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#' @importFrom coda as.mcmc autocorr autocorr.diag effectiveSize HPDinterval
#' @importFrom digest digest
#' @importFrom extraDistr rcat rdirichlet
#' @importFrom graphics abline axis hist mtext par plot points rect text
#' @importFrom grDevices devAskNewPage rgb
#' @importFrom lubridate is.Date
#' @importFrom magrittr %>%
#' @importFrom memoise memoise
#' @importFrom methods is
#' @importFrom mvtnorm rmvnorm
#' @importFrom nnet multinom
#' @importFrom progress progress_bar
#' @importFrom stats acf AIC as.formula coef ecdf logLik median rgeom rnorm
#' runif sd terms var vcov
#' @importFrom topicmodels LDA
#' @importFrom viridis viridis
#'
#' @title Package to conduct two-stage analyses combining Latent Dirichlet
#' Allocation with Bayesian Time Series models
#'
#' @description Performs two-stage analysis of multivariate temporal data
#' using a combination of Latent Dirichlet Allocation (Blei \emph{et al.}
#' 2003) and Bayesian Time Series models (Western and Kleykamp 2004) that we
#' extend for multinomial data using softmax regression (Venables and Ripley
#' 2002) following Christensen \emph{et al.} (2018).
#'
#' @section Documentation:
#' \href{https://github.com/weecology/LDATS/blob/main/LDATS_model.pdf}{Technical mathematical manuscript}
#' \cr \cr
#' \href{https://weecology.github.io/LDATS/articles/rodents-example.html}{End-user-focused vignette worked example}
#' \cr \cr
#' \href{https://weecology.github.io/LDATS/articles/LDATS_codebase.html}{Computational pipeline vignette}
#' \cr \cr
#' \href{https://weecology.github.io/LDATS/articles/paper-comparison.html}{Comparison to Christensen \emph{et al.}}
#'
#' @references
#'
#' Blei, D. M., A. Y. Ng, and M. I. Jordan. 2003. Latent Dirichlet
#' Allocation. \emph{Journal of Machine Learning Research}
#' \strong{3}:993-1022.
#' \href{https://jmlr.csail.mit.edu/papers/v3/blei03a.html}{link}.
#'
#' Christensen, E., D. J. Harris, and S. K. M. Ernest. 2018.
#' Long-term community change through multiple rapid transitions in a
#' desert rodent community. \emph{Ecology} \strong{99}:1523-1529.
#' \href{https://pubmed.ncbi.nlm.nih.gov/29718539/}{link}.
#'
#' Venables, W. N. and B. D. Ripley. 2002. \emph{Modern and Applied
#' Statistics with S}. Fourth Edition. Springer, New York, NY, USA.
#'
#' Western, B. and M. Kleykamp. 2004. A Bayesian change point model for
#' historical time series analysis. \emph{Political Analysis}
#' \strong{12}:354-374.
#' \href{https://www.cambridge.org/core/journals/political-analysis/article/abs/bayesian-change-point-model-for-historical-time-series-analysis/F7D2EDBBC211278EC6C6CB43FE170812}{link}.
#'
#' @name LDATS
#'
#' @docType package
#'
#' @keywords package
#'
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