A series of functions to implement association of covariance for detecting differential co-expression (ACDC), a novel approach for detection of differential co-expression that simultaneously accommodates multiple phenotypes or exposures with binary, ordinal, or continuous data types. Users can use the default method which identifies modules by Partition or may supply their own modules. Also included are functions to choose an information loss criterion (ILC) for Partition using OmicS-data-based Complex trait Analysis (OSCA) and Genome-wide Complex trait Analysis (GCTA). The manuscript describing these methods is as follows: Queen K, Nguyen MN, Gilliland F, Chun S, Raby BA, Millstein J. "ACDC: a general approach for detecting phenotype or exposure associated co-expression" (2023) <doi:10.3389/fmed.2023.1118824>.

Implements parametric modal regression for continuous positive
    distributions of the exponential family under right censoring.
    Provides functions to link the conditional mode to a linear predictor
    using reparameterizations for Gamma, Beta, Weibull, and Inverse Gaussian
    families. Includes maximum likelihood estimation via numerical
    optimization, asymptotic inference based on the observed Fisher
    information matrix, and model diagnostics using randomized quantile
    residuals.

Performs Modal Clustering (MAC) including Hierarchical Modal Clustering (HMAC) along with their parallel implementation (PHMAC) over several processors.  These model-based non-parametric clustering techniques can extract  clusters in very high dimensions with arbitrary density shapes. By default clustering is performed over several resolutions and the results are summarised as a hierarchical tree. Associated plot functions are also provided. There is a package vignette that provides many examples. This version adheres to CRAN policy of not spanning more than two child processes by default.

Implements parametric modal Autoregressive Integrated Moving Average (ARIMA) models utilizing the Skewed Distribution (SKD) family. Current distributions supported are the Skew-Normal, Skewed Student-t, and Skewed Laplace. The conditional mode is parameterized and optimized via maximum likelihood using analytical gradients. Includes comprehensive residual diagnostics, robustness options (heavy tails, asymmetry), robust parametric bootstrap prediction intervals, and classical asymptotic inference via the Fisher Information matrix. Methods are described in Galarza, C.E., Lachos, V.H., Cabral, C.R.B., & Castro, L.M. (2017) <doi:10.1002/sta4.140>.