Inferring demographic history from genetic data

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 |

boo_list | Generate a list of bootstrap resampled arrays |

compare_fits2 | Compare the fit of two qpgraph models |

compare_fits3 | Compare the fit of two qpgraph models |

compare_fits4 | Compare the fit of two qpgraph models |

decomposed_tree_neighbors | Find all trees within SPR distance of 1 of all graph... |

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_qpgraph_ref_results | example_graph fitted using qpGraph |

example_triples | Data frame with population triples |

example_winner | Data frame with one fitted admixture graph |

example_winners | Data frame with fitted admixture graphs |

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_precomp | Read blocked f2 statistics from disk |

f4blockdat_from_geno | f4 from genotype data |

f4blockdat_to_f4blocks | Turn f4 block data to 3d array |

f4_from_f2 | Get per-block f4-statistics |

find_admixedges | Find admixture edges |

find_graphs | 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 |

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_flipadmix | Find all valid graphs which result from flipping one... |

graph_minusone | Find all graphs which result from removing one admixture edge |

graph_minusplus | Find all graphs which result from adding and removing one... |

graphmod_pavel | Return all graphs created from permuting a subclade |

graph_plusone | Find all graphs which result from adding one admixture edge |

graph_splittrees | Find all trees which are part of the admixture graph |

group_samples | Group precomputed data |

insert_admix_igraph | Insert admixture edges into graph |

insert_edge | Insert a single edge into graph |

insert_edges | Insert admixture edges into graph |

insert_leaf | Add population to graph |

isomorphism_classes | Find identical graphs |

isomorphism_classes2 | Find identical graphs |

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_sim | Generate msprime simulation code from admixture graph |

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... |

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_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 |

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 |

plotly_comparison | Compare two models |

plotly_graph | Plot an admixture graph using plotly |

plot_map | Plot samples on a map |

qp3pop | Estimate f3 statistics |

qp3pop_wrapper | Wrapper function around the original qp3Pop program |

qpadm | Estimate admixture weights |

qpadm_models | 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 all pairwise qpadm p-values |

qpadm_wrapper | Wrapper function around the original qpAdm program |

qpdstat | Estimate f4 statistics |

qpdstat_wrapper | Wrapper function around the original qpDstat program |

qpf4ratio | Estimate admixture proportions via f4 ratios |

qpf4ratio_wrapper | Wrapper function around the original qpF4ratio program |

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 |

random_admixturegraph | Generate a random admixture graph |

random_newick | Generate a random binary graph |

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 |

resample_inds | Run models while leaving out individuals |

resample_snps | Run models while leaving out SNP blocks |

run_shiny_admixtools | Launch ADMIXTOOLS 2 GUI |

shortest_unique_prefixes | Return shortest unique prefixes |

simplify_graph | Remove redundant edges |

split_mat | Split a matrix into blocks |

spr_all | Modify a graph by regrafting a subcomponent |

spr_leaves | Modify a graph by regrafting a leaf |

summarize_triples | Summarize triples across graphs |

swap_leaves | Modify a graph by swapping two leaf nodes |

test_cladality | Test if two sets of populations form two clades |

tree_neighbors | Find all trees within SPR distance of 1 |

write_dot | Convert graph to dot format |

write_f2 | Write blocked f2 estimates to disk |

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