tvvarss-package.RdThe tvvarss package uses Stan (mc-stan.org) to fit multi-site multivariate autoregressive (aka vector autoregressive) state space models with a time varying interaction matrix.
The DESCRIPTION file:
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Maintainer: Eric Ward <eric.ward@noaa.gov>
Francis, T.B. E. Wolkovich, S.E. Hampton, M.D. Scheuerell, S.L. Katz, and E.E. Holmes. 2014. Shifting regimes and changing interactions in the Lake Washington, USA, plankton community from 1962–1994. PLoS ONE 9(10): e110363. doi:10.1371/journal.pone.0110363.
Hampton, S. E., Holmes, E. E., Scheef, L. P., Scheuerell, M. D., Katz, S. L., Pendleton, D. E. and Ward, E. J. 2013. Quantifying effects of abiotic and biotic drivers on community dynamics with multivariate autoregressive (MAR) models. Ecology, 94: 2663–2669. doi:10.1890/13-0996.1
Holmes, E. E., E. J. Ward, and M. D. Scheuerell. 2012. Analysis of multivariate time-series using the MARSS package. NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd E., Seattle, WA 98112
Holmes, E. E., E. J. Ward and K. Wills. 2012. MARSS: Multivariate autoregressive state-space models for analyzing time-series data. R Journal 4: 11-19.
Ives, A.R., B. Dennis, K.L. Cottingham, and S.R. Carpenter. 2003. Estimating community stability and ecological interactions from time-series data. Ecological Monographs, 73(2), pp. 301–330.
Ives, A.R. and V. Dakos. 2012. Detecting dynamical changes in nonlinear time series using locally linear state-space models. Ecosphere 3(6):58. http://dx.doi.org/10.1890/ES11-00347.1
Optional links to other man pages, e.g.
#simple examples of the most important functions