Sound Analysis and Synthesis

Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) and Sueur (2018) .

Virtual Machines for R

Manage, provision and use Virtual Machines pre-configured for R. Develop, test and build package in a clean environment. 'Vagrant' tool and a provider (such as 'Virtualbox') have to be installed.

Exploring the Phylogenetic Signal in Continuous Traits

A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.

Data Structure and Manipulations Tool for Host and Viral Population

Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.

Adaptation of Virtual Twins Method from Jared Foster

Research of subgroups in random clinical trials with binary outcome and two treatments groups. This is an adaptation of the Jared Foster method (< https://www.ncbi.nlm.nih.gov/pubmed/21815180>).

Paginate the HTML Output of R Markdown with CSS for Print

Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.

A Procedure to Clean, Decompose and Aggregate Timeseries

Clean, decompose and aggregate univariate time series following the procedure "Cyclic/trend decomposition using bin interpolation" and the Logbox method for flagging outliers, both detailed in Ritter, F.: Technical note: A procedure to clean, decompose, and aggregate time series, Hydrol. Earth Syst. Sci., 27, 349–361, , 2023.

Keyword Assisted Topic Models

Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2024) .

Automatic Description of Factorial Analysis

Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).

Landscape Epidemiology and Evolution

A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) .