Bayesian Models for Partly Interval-Censored Data
Contains functions to fit proportional hazards (PH) model to partly interval-censored (PIC) data (Pan et al. (2020) <doi:10.1177/0962280220921552>), PH model with spatial frailty to spatially dependent PIC data (Pan and Cai (2021) <doi:10.1080/03610918.2020.1839497>), and mixed effects PH model to clustered PIC data. Each random intercept/random effect can follow both a normal prior and a Dirichlet process mixture prior. It also includes the corresponding functions for general interval-censored data.

Self contained gene set analysis for gene- and
pathway-environment interaction analysis
Extension of the ARTP package for gene- and pathway-environment
interaction
'ARTP-GE.R' 'data.to.PIGE.R' 'permutation.snp.R'
'PIGE-package.R' 'compute.p.snp.obs.R' 'LR.inter.cat.R'
'LR.inter.cont.R' 'permutation.wrapper.cont.R' 'LR.cont.R'
'permutation.wrapper.cat.inter.R'
'permutation.wrapper.cont.inter.R'
'permutation.wrapper.cat.inter.Y.and.X.R'
'permutation.wrapper.cont.inter.Y.and.X.R'
'permutation.wrapper.cont.Y.and.X.R' 'LR.cont.surv.R'
'LR.inter.cat.surv.R' 'LR.inter.cont.surv.R'
'data.to.list.gene.snp.R'

Self Contained Gene Set Analysis for Gene- And
Pathway-Environment Interaction Analysis
Benoit Liquet, Therese Truong, Camilo Broc
Extension of the 'ARTP' package (Yu, K., et al. (2009) <doi:10.1002/gepi.20422>) for gene- and pathway-environment interaction. A permutation and a parametric bootstrap approaches have been implemented  for investigating gene- and pathway-environment interaction analysis (Truong, T., et al. (2014) <doi:10.1530/ERC-14-0121>).

Fits models of gene expression evolution to expression data from
coregulated groups of genes, assuming inverse gamma distributed rate
variation

Fits models of gene expression evolution to expression data from
coregulated groups of genes, assuming inverse gamma distributed rate
variation.

Estimates the parameters of a trading-tree model for the
computation of the probability of informed trading
zoo, xts, highfrequency, TTR, timeDate, quantmod
Using information for trade initiation, the package
computes the probability of informed trading of Easley and
O'Hara (1987).