Applied Statistics

R Packages

R package varrank

varrank: Heuristics Tools Based on Mutual Information for Variable Ranking. A computational toolbox of heuristics approaches for performing variable ranking and feature selection based on mutual information well adapted for multivariate system epidemiology datasets. The core function is a general implementation of the minimum redundancy maximum relevance model. Variables ranking can be learned with a sequential forward/backward search algorithm. The two main problems that can be addressed by this package is the selection of the most representative variable within a group of variables of interest (i.e. dimension reduction) and variable ranking with respect to a set of features of interest.

A stable version of the package is posted on CRAN.

R package optimParallel

optimParallel: an R package, that provides parallel versions of the gradient-based optim() methods. The main function of the package is optimParallel(), which has the same usage and output as optim(). Using optimParallel() can significantly reduce the optimization time.

A stable version of the package is posted on CRAN, a development version is posted here.

R package spam

spam: an R package, a collection of functions based in R/Fortran for sparse matrix algebra, tailored for MCMC calculations within GMRF or GRF with compactly supported covariance functions. Emphasis is given on a comprehensive, simple, tutorial structure of the code. 

A stable version of the package is posted on CRAN, a development version is posted here.

R package dotCall64

dotCall64: Enhanced Foreign Function Interface Supporting Long Vectors.
An alternative version of .C() and .Fortran() supporting long vectors and 64-bit integer type arguments. The provided interface .C64() features mechanisms the avoid unnecessary copies of read-only or write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.

A stable version of the package is posted on CRAN, a development version is posted here.

R package spam64

spam64: 64-Bit Extension of the SPArse Matrix R Package 'spam' Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package 'spam' enables the sparse matrix class "spam" to handle huge sparse matrices with more than 2^31-1 non-zero elements.

A stable version of the package is posted on CRAN, a development version is posted here.

R package gapfill

gapfill: Fill Missing Values in Satellite Data A R package Tools to fill missing values in satellite data and to develop new gap-fill algorithms. The methods are tailored to data (images) observed at equally-spaced points in time. The package is illustrated with MODIS NDVI data.abn:

A stable version of the package is posted on CRAN.

R package eggCounts

eggCounts: An R package to assess anthelmintic efficacy using Bayesian hierarchical models for faecal egg count data. We have implemented a new Bayesian inference approach through Stan MCMC sampling scheme. Notice that older version did have some issues with the unpaired setting.
 

A stable version of the package is posted on CRAN.

R package abn

abn: An R package to providing routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data.

A stable version of the package is posted on CRAN.

More information can be found at http://www.r-bayesian-networks.org.  

R package rmbsizerR

mrbsizeR: An R package for the multiresolution analysis of spatial fields and images to capture scale-dependent features. mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales. To infer which of the captured features are credible, Bayesian analysis is used.  The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <doi:10.1016/j.csda.2011.04.011>.

A stable version of the package is posted on CRAN

R package gsbDesign

gsbDesign: An R package to evaluate group sequential operating characteristics for clinical, Bayesian two-arm trials with known Sigma and normal endpoints.

A stable version of the package is posted on CRAN.

R package fields

fields: Tools for Spatial Data for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. 

A stable version of the package is posted on CRAN.