Title: Frequency Domain Analysis for Multivariate Time Series
Description: Methods for the analysis of multivariate time series using frequency domain techniques. Implementations of dynamic principle components analysis (DPCA) and estimators of operators in lagged regression. Examples of usage in functional data analysis setup.
Depends: R (>= 2.15.0), mvtnorm, stats, graphics, base

Title: Frequency Domain Based Analysis: Dynamic PCA
Description: Implementation of dynamic principal component
analysis (DPCA), simulation of VAR and VMA processes and frequency domain tools.
These frequency domain methods for dimensionality reduction of multivariate time series
were introduced by David Brillinger in his book Time Series (1974). We follow implementation
guidelines as described in Hormann, Kidzinski and Hallin (2016),
Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.
Depends: R (>= 2.15.0), mvtnorm, stats, graphics, base, matrixcalc,

Suggests: fda, MASS, MARSS, testthat (>= 3.0.0)

Title: Functional Time Series: Dynamic Functional Principal Components
Description: Implementations of functional dynamic principle components analysis. Related graphic tools and frequency domain methods.
These methods directly use multivariate dynamic principal components implementation,
following the guidelines from Hormann, Kidzinski and Hallin (2016), Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.
Depends: R (>= 2.15.0), mvtnorm, stats, graphics, base, fda, freqdom

Author: Norm Matloff <normmatloff@gmail.com> and Yingkang Xie
Title: Novel Methods for Parallel Coordinates
Description: New approaches to parallel coordinates plots for
multivariate data visualization, including applications to clustering,
outlier hunting and regression diagnostics.  Includes general functions
for multivariate nonparametric density and regression estimation,
Depends: parallel, ggplot2, GGally, FNN, mvtnorm

Title: Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk
person(given="Masaaki", family="Sudo", email="masaaki@sudori.info", role=c("aut", "cre"), comment=c(ORCID="0000-0001-9834-9857"))
Description: Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called "group-testing", this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.
Author: Masaaki Sudo [aut, cre] (<https://orcid.org/0000-0001-9834-9857>)