Implementation of S4 class of sets and multisets of numbers.
    The implementation is based on the hash table from the package 'hash'.
    Quick operations are allowed when the set is a dynamic object.
    The implementation is discussed in detail in Ceoldo and Wit (2023) <arXiv:2304.09809>.

To test the homogeneity of stratum effects in stratified paired binary data.

Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

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>).

Several functions that allow by different methods to infer a piecewise polynomial regression model under regularity constraints, namely continuity or differentiability of the link function. The implemented functions are either specific to data with two regimes, or generic for any number of regimes, which can be given by the user or learned by the algorithm. A paper describing all these methods will be submitted soon. The reference will be added to this file as soon as available.

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. 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. For parameter estimation, at least one sire has to be double 
    heterozygous at the investigated pairs of SNPs.
    Based on recombination rates, genetic distances between markers can be 
    estimated. Markers with unusually large recombination rate to markers in 
    close proximity (i.e. putatively misplaced markers) shall be discarded in 
    this derivation.
    A workflow description is attached as vignette.
    *A pipeline is available at GitHub*
    <https://github.com/wittenburg/hsrecombi>
    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>.