R/spind.R

In spind: Spatial Methods and Indices

#' spind: Spatial Methods and Indices
#'
#' The \code{spind} package provides convenient implementation of Generalized
#' estimating equations (GEEs) and Wavelet-revised models (WRMs)
#' in the context of spatial models. It also provides tools for
#' multi-model inference, stepwise model selection, and spatially
#' corrected model diagnostics. This help section provides brief descriptions
#' of each function and is organized by the type of model they apply to
#' or the scenarios in which you might use them. Of course, these are
#' recommendations - feel free to use them as you see fit. For a more
#' detailed description of the package and its functions, please see
#' the vignette \emph{Intro to spind} (\code{browseVignettes('spind')}).
#'
#' @section GEEs:
#' The \code{GEE} function fits spatial models using a generalized
#' estimating equation and a set of gridded data. The package
#' also includes S3 methods for \code{summary} and \code{predict}
#' so you can interact with these models in the same way you might
#' interact with a \code{glm} or \code{lm}.
#'
#' @section WRMs:
#' The \code{WRM} function fits spatial models using a wavelet-revised
#' model and a set of gridded data. The package
#' also includes S3 methods for \code{summary} and \code{predict}
#' so you can interact with these models in the same way you might
#' interact with a \code{glm} or \code{lm}. There are also a number
#' of helper functions that help you fine tune the fitting process
#' that are specific to WRMs. Please see the documentation for
#' \code{WRM} for more details on those.
#'
#' \code{WRM} also has a few other features specific to it. For example, if
#' you are interested in viewing the variance or covariance of your variables
#' as a function of \code{level}, \code{covar.plot} is useful. \code{upscale}
#' will plot your matrices as a function of \code{level} so you can examine the
#' effect of cluster resolution on your results.
#'
#' @section Multi-model inference and stepwise model selection:
#' \code{spind} includes a couple of functions to help you find the best fit
#' for your data. The first two are multimodel inference tools specific to GEEs
#' and WRMs and are called \code{mmiGEE} and \code{mmiWMRR}. These generate
#' outputs very similar to those from the \code{MuMIn} package. If you would
#' like to see how variable importance changes as a function of the \code{scale} of
#' the WMRR, you can call \code{rvi.plot}. This will generate a model selection
#' table for each degree of \code{level} (from 1 to \code{maxlevel}) and then
#' plot the weight of each variable as a function of \code{level}.
#'
#' \code{spind} also includes a function for stepwise model selection that is
#' loosely based on \code{\link[stats]{step}} and \code{\link[MASS]{stepAIC}}. \code{step.spind} differs
#' from these in that it is specific to classes \code{WRM} and \code{GEE}. It
#' performs model selection using AIC or AICc for WRMs and QIC for GEEs.
#'
#' @section Spatial indices of goodness of fit:
#' Finally, \code{spind} has a number of functions that provide spatially
#' corrected goodness of fit diagnostics for any type of model (i.e. they
#' are not specific to classes \code{WRM} or \code{GEE}). These first appeared
#' in \code{spind v1.0} and have not been updated in this release. The first two are
#' divided into whether or not they are threshold dependent or not. Threshold
#' dependent metrics can be calculated using \code{th.dep} and threshold
#' independent metrics can be calculated using \code{th.indep}.
#'
#' \code{acfft} calculates spatial autocorrelation of residuals from a model
#' using \emph{Moran's I}. You can set the number of distance bins you'd
#' like to examine using \code{dmax} argument and the size of those bins
#' using \code{lim1} and \code{lim2}.
#'
#' @section Conclusion:
#' The vignette titled \emph{Intro to spind} provides more information
#' on these functions and some example workflows that will demonstrate them
#' in greater depth than this document. Of course, if you have suggestions on
#' how to improve this document or any of the other ones in here, please don't
#' hesitate to contact us.
#'
#' @docType package
#' @name spind
#'
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