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ragt2ridges (version 0.3.4)

Ridge Estimation of Vector Auto-Regressive (VAR) Processes

Description

The ragt2ridges-package provides ridge maximum likelihood estimation of vector auto-regressive processes: the VAR(1), VAR(2) and VARX(1) model (more to be added). Prior knowledge may be incorporated in the estimation through a) specification of the edges believed to be absent in the time series chain graph, and b) a shrinkage target towards which the parameter estimate is shrunken for large penalty parameter values. Estimation functionality is accompanied by methodology for penalty parameter selection. In addition, the package offers supporting functionality for the exploitation of estimated models. Among others, i) a procedure to infer the support of the non-sparse ridge estimate (and thereby of the time series chain graph) is implemented, ii) a table of node-wise network summary statistics, iii) mutual information analysis, and iv) impulse response analysis. Cf. Miok et al. (2017) and Miok et al. (2019) for details on the implemented methods.

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install.packages('ragt2ridges')

Monthly Downloads

72

Version

0.3.4

License

GPL (>= 2)

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Maintainer

Wessel van Wieringen

Last Published

January 28th, 2020

Functions in ragt2ridges (0.3.4)

evaluateVAR1fit

Visualize the fit of a VAR(1) model
impulseResponseVAR2

Impulse response analysis of the VAR(2) model
impulseResponseVARX1

Impulse response analysis of the VARX(1) model
array2longitudinal

Convert a time-series array to a longitudinal-object.
centerVAR1data

Zero-centering of time-course data
mutualInfoVAR2

Mutual information analysis of the VAR(2) model
loglikLOOCVVAR2

Leave-one-out (minus) cross-validated log-likelihood of VAR(2) model
loglikLOOCVVARX1

Leave-one-out (minus) cross-validated log-likelihood of VARX(1) model
loglikLOOCVcontourVAR1

Contourplot of LOOCV log-likelihood of VAR(1) model
loglikLOOCVcontourVAR1fused

Contourplot of LOOCV log-likelihood of multiple VAR(1) models
dataVAR2

Sample data from a VAR(2) model
dataVARX1

Sample data from a VARX(1) model
optPenaltyVARX1

Automatic penalty parameter selection for the VARX(1) model.
plotVAR1data

Time series plot
graphVAR2

Graphs of the temporal (or contemporaneous) relations implied by the VAR(2) model
ridgePathVAR1

Visualize the ridge regularization paths of the parameters of the VAR(1) model
nodeStatsVAR1

VAR(1) model node statistics
mutualInfoVAR1

Mutual information analysis of the VAR(1) model
graphVARX1

Graphs of the temporal (or contemporaneous) relations implied by the VARX(1) model
motifStatsVAR1

Network motif detection for the VAR(1) model.
ridgeVAR1

Ridge ML estimation of the VAR(1) model
CIGofVAR1

Conditional independence graphs of the VAR(1) model
CIGofVAR2

Conditional independence graphs of the VAR(2) model
loglikVAR1

Log-likelihood of the VAR(1) model.
hpvP53

Time-course P53 pathway data
impulseResponseVAR1

Impulse response analysis of the VAR(1) model
nodeStatsVAR2

VAR(2) model node statistics
sparsifyVARX1

Function that determines the support of (auto)regression parameters of the VARX(1) model.
sparsifyVAR2

Function that determines the support of autoregression parameters of the VAR(2) model.
longitudinal2array

Convert a longitudinal object into an array.
pruneMotifStats

Network motif list subsetting.
ragt2ridges-package

Ridge Estimation of Vector Auto-Regressive (VAR) Processes
createA

Generation of the VAR(1) autoregression coefficient matrix.
dataVAR1

Sample data from a VAR(1) model
optPenaltyVAR1

Automatic penalty parameter selection for the VAR(1) model.
ridgeVAR2

Ridge ML estimation of the VAR(2) model
ridgeVAR1fused

Fused ridge ML estimation of multiple VAR(1) model
loglikLOOCVcontourVAR2

Contourplot of LOOCV log-likelihood of the VAR(2) model
loglikLOOCVVAR1

Leave-one-out (minus) cross-validated log-likelihood of VAR(1) model
optPenaltyVAR1fused

Automatic penalty parameter selection for multiple VAR(1) models.
ridgeVARX1

Ridge ML estimation of the VARX(1) model
sparsifyVAR1

Function that determines the support of autoregression parameter of the VARX(1) model.
optPenaltyVAR2

Automatic penalty parameter selection for the VAR(2) model.
loglikLOOCVcontourVARX1

Contourplot of the LOOCV log-likelihood of VARX(1) model
loglikLOOCVVAR1fused

Leave-one-out (minus) cross-validated log-likelihood of multiple VAR(1) models
graphVAR1

Graphs of the temporal (or contemporaneous) relations implied by the VAR(1) model