Package index • tekkamaki

Run simulation

tekka(): Run the tekka simulator.

tekka_path() tekka_version(): Get information about the tekka executable

read_tekka(): Read results from tekka

Kinship

find_kinship(): Analyze kinship within samples

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

as_igraph(<sample_family>): Convert sample family data.frames to igraphlight objects

Generate SNPs

make_gene_genealogy() gather_segments() count_uncoalesced() annotate_sampled(): Generate gene genealogy from samples

make_snp() make_snp_chromosome() place_mutations(): Generate SNPs on given samples.

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

Misc.

count_sampled(): Count actually sampled individuals

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

plot_parameters_json(): Visualize parameter json file