Jointly model the accuracy of cognitive responses and item choices
    within a Bayesian hierarchical framework as described by Culpepper and
    Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package
    contains the datasets used within the analysis of the paper.

An implementation of double generalized linear model (DGLM) building with variable selection procedures and handling of interaction terms and other complex situations. We also provide a method of handling convergence issues within the dglm() function. The package offers a simulation function for generating simulated data for testing purposes and utilizes the forward stepwise variable selection procedure in model-building. It also provides a new custom bootstrap function for mean and standard deviation estimation and functions for building crossplots and squareplots from a data set.

A likelihood-based hypothesis testing approach is implemented for
  assessing causal mediation. Described in Millstein, Chen, and Breton (2016),
  <DOI:10.1093/bioinformatics/btw135>, it could be used to test for mediation
  of a known causal association between a DNA variant, the 'instrumental variable',
  and a clinical outcome or phenotype by gene expression or DNA methylation, the
  potential mediator. Another example would be testing mediation of the effect
  of a drug on a clinical outcome by the molecular target. The hypothesis test
  generates a p-value or permutation-based FDR value with confidence intervals
  to quantify uncertainty in the causal inference. The outcome can be represented
  by either a continuous or binary variable, the potential mediator is continuous,
  and the instrumental variable can be continuous or binary and is not limited to
  a single variable but may be a design matrix representing multiple variables.

Supports quantitative
    research in scientometrics and bibliometrics. Provides
    various tools for preprocessing bibliographic
    data retrieved, e.g., from Elsevier's SciVerse Scopus,
    computing bibliometric impact of individuals,
    or modelling phenomena encountered in the social sciences.
    This package is deprecated, see 'agop' instead.