Author: Taryn B. T. Athey [aut, cre], Paul D. McNicholas [aut, cre], Jarrett D. Phillips [ctb]
Maintainer: Taryn B. T. Athey <taryn.athey@gmail.com>
Description: Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences.  The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs.  The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another.  Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992>.
Packaged: 2022-08-17 21:23:08 UTC; jarrettphillips

Note:    ====== vlmc.version in R/vlmc.R
Title: VLMC -- Variable Length Markov Chains
Description: Functions, Classes & Methods for estimation, prediction, and
simulation (bootstrap) of VLMC -- Variable Length Markov Chain -- Models
Packaged: Mon Sep 18 10:34:09 2006; maechler

Description: Functions, Classes & Methods for estimation, prediction,
and simulation (bootstrap) of VLMC -- Variable Length Markov

Versionnote: == vlmc.version in R/vlmc.R

Packaged: Wed May  5 18:42:49 2004; maechler

Packaged: Fri Mar 25 15:21:48 2005; maechler

Packaged: Thu Oct  6 15:00:09 2005; maechler

Title: Variable Length Markov Chains ('VLMC') Models
simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.

Title: Variable-Lag Time Series Causality Inference Framework
Description: A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2019) <https://www.cs.uic.edu/~elena/pubs/amornbunchornvej-dsaa19.pdf> when referring to this package in publications.
Depends: R (>= 3.5.0), dtw, tseries, RTransferEntropy
Packaged: 2019-12-20 02:09:46 UTC; Chainarong