This package provides a micro-package for reading "passwords", i.e. reading user input with masking, so that the input is not displayed as it is typed. Currently, RStudio, the command line (every OS), and any platform where tcltk is present are supported.

This is a package supporting cluster analysis for cognitive diagnosis based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; doi:10.1007/s11336-009-9125-0). Given the sample statistic of sum-scores, cluster analysis techniques can be used to classify examinees into latent classes based on their attribute patterns. In addition to the algorithms used to classify data, three labeling approaches are proposed to label clusters so that examinees' attribute profiles can be obtained.

This package extends the fitdistr function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.

This package lets you determine the significance of pre-defined sets of genes with respect to an outcome variable, such as a group indicator, a quantitative variable or a survival time.

This package provides utility functions useful when programming and developing R packages.

This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools.

This package lets you construct Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Results Data objects. These objects are used and re-used to construct summary tables, visualizations, and written reports. The package also exports utilities for working with these objects and creating new Analysis Results Data objects.

This package provides tools for the computation of matrix and scalar exponentiation.

The Tweedie compound Poisson distribution is a mixture of a degenerate distribution at the origin and a continuous distribution on the positive real line. It has been applied in a wide range of fields in which continuous data with exact zeros regularly arise. The cplm package provides likelihood based and Bayesian procedures for fitting common Tweedie compound Poisson linear models. In particular, models with hierarchical structures or extra zero inflation can be handled. Further, the package implements the Gini index based on an ordered version of the Lorenz curve as a robust model comparison tool involving zero-inflated and highly skewed distributions.

This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.

This package provides an interface (wrapper) to MPI APIs. It also provides an interactive R manager and worker environment.

Implementation of the web-based Practical Meta-Analysis Effect Size Calculator from David B. Wilson in R. Based on the input, the effect size can be returned as standardized mean difference, Cohen's f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds, or eta squared effect size.

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an XPath "interpreter".

Tools to clean and process text. Tools are geared at checking for substrings that are not optimal for analysis and replacing or removing them (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, Kumar, Ostendorf, & Richards (2001) doi:10.1006/csla.2001.0169) or extracting them into new variables. For example, emoticons are often used in text but not always easily handled by analysis algorithms. The replace_emoticon() function replaces emoticons with word equivalents.

This package provides a means to mock a package function, i.e., temporarily substitute it for testing. It was designed as a drop-in replacement for the now deprecated testthat::with_mock() and testthat::local_mock().

This package provides functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.

This package provides a method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.

This package abbreviates strings to a specified minimum number of characters, such that the strings remain unique (if they originally were).

This package provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.

This package provides tools for the analysis of epidemiological and surveillance data. It contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.

This package can be used to conduct post hoc analyses of resampling results generated by models. For example, if two models are evaluated with the root mean squared error (RMSE) using 10-fold cross-validation, there are 10 paired statistics. These can be used to make comparisons between models without involving a test set.

This package generates version 2 and 4 request signatures for Amazon Web Services (AWS) and provides a mechanism for retrieving credentials from environment variables, AWS credentials files, and EC2 instance metadata. For use on EC2 instances, the package 'aws.ec2metadata' is suggested.

This package provides a color mapping is generated according to the break values and corresponding colors. Other colors are generated by interpolating in a certain color space. The functions were part of the circlize package.

This package provides logicless templating, with a syntax that is not limited to R.