Provides tools for performing Bayesian inference on epidemiological 
  data to estimate the time-varying reproductive number and other related metrics.
  These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>.
  This package supports analyses based on aggregated case count data and individual line list 
  data, facilitating enhanced surveillance and intervention planning for infectious 
  diseases like COVID-19.

Create maps made of lines. The package contains one function:
    linemap(). linemap() displays a map made of lines using a
    raster or gridded data.

Fits a linear excess relative risk model by maximum likelihood, possibly including several variables and allowing for lagged exposures.

Tools for detecting and correcting sample mix-ups between two sets
    of measurements, such as between gene expression data on two tissues.
    Broman et al. (2015) <doi:10.1534/g3.115.019778>.

Tools for detecting and correcting sample mix-ups between two sets
    of measurements, such as between gene expression data on two
    tissues. This is a revised version of the 'lineup' package, to be
    more general and not tied to the 'qtl' package.

'LineUp' is an interactive technique designed to create, visualize and explore rankings of items based on a set of heterogeneous attributes.
  This is a 'htmlwidget' wrapper around the JavaScript library 'LineUp.js'.
  It is designed to be used in 'R Shiny' apps and 'R Markddown' files.
  Due to an outdated 'webkit' version of 'RStudio' it won't work in the integrated viewer.

Create interactive time series visualizations.
    'linevis' includes an extensive API to manipulate time series after creation,
    and supports getting data out of the visualization. Based on the
    'timevis' package and the 'vis.js' Timeline 'JavaScript' library <https://visjs.github.io/vis-timeline/docs/graph2d/>.

A fast generalized edit distance and string alignment computation mainly for linguistic aims. As a generalization to the classic edit distance algorithms, the package allows users to define custom cost for every symbol's insertion, deletion, and substitution. The package also allows character combinations in any length to be seen as a single symbol which is very useful for International Phonetic Alphabet (IPA) transcriptions with diacritics. In addition to edit distance result, users can get detailed alignment information such as all possible alignment scenarios between two strings which is useful for testing, illustration or any further usage. Either the distance matrix or its long table form can be obtained and tools to do such conversions are provided. All functions in the package are implemented in 'C++' and the distance matrix computation is parallelized leveraging the 'RcppThread' package.