diff --git a/R/GxESelection.R b/R/GxESelection.R index 220716f..6a215c4 100644 --- a/R/GxESelection.R +++ b/R/GxESelection.R @@ -11,7 +11,7 @@ #' #' @references #' Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y. and Wu, C. (2023) Robust Bayesian variable selection for -#' gene-environment interactions. \emph{Biometrics}, 79(2):684-694. doi: \url{https://doi.org/10.1111/biom.13670}. PMID: 35394058. +#' gene-environment interactions. \emph{Biometrics}, 79(2):684-694. \doi{10.1111/biom.13670}. PMID: 35394058. #' #' Barbieri, M.M. and Berger, J.O. (2004). Optimal predictive model selection. {\emph{Ann. Statist}, 32(3):870–897} #' diff --git a/R/roben-package.R b/R/roben-package.R index ed80e1a..3483ddb 100644 --- a/R/roben-package.R +++ b/R/roben-package.R @@ -25,35 +25,35 @@ NULL #' predict() takes a roben object and returns the predicted values for new observations. #' #' @references -#' Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y. and Wu, C. (2023) Robust Bayesian variable selection for -#' gene-environment interactions. \emph{Biometrics}, 79(2):684-694. doi: \url{https://doi.org/10.1111/biom.13670}. PMID: 35394058. +#' Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y., and Wu, C. (2023). Robust Bayesian variable selection for gene-environment interactions. +#' \emph{Biometrics}, 79(2):684-694. \doi{10.1111/biom.13670}. PMID: 35394058. #' -#' Wu, C. and Ma, S. (2015). A selective review of robust variable selection with applications in bioinformatics. -#' {\emph{Briefings in Bioinformatics}, 16(5), 873–883} \url{https://doi.org/10.1093/bib/bbu046} +#' Wu, C., and Ma, S. (2015). A selective review of robust variable selection with applications in bioinformatics. +#' \emph{Briefings in Bioinformatics}, 16(5), 873–883. \doi{10.1093/bib/bbu046}. #' -#' Zhou, F., Ren, J., Lu, X., Ma, S. and Wu, C. (2021). Gene-Environment Interaction: A Variable Selection Perspective. -#' \emph{Methods in Molecular Biology}, 2212:191-223. doi: \url{https://doi.org/10.1007/978-1-0716-0947-7_13}. PMID: 33733358. +#' Zhou, F., Ren, J., Lu, X., Ma, S., and Wu, C. (2021). Gene-Environment Interaction: A Variable Selection Perspective. +#' \emph{Methods in Molecular Biology}, 2212:191-223. \doi{10.1007/978-1-0716-0947-7_13}. PMID: 33733358. #' -#' Ren, J., Zhou, F., Li, X., Chen, Q., Zhang, H., Ma, S., Jiang, Y. and Wu, C. (2020) Semi-parametric Bayesian variable selection for gene-environment interactions. -#' {\emph{Statistics in Medicine}, 39: 617– 638} \url{https://doi.org/10.1002/sim.8434} +#' Ren, J., Zhou, F., Li, X., Chen, Q., Zhang, H., Ma, S., Jiang, Y., and Wu, C. (2020). Semi-parametric Bayesian variable selection for +#' gene-environment interactions. \emph{Statistics in Medicine}, 39: 617–638. \doi{10.1002/sim.8434}. #' -#' Ren, J., Zhou, F., Li, X., Wu, C. and Jiang, Y. (2019) spinBayes: Semi-Parametric Gene-Environment Interaction via Bayesian Variable Selection. -#' R package version 0.1.0. \url{https://CRAN.R-project.org/package=spinBayes} +#' Ren, J., Zhou, F., Li, X., Wu, C., and Jiang, Y. (2019). spinBayes: Semi-Parametric Gene-Environment Interaction via +#' Bayesian Variable Selection. R package version 0.1.0. \url{https://CRAN.R-project.org/package=spinBayes}. #' -#' Wu, C., Jiang, Y., Ren, J., Cui, Y. and Ma, S. (2018). Dissecting gene-environment interactions: A penalized robust approach accounting for hierarchical structures. -#' {\emph{Statistics in Medicine}, 37:437–456} \url{https://doi.org/10.1002/sim.7518} +#' Wu, C., Jiang, Y., Ren, J., Cui, Y., and Ma, S. (2018). Dissecting gene-environment interactions: A penalized robust approach +#' accounting for hierarchical structures. \emph{Statistics in Medicine}, 37:437–456. \doi{10.1002/sim.7518}. #' -#' Wu, C., Shi, X., Cui, Y. and Ma, S. (2015). A penalized robust semiparametric approach for gene-environment interactions. -#' {\emph{Statistics in Medicine}, 34 (30): 4016–4030} \url{https://doi.org/10.1002/sim.6609} +#' Wu, C., Shi, X., Cui, Y., and Ma, S. (2015). A penalized robust semiparametric approach for gene-environment interactions. +#' \emph{Statistics in Medicine}, 34(30): 4016–4030. \doi{10.1002/sim.6609}. #' -#' Wu, C., Cui, Y., and Ma, S. (2014). Integrative analysis of gene–environment interactions under a multi–response partially linear varying coefficient model. -#' {\emph{Statistics in Medicine}, 33(28), 4988–4998} \url{https://doi.org/10.1002/sim.6287} +#' Wu, C., Cui, Y., and Ma, S. (2014). Integrative analysis of gene–environment interactions under a multi–response partially linear +#' varying coefficient model. \emph{Statistics in Medicine}, 33(28): 4988–4998. \doi{10.1002/sim.6287}. #' -#' Wu, C., Zhong, P.S. and Cui, Y. (2018). Additive varying–coefficient model for nonlinear gene–environment interactions. -#' {\emph{Statistical Applications in Genetics and Molecular Biology}, 17(2)} \url{https://doi.org/10.1515/sagmb-2017-0008} +#' Wu, C., Zhong, P.S., and Cui, Y. (2018). Additive varying–coefficient model for nonlinear gene–environment interactions. +#' \emph{Statistical Applications in Genetics and Molecular Biology}, 17(2). \doi{10.1515/sagmb-2017-0008}. #' -#' Wu, C., Zhong, P.S. and Cui, Y. (2013). High dimensional variable selection for gene-environment interactions. -#' {\emph{Technical Report. Michigan State University.}} +#' Wu, C., Zhong, P.S., and Cui, Y. (2013). High dimensional variable selection for gene-environment interactions. +#' \emph{Technical Report. Michigan State University.} #' #' @seealso \code{\link{roben}} NULL diff --git a/man/GxESelection.Rd b/man/GxESelection.Rd index 2e5c11a..0e500f8 100644 --- a/man/GxESelection.Rd +++ b/man/GxESelection.Rd @@ -56,7 +56,7 @@ selected } \references{ Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y. and Wu, C. (2023) Robust Bayesian variable selection for -gene-environment interactions. \emph{Biometrics}, 79(2):684-694. doi: \url{https://doi.org/10.1111/biom.13670}. PMID: 35394058. +gene-environment interactions. \emph{Biometrics}, 79(2):684-694. \doi{10.1111/biom.13670}. PMID: 35394058. Barbieri, M.M. and Berger, J.O. (2004). Optimal predictive model selection. {\emph{Ann. Statist}, 32(3):870–897} } diff --git a/man/roben-package.Rd b/man/roben-package.Rd index 786b116..b69ae28 100644 --- a/man/roben-package.Rd +++ b/man/roben-package.Rd @@ -25,35 +25,35 @@ GxESelection() takes a roben object and returns the variable selection results. predict() takes a roben object and returns the predicted values for new observations. } \references{ -Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y. and Wu, C. (2023) Robust Bayesian variable selection for -gene-environment interactions. \emph{Biometrics}, 79(2):684-694. doi: \url{https://doi.org/10.1111/biom.13670}. PMID: 35394058. +Ren, J., Zhou, F., Li, X., Ma, S., Jiang, Y., and Wu, C. (2023). Robust Bayesian variable selection for gene-environment interactions. +\emph{Biometrics}, 79(2):684-694. \doi{10.1111/biom.13670}. PMID: 35394058. -Wu, C. and Ma, S. (2015). A selective review of robust variable selection with applications in bioinformatics. -{\emph{Briefings in Bioinformatics}, 16(5), 873–883} \url{https://doi.org/10.1093/bib/bbu046} +Wu, C., and Ma, S. (2015). A selective review of robust variable selection with applications in bioinformatics. +\emph{Briefings in Bioinformatics}, 16(5), 873–883. \doi{10.1093/bib/bbu046}. -Zhou, F., Ren, J., Lu, X., Ma, S. and Wu, C. (2021). Gene-Environment Interaction: A Variable Selection Perspective. -\emph{Methods in Molecular Biology}, 2212:191-223. doi: \url{https://doi.org/10.1007/978-1-0716-0947-7_13}. PMID: 33733358. +Zhou, F., Ren, J., Lu, X., Ma, S., and Wu, C. (2021). Gene-Environment Interaction: A Variable Selection Perspective. +\emph{Methods in Molecular Biology}, 2212:191-223. \doi{10.1007/978-1-0716-0947-7_13}. PMID: 33733358. -Ren, J., Zhou, F., Li, X., Chen, Q., Zhang, H., Ma, S., Jiang, Y. and Wu, C. (2020) Semi-parametric Bayesian variable selection for gene-environment interactions. -{\emph{Statistics in Medicine}, 39: 617– 638} \url{https://doi.org/10.1002/sim.8434} +Ren, J., Zhou, F., Li, X., Chen, Q., Zhang, H., Ma, S., Jiang, Y., and Wu, C. (2020). Semi-parametric Bayesian variable selection for +gene-environment interactions. \emph{Statistics in Medicine}, 39: 617–638. \doi{10.1002/sim.8434}. -Ren, J., Zhou, F., Li, X., Wu, C. and Jiang, Y. (2019) spinBayes: Semi-Parametric Gene-Environment Interaction via Bayesian Variable Selection. -R package version 0.1.0. \url{https://CRAN.R-project.org/package=spinBayes} +Ren, J., Zhou, F., Li, X., Wu, C., and Jiang, Y. (2019). spinBayes: Semi-Parametric Gene-Environment Interaction via +Bayesian Variable Selection. R package version 0.1.0. \url{https://CRAN.R-project.org/package=spinBayes}. -Wu, C., Jiang, Y., Ren, J., Cui, Y. and Ma, S. (2018). Dissecting gene-environment interactions: A penalized robust approach accounting for hierarchical structures. -{\emph{Statistics in Medicine}, 37:437–456} \url{https://doi.org/10.1002/sim.7518} +Wu, C., Jiang, Y., Ren, J., Cui, Y., and Ma, S. (2018). Dissecting gene-environment interactions: A penalized robust approach +accounting for hierarchical structures. \emph{Statistics in Medicine}, 37:437–456. \doi{10.1002/sim.7518}. -Wu, C., Shi, X., Cui, Y. and Ma, S. (2015). A penalized robust semiparametric approach for gene-environment interactions. -{\emph{Statistics in Medicine}, 34 (30): 4016–4030} \url{https://doi.org/10.1002/sim.6609} +Wu, C., Shi, X., Cui, Y., and Ma, S. (2015). A penalized robust semiparametric approach for gene-environment interactions. +\emph{Statistics in Medicine}, 34(30): 4016–4030. \doi{10.1002/sim.6609}. -Wu, C., Cui, Y., and Ma, S. (2014). Integrative analysis of gene–environment interactions under a multi–response partially linear varying coefficient model. -{\emph{Statistics in Medicine}, 33(28), 4988–4998} \url{https://doi.org/10.1002/sim.6287} +Wu, C., Cui, Y., and Ma, S. (2014). Integrative analysis of gene–environment interactions under a multi–response partially linear +varying coefficient model. \emph{Statistics in Medicine}, 33(28): 4988–4998. \doi{10.1002/sim.6287}. -Wu, C., Zhong, P.S. and Cui, Y. (2018). Additive varying–coefficient model for nonlinear gene–environment interactions. -{\emph{Statistical Applications in Genetics and Molecular Biology}, 17(2)} \url{https://doi.org/10.1515/sagmb-2017-0008} +Wu, C., Zhong, P.S., and Cui, Y. (2018). Additive varying–coefficient model for nonlinear gene–environment interactions. +\emph{Statistical Applications in Genetics and Molecular Biology}, 17(2). \doi{10.1515/sagmb-2017-0008}. -Wu, C., Zhong, P.S. and Cui, Y. (2013). High dimensional variable selection for gene-environment interactions. -{\emph{Technical Report. Michigan State University.}} +Wu, C., Zhong, P.S., and Cui, Y. (2013). High dimensional variable selection for gene-environment interactions. +\emph{Technical Report. Michigan State University.} } \seealso{ Useful links: diff --git a/roben.pdf b/roben.pdf index 73e4ef2..628e1b7 100644 Binary files a/roben.pdf and b/roben.pdf differ