R/dsmextra-package.R

In densitymodelling/dsmextra: A Toolkit for Extrapolation Assessments in Density Surface Models

#' Extrapolation detection in density surface models
#'
#' The \code{dsmextra} package provides functions for detecting, diagnosing and visualising extrapolation in multivariate environmental space, with applications to density surface models (DSMs) created in the \code{\link[dsm]{dsm}} package, as well as other types of spatially-explicit predictive ecological models.
#'
#' Consult the package website at \href{https://densitymodelling.github.io/dsmextra/}{https://densitymodelling.github.io/dsmextra/} for a step-by-step tutorial.
#'
#' Further information on distance sampling methods and example code is available at \href{http://distancesampling.org/R/}{http://distancesampling.org/R/}.
#'
#' For help with distance sampling, there is a Google Group \href{https://groups.google.com/forum/#!forum/distance-sampling}{https://groups.google.com/forum/#!forum/distance-sampling}.
#'
#' @author Phil J. Bouchet, Laura Mannocci, David Miller
#' @docType package
#' @name dsmextra
#' @importFrom dplyr %>%
#' @importFrom purrr %||%
NULL

# Quiets concerns of R CMD check re: the .'s that appear in pipelines
if(getRversion() >= "2.15.1")  utils::globalVariables(c("."))

#' Sperm whale sightings in the Mid-Atlantic
#'
#' Data from a combination of several NOAA visual surveys conducted for cetaceans in the U.S. Mid-Atlantic. Survey tracklines were split into segments for analysis in the \code{\link[dsm]{dsm}} R package. Spatial coordinates (\code{x}, \code{y}) and values of both static and dynamic environmental covariates are availble for each segment mid-point and for the centroids of a 10 km grid overlaid on the study area. Covariates include: depth, sea surface temperature (\code{SST}), net primary production (\code{NPP}), distance to nearest canyon or seamount (\code{DistToCAS}), and eddy kinetic energy (\code{EKE}).
#'
#' An example extrapolation assessment is provided at \url{https://densitymodelling.github.io/dsmextra/articles/dsmextra-vignette.html}.
#'
#' @references NOAA Northeast Fisheries Science Center (2004). A survey for abundance and distribution of cetaceans in the U.S. Mid-Atlantic with an emphasis on pilot whales. Report of a survey conducted aboard NOAA Ship Gordon Gunter Cruise GU-04-03 (028).
#'
#' NOAA Northeast Fisheries Science Center (2004). Report on the 2004 Mid-Atlantic Marine Mammal Shipboard Abundance Survey aboard the R/V Endeavor, Cruise No. EN 04-395/396.
#'
#' Palka DL (2012). Cetacean abundance estimates in US northwestern Atlantic Ocean waters from summer 2011 line transect survey. Northeast Fisheries Science Center Reference Document 12-29, 37 p.
#'
#' Palka DL (2006) Summer abundance estimates of cetaceans in US North Atlantic Navy operating areas. Northeast Fisheries Science Center Reference Document 06-03, 41 p.
#'
#' @format A list of two
#' \describe{
#'   \item{segs}{segment-level data, as used in the \code{\link[dsm]{dsm}} package}
#'   \item{predgrid}{prediction data.frame}
#' }
#'
#' @name spermwhales
#' @docType data
#' @source Data provided by Debi Palka (NOAA North East Fisheries Science Center) and Lance Garrison (NOAA South East Fisheries Science Center). Initial data processing by Jason Roberts (Marine Geospatial Ecology Lab, Duke University). A subset of the data are held and described on OBIS-SEAMAP at: \url{http://seamap.env.duke.edu/dataset/396}.
#' @keywords datasets
NULL


#' Native and introduced range of Acacia cyclops
#'
#' Spatial extents of the native and introduced ranges of A. cyclops, a small shrub species.
#'
#'#' Mesgaran MB, Cousens RD, Webber BL (2014). Here be dragons: a tool for quantifying novelty due to covariate range and correlation change when projecting species distribution models. Diversity & Distributions, 20: 1147-1159, DOI: \href{https://onlinelibrary.wiley.com/doi/full/10.1111/j.1472-4642.2011.00811.x}{10.1111/j.1472-4642.2011.00811.x}
#'
#' Webber BL, Yates, CJ, Le Maitre DC, Scott JK, Kriticos DJ, Ota N, McNeill A, Le Roux JJ, Midgley GF (2011). Modelling horses for novel climate courses: Insights from projecting potential distributions of native and alien Australian acacias with correlative and mechanistic models. Diversity and Distributions, 17: 978–1000. DOI: \href{https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12209}{10.1111/ddi.12209}
#'
#' @format A list of two
#' \describe{
#'   \item{south_australia}{\code{SpatialPolygonsDataFrame} of the native range (reference area).}
#'   \item{south_africa}{\code{SpatialPolygonsDataFrame} of the introduced range (target area).}
#' }
#'
#' @name acacia
#' @docType data
#' @source Sample data from the ExDet tutorial available from https://www.climond.org/ExDet.aspx.
#' @keywords datasets
NULL