gibbs_update_one_indiv_in_place: does a gibbs update of the full sibling group of individual...

Description Usage Arguments

Description

does a gibbs update of the full sibling group of individual Ind

Usage

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gibbs_update_one_indiv_in_place(FSL, IFS, LMMI, LMMFS, PMMFS, KidProngs, Pile,
  MatPile, AFSL, Gfreqs, UPG, TP, IndLiks, Ind)

Arguments

FSL

list of integer vectors. Each component is a list of two componontes: LMMI_Idx = the index of the sibgroup in LMMI (see below). It also is the column that Ind's current full sib group occuppies in LMMFS

IFS

individual full siblings group vector. A vector such that element i contains the base-0 index of the sibship to which the individual with index i belongs. and PMMFS, and KidProngs Indivs = the the base-0 indices of individuals in the full sibship.

LMMI

Likelihood matrix of marriages given individuals.

LMMFS

Likelihood matrix of marriages given full sibships.

PMMFS

Posterior matrix of marriages given full sibships.

KidProngs

Posterior predictives for the next individuals to be sampled from a full sibship.

Pile

An integer vector that we will use as a stack to hold the indices of empty FSL list elements that we can put newly formed sibships into

MatPile

An integer vector that is parallel to Pile that holds the corresponding column of LMMFS that go along with the elements of Pile. can be renewed.

AFSL

The acceptable full siblings list. Component i is a vector of the base-0 indices of the individuals that indiv i has high full-sibling LOD with.

Gfreqs

The genotype frequencies.

UPG

Unrelated Pair Genotype Frequencies.

TP

Transmission probabilities

IndLiks

Individual likelihoods

Ind

the index of the individual to be updated.


eriqande/fullsniplings documentation built on May 16, 2019, 8:45 a.m.