R/CarolinaWrenPA.R

In zoonproject/modules: Species Distribution Modelling Code Modules for the ZOON Package

#' @name CarolinaWrenPA
#'   
#' @title Presence/absence data for the Carolina Wren in the USA
#'   
#' @description Presence/absence of the Carolina Wren \emph{Thryothorus 
#'   ludovicianus} at Breeding Bird Survey transects in 2006. These data are 
#'   made available in the maxlike R package. See 
#'   \code{\link[maxlike]{carw.data}} for more details. This module loads them 
#'   data transform the coordinates to lat/longs and formats the data for use in
#'   a zoon workflow. To use these data for validation rather than model
#'   fitting, see \code{CarolineWrenValidation}.
#'   
#' @details
#' 
#'
#' @family occurrence
#'
#' @author Nick Golding, \email{nick.golding.research@@gmail.com}
#'
#' @section Data type: presence/absence
#'
#' @section Version: 0.1
#'
#' @section Date submitted:  2016-05-21
CarolinaWrenPA <- function () 
{
    zoon::GetPackage("maxlike")
    data(carw, envir = environment())
    occ <- na.omit(carw.data$pa.data)
    coords_raw <- sp::SpatialPoints(occ[, c("X", "Y")], proj4string = CRS("+proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs"))
    coords <- sp::spTransform(coords_raw, "+init=epsg:4326")
    data.frame(longitude = coords@coords[, "X"], latitude = coords@coords[, 
        "Y"], value = occ$y, type = ifelse(occ$y, "presence", 
        "absence"), fold = 1, stringsAsFactors = FALSE)
}