data frame with population triples
`extract_afs()`	Compute and store blocked allele frequency data
`extract_afs_simple()`	Compute and store blocked allele frequency data
`extract_counts()`	Extract and store data needed to compute blocked f2
`extract_f2()`	Compute and store blocked f2 statistics
`extract_f2_large()`	Compute and store blocked f2 statistics
`extract_f2_subset()`	Copy f2-statistics
`extract_samples()`	Extract samples from PLINK files
`f2()`	Estimate f2 statistics
`f2_from_geno()`	Compute blocked f2 statistics
`f2_from_msprime()`	Simulate an admixture graph in msprime
`f2_from_precomp()`	Read blocked f2 statistics from disk
`f2dat_f4dat()`	Turn f2 data to f4 data
`f3blockdat_from_geno()`	f3 from genotype data
`f4_from_afdat()`	Compute f4 from allele frequencies
`f4_from_f2()`	Get per-block f4-statistics
`f4blockdat_from_geno()`	f4 from genotype data
`f4blockdat_to_f4blocks()`	Turn f4 block data to 3d array
`find_admixedges()`	Find admixture edges
`find_graphs()`	Find well fitting admixture graphs
`find_graphs_old()`	Find well fitting admixture graphs
`find_newedges()`	Find possible new edges
`find_normedges()`	Find drift edges
`flipadmix_random()`	Modify a graph flipping the direction of an admixture edge
`fst()`	Compute Fst
`generate_all_graphs()`	Generate all graphs
`generate_all_trees()`	Generate all trees
`get_block_lengths()`	Find LD-independent blocks
`get_f2()`	Turns f2_data into f2_blocks
`get_leafnames()`	Get the population names of a graph
`get_outpop()`	Get the outgroup from a graph (if it exists)
`get_rootname()`	Get the root name
`graph_addleaf()`	Add a population to an admixture graph
`graph_distances()`	Pairwise distance estimates for graphs
`graph_equations()`	Find well fitting admixture graphs
`graph_f2_function()`	Make a function representing a graph
`graph_flipadmix()`	Find all valid graphs which result from flipping one admixture edge
`graph_hash()`	Get unique hash of an admixture graph
`graph_minusone()`	Find all graphs which result from removing one admixture edge
`graph_minusplus()`	Find all graphs which result from adding and removing one admixture edge
`graph_plusone()`	Find all graphs which result from adding one admixture edge
`graph_splittrees()`	Find all trees which are part of the admixture graph
`graph_to_afs()`	Simulate allele frequncies under an admixture graph
`graph_to_pcs()`	Simulate PCs under an admixture graph
`graph_to_qpadm()`	Get all qpadm models for a graph
`graphmod_pavel()`	Return all graphs created from permuting a subclade
`group_samples()`	Group precomputed data
`igraph_to_agraph()`	Convert igraph to agraph
`insert_admix()`	Insert a single edge into graph
`insert_admix_n()`	Insert admixture edges into graph
`insert_admix_old()`	Insert admixture edges into graph
`insert_leaf()`	Add population to graph
`is_valid()`	Test if an admixture graph is valid
`isomorphism_classes()`	Find identical graphs
`isomorphism_classes2()`	Find identical graphs
`joint_sfs()`	Joint site frequency spectrum
`joint_spectrum()`	Estimate joint allele frequency spectrum
`lazadm()`	Estimate admixture weights
`loo_list()`	Generate a list of leave-one-out arrays
`loo_to_est()`	Turn leave-one-out estimates to per-block estimates
`move_admixedge_once()`	Modify a graph by moving an admixture edge
`msprime_genome()`	Simulate an admixture graph in msprime v1.x.
`msprime_sim()`	Simulate an admixture graph in msprime v1.x
`mutate_n()`	Modify a graph by applying n mutation functions
`newick_to_edges()`	Turn a newick format tree to a matrix of edges
`node_counts()`	Count how often each node in graph occurs in other graphs
`node_signature()`	Returns a signature of a graph consisting of the left and right descendent leaf nodes of each internal node (sorted and concatenated)
`numadmix()`	Count number of admixture nodes
`packedancestrymap_to_afs()`	Read allele frequencies from packedancestrymap files
`packedancestrymap_to_plink()`	Convert EIGENSTRAT or PACKEDANCESTRYMAP to PLINK
`parse_dot()`	Read graph in dot format
`parse_qp3pop_output()`	Read qp3Pop output file
`parse_qpadm_output()`	Read qpAdm output file
`parse_qpdstat_output()`	Read qpDstat output file
`parse_qpf4ratio_output()`	Read qpF4ratio output file
`parse_qpgraph_graphfile()`	Read qpGraph graph file
`parse_qpgraph_output()`	Read qpGraph output file
`permute_leaves()`	Modify a graph by permuting leaf nodes
`place_root_random()`	Modify a graph by changing the position of the root node
`plink_to_afs()`	Read allele frequencies from `PLINK` files
`plot_comparison()`	Compare two models
`plot_graph()`	Plot an admixture graph
`plot_graph_map()`	Plot an admixture graph on a map
`plot_map()`	Plot samples on a map
`plotly_comparison()`	Compare two models
`plotly_graph()`	Plot an admixture graph using plotly
`pseudo_dates()`	Get pseudo dates for graph nodes
`qp3pop()`	Estimate f3 statistics
`qp3pop_wrapper()`	Wrapper function around the original qp3Pop program
`qpadm()`	Estimate admixture weights
`qpadm_models()`	Partition a list of populations into left and right populations
`qpadm_models_old()`	Return all valid qpAdm models for an admixturegraph
`qpadm_multi()`	Run multiple qpadm models
`qpadm_p()`	Faster version of `qpadm` with reduced output
`qpadm_rotate()`	Compute p-values for many qpadm models
`qpadm_wrapper()`	Wrapper function around the original qpAdm program
`qpdstat()`	Estimate f4 statistics
`qpdstat_wrapper()`	Wrapper function around the original qpDstat program
`qpf4diff()`	Estimate f4 differences
`qpf4ratio()`	Estimate admixture proportions via f4 ratios
`qpf4ratio_wrapper()`	Wrapper function around the original qpF4ratio program
`qpfstats()`	Get smoothed f2-statistics
`qpgraph()`	Compute the fit of an admixture graph
`qpgraph_precompute_f3()`	Compute f3-statistics from f2-statistics.
`qpgraph_resample_multi()`	Evaluate a qpgraph models many times
`qpgraph_resample_snps2()`	Evaluate a qpgraph model many times
`qpgraph_wrapper()`	Wrapper function around the original qpGraph program
`qpwave()`	Estimate admixture waves
`qpwave_pairs()`	Compute all pairwise qpwave p-values
`qpwave_wrapper()`	Wrapper function around the original qpWave program
`random_admixturegraph()`	Generate a random admixture graph
`random_dates()`	Get random dates for graph nodes
`random_newick()`	Generate a random binary graph
`random_sim()`	Generate a random graph and simulate it in msprime v1.x
`read_eigenstrat()`	Read genotype data from EIGENSTRAT files
`read_f2()`	Read blocked f2 estimates from disk
`read_packedancestrymap()`	Read genotype data from packedancestrymap files
`read_plink()`	Read genotype data from `PLINK` files
`qp3pop_resample_inds()` `qpdstat_resample_inds()` `qpwave_resample_inds()` `qpadm_resample_inds()` `qpgraph_resample_inds()`	Run models while leaving out individuals
`qp3pop_resample_snps()` `qpdstat_resample_snps()` `qpwave_resample_snps()` `qpadm_resample_snps()` `qpgraph_resample_snps()`	Run models while leaving out SNP blocks
`rotate_models()`	Rotate populations between left and right
`run_shiny_admixtools()`	Launch ADMIXTOOLS 2 GUI
`satisfies_constraints()`	Test constraints on a graph
`satisfies_eventorder()`	Test f4 constraints on a graph
`satisfies_nonzerof4()`	Test f4 constraints on a graph
`satisfies_numadmix()`	Test admixture constraints on a graph
`satisfies_zerof4()`	Test f4 constraints on a graph
`shortest_unique_prefixes()`	Return shortest unique prefixes
`simplify_graph()`	Remove redundant edges
`split_mat()`	Split a matrix into blocks
`split_multifurcations()`	Split nodes with more than two edges
`spr_all()`	Modify a graph by regrafting a subcomponent
`spr_leaves()`	Modify a graph by regrafting a leaf
`summarize_descendants()`	List leaf nodes for all internal nodes
`summarize_descendants_list()`	List leaf nodes for all internal nodes in a list of graphs
`summarize_eventorder()`	List population split events in a graph
`summarize_eventorder_list()`	List population split events in a list of graphs
`summarize_fits()`	Summarize graph fits
`summarize_numadmix()`	List number of admixture events for each population
`summarize_numadmix_list()`	List number of admixture events for each population in a list of graphs
`summarize_proxies()`	Assign proxy populations to admixed populations
`summarize_proxies_list()`	List proxy populations in graphlist
`summarize_triples()`	Summarize triples across graphs
`summarize_zerof4()`	List clades in a graph
`summarize_zerof4_list()`	List clades in a list of graphs
`swap_leaves()`	Modify a graph by swapping two leaf nodes
`test_cladality()`	Test if two sets of populations form two clades
`tree_in_graph()`	Test if a tree is part of a graph
`tree_neighbors()`	Find all trees within SPR distance of 1
`unidentifiable_edges()`	Find all unidentifiable edges
`write_dot()`	Convert graph to dot format
`write_f2()`	Write blocked f2 estimates to disk

Reference

ADMIXTOOLS programs

Wrapper functions

Parsing functions

Plotting functions

Resampling functions

Reading and writing

Model exploration

Everything