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‎DESCRIPTION‎

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Package: SelectBoost
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Type: Package
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Title: A General Algorithm to Enhance the Performance of Variable Selection Methods in Correlated Datasets
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Version: 2.2.2
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Date: 2022-11-29
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Depends: R (>= 2.10)
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Version: 2.3.0
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Date: 2025-09-10
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Depends:
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R (>= 3.5)
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biocViews:
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Imports: lars, glmnet, igraph, parallel, msgps, Rfast, methods, Cascade, graphics, grDevices, varbvs, spls, abind
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Suggests:
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knitr,
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markdown,
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rmarkdown,
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mixOmics,
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CascadeData
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CascadeData,
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testthat (>= 3.0.0)
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Authors@R: c(
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person(given = "Frederic", family= "Bertrand", role = c("cre", "aut"), email = "frederic.bertrand@utt.fr", comment = c(ORCID = "0000-0002-0837-8281")),
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person(given = "Myriam", family= "Maumy-Bertrand", role = c("aut"), email = "myriam.maumy-bertrand@utt.fr", comment = c(ORCID = "0000-0002-4615-1512")),
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person(given = "Frederic", family= "Bertrand", role = c("cre", "aut"), email = "frederic.bertrand@lecnam.net", comment = c(ORCID = "0000-0002-0837-8281")),
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person(given = "Myriam", family= "Maumy-Bertrand", role = c("aut"), email = "myriam.maumy@ehesp.fr", comment = c(ORCID = "0000-0002-4615-1512")),
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person(given = "Ismail", family= "Aouadi", role = c("ctb"), email = "[email protected]"),
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person(given = "Nicolas", family= "Jung", role = c("ctb"), email = "[email protected]"))
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Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>), Ismail Aouadi [ctb], Nicolas Jung [ctb]
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Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
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Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
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Description: An implementation of the selectboost algorithm (Bertrand et al. 2020, 'Bioinformatics', <doi:10.1093/bioinformatics/btaa855>), which is a general algorithm that improves the precision of any existing variable selection method. This algorithm is based on highly intensive simulations and takes into account the correlation structure of the data. It can either produce a confidence index for variable selection or it can be used in an experimental design planning perspective.
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License: GPL-3
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Encoding: UTF-8
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Classification/MSC: 62H11, 62J12, 62J99
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LazyData: true
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VignetteBuilder: knitr
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RoxygenNote: 7.2.1
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RoxygenNote: 7.3.2
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URL: https://fbertran.github.io/SelectBoost/, https://github.com/fbertran/SelectBoost/
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BugReports: https://github.com/fbertran/SelectBoost/issues/
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Config/testthat/edition: 3

‎NEWS.md‎

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# SelectBoost 2.3.0
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* Maintainer email update
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* Added unit tests
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* Fix the package to get rid of CRAN check notes
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# SelectBoost 2.2.2
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* Update email maintainer address
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* Maintainer email update
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# SelectBoost 2.2.1
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‎R/BIC_AICc_glmnet.R‎

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#' @name AICc_BIC_glmnetB
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#'
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#' @return A list relevant to model selection.
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{Robust Parametric Classification and Variable Selection by a Minimum Distance Criterion}, Chi and Scott, Journal of Computational and Graphical Statistics, \bold{23}(1), 2014, p111--128, \doi{10.1080/10618600.2012.737296}.
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#' @seealso \code{\link{var_select}}
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#' @examples

‎R/SelectBoost-package.R‎

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#' SelectBoost
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#'
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#' Motivation: With the growth of big data, variable selection has become one of the major
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#' challenges in statistics. Although many methods have been proposed in the literature their
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#' performance in terms of recall and precision are limited in a context where the number of
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#' variables by far exceeds the number of observations or in a high correlated setting.
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#' Results: This package implements a new general algorithm which improves the precision of any
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#' existing variable selection method. This algorithm is based on highly intensive simulations and
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#' takes into account the correlation structure of the data. Our algorithm can either produce a
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#' confidence index for variable selection or it can be used in an experimental design planning
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#' perspective.
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#'
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#' @docType package
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#' @name SelectBoost
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#' @keywords internal
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#' @aliases SelectBoost-package SelectBoost NULL
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#'
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#' @references F. Bertrand, I. Aouadi, N. Jung, R. Carapito, L. Vallat, S. Bahram, M. Maumy-Bertrand (2020). SelectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets, \emph{Bioinformatics}. \doi{10.1093/bioinformatics/btaa855}
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#'
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#' SelectBoost was used to decypher networks in
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#' C. Schleiss, [...], M. Maumy-Bertrand, S. Bahram, F. Bertrand, and L. Vallat. (2021). Temporal multiomic modelling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia. \emph{Leukemia}.
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#'
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# @import parallel doMC foreach
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#' @import lars glmnet msgps spls varbvs
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#' @importFrom abind abind
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#' @importFrom methods new
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#' @importFrom utils head tail
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#' @importFrom stats coef cor heatmap predict var
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#' @importFrom grDevices rainbow
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#' @importFrom graphics abline axis barplot matplot mtext par plot points segments
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#' @importFrom stats binom.test median plogis pt qbinom quantile rbinom rnorm runif sd t.test wilcox.test
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#' @importFrom Rfast vmf.mle rvmf
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# #' @importFrom parallel detectCores makeCluster clusterEvalQ clusterExport parLapply stopCluster
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# #' @importFrom doMC registerDoMC
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# #' @importFrom foreach foreach "%dopar%"
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#' @importFrom igraph graph.adjacency infomap.community communities
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#' @importFrom grDevices rgb gray
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#' @importFrom graphics image layout
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#' @importFrom parallel detectCores
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#'#' @author This package has been written by Frédéric Bertrand, Myriam
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#' Maumy-Bertrand, Ismail Aouadi and Nicolas Jung.
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#' Maintainer: Frédéric Bertrand <frederic.bertrand@@lecnam.net>
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#'
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#' @examples
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#' set.seed(314)
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#' xran=matrix(rnorm(75),15,5)
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#' #Binary logistic regression
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#' fastboost(xran,ybin,func=lasso_cv_glmnet_bin_min)
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#'}
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#'
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"_PACKAGE"
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# @import parallel doMC foreach
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#' @import lars glmnet msgps spls varbvs
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#' @importFrom abind abind
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#' @importFrom methods new
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#' @importFrom utils head tail
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#' @importFrom stats coef cor heatmap predict var
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#' @importFrom grDevices rainbow
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#' @importFrom graphics abline axis barplot matplot mtext par plot points segments
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#' @importFrom stats binom.test median plogis pt qbinom quantile rbinom rnorm runif sd t.test wilcox.test
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#' @importFrom Rfast vmf.mle rvmf
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# #' @importFrom parallel detectCores makeCluster clusterEvalQ clusterExport parLapply stopCluster
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# #' @importFrom doMC registerDoMC
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# #' @importFrom foreach foreach "%dopar%"
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#' @importFrom igraph graph.adjacency infomap.community communities
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#' @importFrom grDevices rgb gray
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#' @importFrom graphics image layout
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#' @importFrom parallel detectCores
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#'
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NULL

‎R/autoboost.R‎

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#'
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#' @return A numeric matrix with attributes.
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#' @family Selectboost functions
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{boost}}, \code{\link{fastboost}}, \code{\link{plot.selectboost}}
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#' @examples
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#'
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#' @family Selectboost functions
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{boost}}, \code{\link{autoboost}}, \code{\link{plot.selectboost}}
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#' @examples
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#'
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#' @family Selectboost analyse functions
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{fastboost}}, \code{\link{autoboost}}
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#'
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#' @family Selectboost analyse functions
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @examples
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#' @family Selectboost analyse functions
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{fastboost}}, \code{\link{autoboost}} and \code{\link{summary.selectboost}}
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#'
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#' @family Selectboost analyze functions
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#'
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#'
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{fastboost}} and \code{\link{autoboost}}

‎R/boost.R‎

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#'
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#' @return Various types depending on the function.
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#' @family Selectboost functions
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#' @author Frederic Bertrand, \email{frederic.bertrand@@utt.fr}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{fastboost}}, \code{\link{autoboost}}
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#' @examples

‎R/datasets.R‎

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#' @docType data
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‎R/group_func_1.R‎

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#' \item "type": "normal"
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#' \item "length.groups" the length of each groups.
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#' }
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{group_func_2}} and \code{\link{boost.findgroups}}
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#' @examples

‎R/group_func_2.R‎

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#' \item "type": "normal"
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#' \item "length.groups" the length of each groups.
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link{group_func_2}} \code{\link{boost.findgroups}}, \code{\link[igraph]{infomap.community}} and \code{\link[igraph]{igraph}}.
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‎R/lasso_cv.R‎

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#'
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link[glmnet]{glmnet}}, \code{\link[glmnet]{cv.glmnet}}, \code{\link{AICc_BIC_glmnetB}}, \code{\link[lars]{lars}}, \code{\link[lars]{cv.lars}}, \code{\link[msgps]{msgps}}
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#' @author Frederic Bertrand, \email{frederic.bertrand@@lecnam.net}
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#' @references \emph{selectBoost: a general algorithm to enhance the performance of variable selection methods in correlated datasets}, Frédéric Bertrand, Ismaïl Aouadi, Nicolas Jung, Raphael Carapito, Laurent Vallat, Seiamak Bahram, Myriam Maumy-Bertrand, Bioinformatics, 2020. \doi{10.1093/bioinformatics/btaa855}
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#' @seealso \code{\link[glmnet]{glmnet}}, \code{\link[glmnet]{cv.glmnet}}, \code{\link[msgps]{msgps}}, \code{\link{AICc_BIC_glmnetB}}, \code{\link[spls]{spls}}, \code{\link[spls]{cv.spls}}, \code{\link[spls]{correct.spls}}, \code{\link[spls]{splsda}}, \code{\link[spls]{cv.splsda}}, \code{\link[spls]{sgpls}}, \code{\link[spls]{cv.sgpls}}, \code{\link[varbvs]{varbvs}}
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#' @examples

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