Latent Factor Mixed Models

Fast and accurate inference of gene-environment associations (GEA) in genome-wide studies (Caye et al., 2019, ). We developed a least-squares estimation approach for confounder and effect sizes estimation that provides a unique framework for several categories of genomic data, not restricted to genotypes. The speed of the new algorithm is several times faster than the existing GEA approaches, then our previous version of the 'LFMM' program present in the 'LEA' package (Frichot and Francois, 2015, ).

Visualize Data for Host and Viral Population from 'SMITIDstruct' using 'HTMLwidgets'

Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using 'HTMLwidgets'. It mainly using 'D3JS' javascript framework.

Shared Memory Multithreading

This project extends 'R' with a mechanism for efficient parallel data access by utilizing 'C++' shared memory. Large data objects can be accessed and manipulated directly from 'R' without redundant copying, providing both speed and memory efficiency.

Add Even More Interactivity to Interactive Charts

Like package 'manipulate' does for static graphics, this package helps to easily add controls like sliders, pickers, checkboxes, etc. that can be used to modify the input data or the parameters of an interactive chart created with package 'htmlwidgets'.

Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.

Interface for Masked Autoregressive Flows

Interfaces the Python library 'zuko' implementing Masked Autoregressive Flows. See Rozet, Divo and Schnake (2023) and Papamakarios, Pavlakou and Murray (2017) .

Population Fisher Information Matrix

Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) , Retout S, Comets E, Samson A, Mentré F (2007) , Bazzoli C, Retout S, Mentré F (2009) , Le Nagard H, Chao L, Tenaillon O (2011) , Combes FP, Retout S, Frey N, Mentré F (2013) and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) .

Deprecated 'classic' 'Rcpp' 'API'

The 'RcppClassic' package provides a deprecated C++ library which facilitates the integration of R and C++. New projects should use the new 'Rcpp' 'API' in the 'Rcpp' package.

GPL Palettes Copied from 'Gimp' and 'Inkscape'

A set of palettes imported from 'Gimp' distributed under GPL3 (< https://www.gimp.org/about/COPYING>), and 'Inkscape' distributed under GPL2 (< https://inkscape.org/about/license/>).

Perform Factorial Analysis from 'FactoMineR' with a Shiny Application

Perform factorial analysis with a menu and draw graphs interactively thanks to 'FactoMineR' and a Shiny application.