compile_related_pairs {CKMRpop}

compile pairwise relationships from the samples

Description

Run this on some of the output from slurp_spip().

Usage

compile_related_pairs(S)

Arguments

S

a tibble. In the context of this package this tibble is typically going to often be the samples component of the output slurped up from spip with slurp_spip(). More generally, it is a tibble that must have the columns:

• ID: the id of the sample

• ancestors: a list column of the ancestor vectors of each individual

• relatives: a list column of the vectors of individual samples (including self) that each individual is related to.

Value

a tibble with columns id_1 and id_2 for each pair. Any additional columns outside of relatives will be joined with ⁠_1⁠ and ⁠_2⁠ suffixes. In a typical run slurped up from spip this leads to the following columns:

• id_1: the id of the first sample of the pair,

• id_2: the id of the 2nd sample of the pair,

• conn_comp: the index of the connected component to which the pair belongs,

• dom_relat: the dominant relationship that the pair shares,

• max_hit: the number of shared ancestors at the level of the dominant relationship

• dr_hits: a list column of two-vectors—the number of shared ancestors at the level of the dominant relationship in the upper and lower quadrants, respectively of the ancestry match matrix. If the relationship is symmetrical, the two values are the same.

• upper_member: for non-symmetrical relationships, a 1 or a 2 indicating which member of the pair is the one that is typically older (i.e. the uncle in an uncle-nephew relationship), or NA if the relationship is symmetrical.

• times_encountered: the number of times this pair was encountered when processing the output of the depth first search algorithm that found these pairs. Not typically used for downstream analyses.

• primary_shared_ancestors: a list columns of two-vectors. The first element of each is the the position in the ancestry vector of id_1's primary shared ancestor. The second element is the same for id_2.

• psa_tibs: like primary_shared_ancestor but a list column of tibbles.

• pop_pre_1, pop_post_1, pop_dur_1: the population from which the id_1 individual was sampled during the prekill, postkill, or during-reproduction sampling episodes, respectively. NA for episodes in which the individual was not sampled

• pop_pre_2, pop_post_2, pop_dur_2: same as above for the id_2 individual.

• sex_1: sex of the id_1 individual,

• sex_2: sex of the id_2 individual,

• born_year_1: birth year of the id_1 individual,

• born_year_2: birth year of the id_2 individual,

• samp_years_list_pre_1: list column of years during which the id_1 individual was sampled during the prekill episode.

• samp_years_list_dur_1: list column of years during which the id_1 individual was sampled during reproduction.

• samp_years_list_post_1: list column of years during which the id_1 individual was sampled during the postkill episode.

• samp_years_list_1: by default this column is identical to samp_years_list_post_1 and is the column used in downstream plotting by some functions. If you want to use a different column, for example samp_years_list_pre_1 for the downstream plotting, then set the value of samp_years_list_1 to the same values,

• samp_years_list_pre_2, samp_years_list_dur_2, samp_years_list_post_2, samp_years_list_2: same as above but for individual with id_2,

• born_pop_1: index of population in which id_1 was born,

• ancestors_1: ancestry vector of id_1,

• born_pop_2: index of population in which id_2 was born,

• ancestors_2: ancestry vector of id_2,

• anc_match_matrix: the ancestry match matrix (a logical matrix) for the pair.

Examples

C <- compile_related_pairs(three_pops_with_mig_slurped_results$samples)