Software

R packages

SOMbrero

SOMbrero is an R package that implements stochastic self-organizing maps (SOM) variants for numeric and non numeric datasets.

Role in the project: Maintainer and author
Project home page on CRAN
Current version: 1.2 (Sept 2016)
Install SOMbrero with
install.packages("SOMbrero")
SOMbrero comes with a Web User Interface (using shiny) that can be used by typing the command line:
sombreroWUI()

Archives (package source and Windows built prior version 1.0)

If you are using SOMbrero, please cite:
  • Olteanu M., Villa-Vialaneix N. (2015) On-line relational and multiple relational SOM. Neurocomputing, 147, 15-30.

SISIR

SISIR is an R package that implements the sparse interval sliced inverse regression. It also provides an implementation of standard ridge and sparse SIR for high dimensional data

Role in the project: Maintainer and author
Project home page on CRAN
Current version: 0.1 (Dec 2016)
Install SISIR with
install.packages("SISIR")

If you are using SISIR, please cite:
  • Picheny V., Servien R., Villa-Vialaneix N. (2016) Interpretable sparse SIR for digitized functional data. Preprint.

SirStatis

SirStatis is an R package that implements an extension of the DUAL-STATIS method to a SIR framework. It can be used to analyse multiway datasets in relation with a numeric target variable.

Role in the project: Author (Maintainer is Valérie Sautron)
Current version: 0.1 (April 2016)
Install SirStatis by first installing its dependancies
install.packages(c("ggplot2", "ggrepel", "expm", "MASS"))
and by then downloading the source package at this link.
Archives (package source; we do not provide Windows built)

therese

therese is an R package for inferring networks from expression data obtained in various experimental conditions. The "cLasso " (consensus Lasso) method is implemented (see reference below). Not maintained anymore

Role in the project: Maintainer and author
Project home page on R-Forge
Current version: 0.3-beta (Sept. 2014)
Install SOMbrero with
install.packages("therese", repos="http://R-Forge.R-project.org")
Sources can be fetched (from Git) with
git clone http://mulcyber.toulouse.inra.fr/anonscm/git/therese/therese.git
Archives (package source and Windows built)

If you are using therese, please cite:
  • Villa-Vialaneix N., Vignes M., Viguerie N., San Cristobal M. (2014) Inferring networks from multiple samples with consensus LASSO. Quality Technology & Quantitative Management, 11(1), 39-60.

NiLeDAM

NiLeDAM is an R package for dating monazites from measurements of triplets (U,Th,Pb) obtained by a microprobe technique. The implemented method is the one described in the article (Montel et al., 1996) and the package has been developed from the original programs made in basic language by Jean-Marc Montel (École Nationale Supérieure de Géologie, France). An example, kindly provided by Anne-Magali Seydoux-Guillaume is included in the package and is the one described in the article (Seydoux-Guillaume et al., 2012). Not maintained anymore
Monazite image by Aangelo (personal work) - licence GFDL or CC-BY-SA-3.0-2.5-2.0-1.0, via Wikimedia Commons

Role in the project: Maintainer and author
Project home page on R-Forge
Current version: 0.1-alpha (Aug. 2013)
Install NiLeDAM with
install.packages("NiLeDAM", repos="http://R-Forge.R-project.org")
(the package nleqslv must have been previously installed from CRAN).
A Web User Interface (using shiny) can be used directly on-line for those who are not familiar with R programming language. It is available at http://shiny.nathalievilla.org/niledam. The script of the web user interface is provided on GitHub:
git clone https://github.com/tuxette/niledam.git

If you are using NiLeDAM, please cite:
  • Villa-Vialaneix N., Montel J.M., Seydoux-Guillaume A.M. (2013) NiLeDAM: Monazite Datation for the NiLeDAM team. R package version 0.1.
  • Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37-53.
  • Seydoux-Guillaume A.M., Montel J.M., Bingen B., Bosse V., de Parseval P., Paquette J.L., Janots E., Wirth R. (2012) Low-temperature alteration of monazite: fluid mediated coupled dissolution-precipitation, irradiation damage and disturbance of the U-Pb and Th-Pb chronometers. Chemical Geology, 330-331, 140-158.
Cited in:
  • Laurent A.T., Seydoux-Guillaume, A.M., Duchene S., Bingen B., Bosse V., Datas L. (2016) Sulphate incorporation in monazite lattice and dating the cycle of sulphur in metamorphic belts. Contributions to Mineralogy and Petrology, 171, 94.

Other R programs

Other

  • For the SFdS, I also developed a generic website to administer conferences (PhP/MySQL scripts). This solution is based on wordpress and includes a registration form (connected to a credit card plateform), an automatic sending of invoice by emails and tools to administer the participants and check the payment of registration fees. It also comprises a script that automatically generates the program of the conference based on MyReview. An example of my work can be seen on this page. The programs have been documented so that they can be used by any webmaster. The scripts are available on GitHub:
git clone https://github.com/tuxette/jdsxxx.git