Phasing, sire imputation, recombination events identification
and pedigree reconstruction of half-sib families using SNP data

Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data

Mohammad Ferdosi <mferdosi@myune.edu.au>, Cedric Gondro <gondroce@msu.edu>
Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

c(person("Gianfranco", "Piras", role = c("aut", "cre"),
email = "gpiras@mac.com",
comment = c(ORCID = "0000-0003-0225-6061")),
person("Mauricio", "Sarrias", role = c("aut"),
email = "msarrias86@gmail.com",
comment = c(ORCID = "0000-0001-5932-4817")))
Spatial heterogeneity can be specified in various ways. 'hspm' is an ambitious project that aims at implementing various methodologies to control for heterogeneity in spatial models. The current version of 'hspm' deals with spatial and (non-spatial) regimes models. In particular, the package allows to estimate a general spatial regimes model with additional endogenous variables, specified in terms of a spatial lag of the dependent variable, the spatially lagged regressors, and, potentially, a spatially autocorrelated error term. Spatial regime models are estimated by instrumental variables and generalized methods of moments (see Arraiz et al., (2010) <doi:10.1111/j.1467-9787.2009.00618.x>, Bivand and Piras, (2015) <doi:10.18637/jss.v063.i18>, Drukker et al., (2013) <doi:10.1080/07474938.2013.741020>, Kelejian and Prucha, (2010) <doi:10.1016/j.jeconom.2009.10.025>).
Gianfranco Piras [aut, cre] (<https://orcid.org/0000-0003-0225-6061>),
Mauricio Sarrias [aut] (<https://orcid.org/0000-0001-5932-4817>)

Estimation of Recombination Rate and Maternal LD in Half-Sibs
c(person("Dörte","Wittenburg", role = c("aut", "cre"),
email = "wittenburg@fbn-dummerstorf.de"))
Paternal recombination rate and maternal linkage disequilibrium
(LD) are estimated for pairs of biallelic markers such as single nucleotide
polymorphisms (SNPs) from progeny genotypes and sire haplotypes. At least
one sire has to be double heterozygous at the investigated pairs of SNPs.
The implementation relies on paternal half-sib families. If maternal half-
sib families are used, the roles of sire/dam are swapped. Multiple families
can be considered.
Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of
recombination rate and maternal linkage disequilibrium in half-sibs"
<doi:10.3389/fgene.2018.00186>.
Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium
in half-sib families" <doi:10.1534/genetics.111.137521>.
Rcpp (>= 1.0.3), hsphase, dplyr, data.table, rlist