Functions to infer co-mapping trait hotspots and causal models.
  Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) 
  Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355-1365. 
  <doi:10.1534/genetics.112.139451>.
  Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013)
  Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003-1013.
  <doi:10.1534/genetics.112.147124>.

Functions to Simultaneously Infer Causal Graphs and Genetic Architecture.
  Includes acyclic and cyclic graphs for data from an experimental cross with a modest number (<10) of phenotypes driven by
  a few genetic loci (QTL).
  Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010)
  Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes.
  Annals of Applied Statistics 4: 320-339.
  <doi:10.1214/09-AOAS288>.

This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.

Provides methods for estimation of mean- and quantile-optimal treatment regimes from censored data. 
    Specifically, we have developed distinct functions for three types of right censoring for static treatment using quantile criterion: (1) independent/random censoring, (2) treatment-dependent random censoring, and (3) covariates-dependent random censoring. It also includes a function to estimate quantile-optimal dynamic treatment regimes for independent censored data. Finally, this package also includes a simulation data generative model of a dynamic treatment experiment proposed in literature.