adegenet - Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Last updated 2 years ago

12.35 score 168 stars 28 packages 2.1k scripts 11k downloads

epitrix - Small Helpers and Tricks for Epidemics Analysis

A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.

Last updated 2 years ago

epidemiology

8.48 score 11 stars 4 packages 227 scripts 474 downloads

treespace - Statistical Exploration of Landscapes of Phylogenetic Trees

Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.

Last updated 1 years ago

7.38 score 27 stars 63 scripts 309 downloads

apex - Phylogenetic Methods for Multiple Gene Data

Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>. 'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.

Last updated 10 months ago

6.65 score 5 stars 54 scripts 1.1k downloads

earlyR - Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

Last updated 4 years ago

6.59 score 9 stars 95 scripts 202 downloads

projections - Project Future Case Incidence

Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.

Last updated 2 years ago

6.47 score 14 stars 174 scripts 397 downloads

reportfactory - Lightweight Infrastructure for Handling Multiple R Markdown Documents

Provides an infrastructure for handling multiple R Markdown reports, including automated curation and time-stamping of outputs, parameterisation and provision of helper functions to manage dependencies.

Last updated 2 years ago

infrastructureknitrrmarkdownrmarkdown-document

5.99 score 83 stars 47 scripts 315 downloads

trending - Model Temporal Trends

Provides a coherent interface to multiple modelling tools for fitting trends along with a standardised approach for generating confidence and prediction intervals.

Last updated 2 years ago

5.58 score 8 stars 1 packages 16 scripts 219 downloads

trendeval - Evaluate Trending Models

Provides a coherent interface for evaluating models fit with the trending package. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

Last updated 2 years ago

3.00 score 2 stars 7 scripts 157 downloads