Package index • tekkamaki

Run simulation

tekka(): Run C++ simulation.

tekka_path() tekka_version(): Get the path to the tekka installation.

read_result(): Read functions

make_gene_genealogy() gather_segments() count_uncoalesced() annotate_sampled(): Functions to generate gene genealogy from sample family table

make_snp() make_snp_chromosome() place_mutations(): Functions to generate SNPs on given samples.

as_vcf() write_vcf() read_vcf() as_vcf_gt() add_pos_id(): Utilities for VCF format

Kinship

find_kinship(): Analyze kinship with igraph

as_hsp() write_hsp() read_hsp(): Count half-sib pairs in HSP format

as_hsp2() write_hsp2() read_hsp2(): Count half-sib pairs in HSP2 format

as_pop() write_pop() read_pop(): Count parent-offspring pairs in POP format

as_pop2() write_pop2() read_pop2(): Count parent-offspring pairs in POP2 format

Misc.

as_igraph(<sample_family>): Convert genealogy to igraph

augment(<sample_family>) augment(<genealogy>) layout_demography() plot(<genealogy>) plot(<sample_family>): Methods for quick visualization

plot_parameters_json(): Visualize parameter json file