R/sars.R

In txm676/mmSAR2: Fit and Compare Species-Area Relationship Models Using Multimodel Inference

"_PACKAGE"
#' sars: Fit and compare species-area relationship models using multimodel inference
#'
#' @name sars-package
#'
#' @description This package provides functions to fit twenty models to
#'   species-area relationship (SAR) data (see Triantis et al. 2012), plot the
#'   model fits, and to construct a multimodel SAR curve using information
#'   criterion weights. A number of additional SAR functions are provided, e.g.
#'   to fit the log-log power model, the general dynamic model of island
#'   biogeography (GDM), Coleman's Random Placement model, and piecewise ISAR
#'   models (i.e. models with thresholds in the ISAR).
#' @details Functions are provided to fit 20 individual SAR models. Nineteen are
#'   fitted using non-linear regression, whilst a single model (the linear
#'   model) is fitted using linear regression. Each model has its own function
#'   (e.g. \code{\link{sar_power}}). A set of multiple model fits can be
#'   combined into a fit collection (\code{\link{sar_multi}}). Plotting
#'   functions (\code{\link{plot.sars}}) are provided that enable individual
#'   model fits to be plotted on their own, or the fits of multiple models to be
#'   overlayed on the same plot. Model fits can be validated using a number of
#'   checks, e.g. the normality and homogeneity of the model residuals can be
#'   assessed.
#'
#'   A multimodel SAR curve can be constructed using the
#'   \code{\link{sar_average}} function. This fits up to twenty SAR models and
#'   constructs the multimodel curve (with confidence intervals) using
#'   information criterion weights (see \code{\link{summary.sars}} to calculate
#'   a table of models ranked by information criterion weight). The
#'   \code{\link{plot.multi}} functions enables the multimodel SAR curve to be
#'   plotted with or without the fits of the individual models.
#'
#'   Other SAR related functions include: (i) \code{\link{lin_pow}}, which fits
#'   the log-log power model and enables comparison of the model parameters with
#'   those calculated using the non-linear power model, (ii) \code{\link{gdm}},
#'   which fits the general dynamic model of island biogeography (Whittaker et
#'   al. 2008) using several different functions, and (iii)
#'   \code{\link{coleman}}, which fits Coleman's  (1981) random placement model
#'   to a species-site abundance matrix. Version 1.3.0 has added functions for
#'   fitting, evaluating and plotting a range of commonly used piecewise SAR
#'   models (\code{\link{sar_threshold}}).
#' @author Thomas J. Matthews and Francois Guilhaumon
#' @references Coleman, B. D. (1981). On random placement and species-area
#'   relations. Mathematical Biosciences, 54, 191-215.
#'
#'   Guilhaumon, F., Mouillot, D., & Gimenez, O. (2010). mmSAR: an R-package for
#'   multimodel species–area relationship inference. Ecography, 33, 420-424.
#'
#'   Matthews, T.J., Guilhaumon, F., Triantis, K.A, Borregaard, M.K., &
#'   Whittaker, R.J. (2015b) On the form of species–area relationships in
#'   habitat islands and true islands. Global Ecology & Biogeography. DOI:
#'   10.1111/geb.12269.
#'
#'   Triantis, K.A., Guilhaumon, F. & Whittaker, R.J. (2012) The island
#'   species–area relationship: biology and statistics. Journal of Biogeography,
#'   39, 215-231.
#'
#'   Whittaker, R.J., Triantis, K.A. & Ladle, R.J. (2008) A general dynamic
#'   theory of oceanic island biogeography. Journal of Biogeography, 35,
#'   977-994.
#' @seealso \url{https://github.com/txm676/sars}
#' @examples
#' data(galap, package = "sars")
#' #fit the power model
#' fit <- sar_power(galap)
#' summary(fit)
#' plot(fit)
#' 
#' #Construct a multimodel averaged SAR curve, using no grid_start simply
#' #for speed (not recommended - see documentation for sar_average())
#' fit_multi <- sar_average(data = galap, grid_start = "none")
#' summary(fit_multi)
#' plot(fit_multi)

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