A Toolbox for Manipulating Biological Sequences

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) . Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.

An Interface to the Nexus Class Library

An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.

Black Box Optimization and Exploration of Parameter Space

Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 ; Leblois et al., 2014 ; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.

Functions to Make Surveys Processing Easier

Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.

Quick Serialization of R Objects

Provides functions for quickly writing and reading any R object to and from disk.

Knowledge Synthesis in Agriculture - From Experimental Network to Meta-Analysis

Demo and dataset accompaying the books : De l'analyse des réseaux expérimentaux à la méta-analyse: Méthodes et applications avec le logiciel R pour les sciences agronomiques et environnementales (Published 2018-06-28, Quae, for french version) by David Makowski, Francois Piraux and Francois Brun - < https://www.quae.com/produit/1514/9782759228164/de-l-analyse-des-reseaux-experimentaux-a-la-meta-analyse> Knowledge Synthesis in Agriculture : from Experimental Network to Meta-Analysis (in preparation for 2018-06, Springer , for English version) by David Makowski, Francois Piraux and Francois Brun A full description of all the material is in both books. ACKNOWLEDGMENTS : The French network "RMT modeling and data analysis for agriculture" (< http://www.modelia.org>) have contributed to the development of this R package. This project and network are lead by ACTA (French Technical Institute for Agriculture) and was funded by a grant from the Ministry of Agriculture and Fishing of France.

Tools for Approximate Bayesian Computation (ABC)

Implements several ABC algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.

Authoring Books and Technical Documents with R Markdown

Output formats and utilities for authoring books and technical documents with R Markdown.

Interface to the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

Wrappers for Tools in Other Packages for IDE Friendliness

Set of tools aimed at wrapping some of the functionalities of the packages tools, utils and codetools into a nicer format so that an IDE can use them.