Package: SimRepeat
Type: Package
Title: Simulation of Correlated Systems of Equations with Multiple
        Variable Types
Version: 0.1.0
Author: Allison Cynthia Fialkowski
Maintainer: Allison Cynthia Fialkowski <allijazz@uab.edu>
Description: Generate correlated systems of statistical equations which represent 
    repeated measurements or clustered data.  These systems contain either: a) continuous normal, 
    non-normal, and mixture variables based on the techniques of Headrick and Beasley (2004) 
    <DOI:10.1081/SAC-120028431> or b) continuous (normal, non-normal and mixture), ordinal, 
    and count (regular or zero-inflated, Poisson and Negative Binomial) variables based on the 
    hierarchical linear models (HLM) approach.  Headrick and Beasley's method for continuous 
    variables calculates the beta (slope) coefficients based on the target correlations between 
    independent variables and between outcomes and independent variables.  The package provides 
    functions to calculate the expected correlations between outcomes, between outcomes and error 
    terms, and between outcomes and independent variables, extending Headrick and Beasley's 
    equations to include mixture variables.  These theoretical values can be compared to the 
    simulated correlations.  The HLM approach requires specification of the beta coefficients, 
    but permits group and subject-level independent variables, interactions among independent 
    variables, and fixed and random effects, providing more flexibility in the system of 
    equations.  Both methods permit simulation of data sets that mimic real-world clinical or 
    genetic data sets (i.e. plasmodes, as in Vaughan et al., 2009, <10.1016/j.csda.2008.02.032>).  
    The techniques extend those found in the 'SimMultiCorrData' and 'SimCorrMix' packages.  
    Standard normal variables with an imposed intermediate correlation matrix are transformed 
    to generate the desired distributions.  Continuous variables are simulated using either 
    Fleishman's third-order (<DOI:10.1007/BF02293811>) or Headrick's fifth-order 
    (<DOI:10.1016/S0167-9473(02)00072-5>) power method transformation (PMT).  Simulation 
    occurs at the component-level for continuous mixture distributions.  These components are 
    transformed into the desired mixture variables using random multinomial variables based on 
    the mixing probabilities.  The target correlation matrices are specified in terms of 
    correlations with components of continuous mixture variables.  Binary and ordinal variables 
    are simulated by discretizing the normal variables at quantiles defined by the marginal 
    distributions.  Count variables are simulated using the inverse CDF method.  There are 
    two simulation pathways for the multi-variable type systems which differ by intermediate 
    correlations involving count variables.  Correlation Method 1 adapts Yahav and Shmueli's 
    2012 method <DOI:10.1002/asmb.901> and performs best with large count variable means and 
    positive correlations or small means and negative correlations.  Correlation Method 2 
    adapts Barbiero and Ferrari's 2015 modification of the 'GenOrd' package 
    <DOI:10.1002/asmb.2072> and performs best under the opposite scenarios.  There are 
    three methods available for correcting non-positive definite correlation matrices.  The 
    optional error loop may be used to improve the accuracy of the final correlation matrices.  
    The package also provides function to check parameter inputs and summarize the simulated 
    systems of equations.
Depends: R (>= 3.4.0), SimMultiCorrData (>= 0.2.1), SimCorrMix (>=
        0.1.0)
License: GPL-2
Imports: BB, nleqslv, MASS, Matrix, VGAM, triangle, ggplot2, grid,
        stats, utils
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, printr, bookdown, nlme, reshape2, testthat
VignetteBuilder: knitr
URL: https://github.com/AFialkowski/SimRepeat
NeedsCompilation: no
Packaged: 2018-04-16 11:30:02 UTC; Allison
Repository: CRAN
Date/Publication: 2018-04-16 14:09:07 UTC
Built: R 3.4.4; ; 2019-04-25 22:38:06 UTC; windows
