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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.
Mini Charts for Interactive Maps
Add and modify small charts on an interactive map created with package 'leaflet'. These charts can be used to represent at same time multiple variables on a single map.
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>).
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,
Collecting Twitter Data
An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: < https://developer.twitter.com/en/docs>.
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)
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)
A DNA Reference Library Manager
Reference database manager offering a set of functions to import, organize, clean, filter, audit and export reference genetic data. Provide functions to download sequence data from Bold Systems (< https://www.boldsystems.org/>) and NCBI GenBank < https://www.ncbi.nlm.nih.gov/genbank/>. Designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in barcoding and metabarcoding studies.
Latent Factor Mixed Models
Fast and accurate inference of
gene-environment associations (GEA) in genome-wide studies
(Caye et al., 2019,