R/BIRDS_pkg.r

In BIRDS: Biodiversity Information Review and Decision Support

#' BIRDS: Biodiversity Information Review and Decision Support.
#'
#' @description The primary aim of this package is to provide tools for Biodiversity Informatics
#' in order to understand the species information data and decide about what analyses
#' we can perform and draw appropriate conclusions. For this we need to understand
#' the data generation process. With this R package we want to take the
#' user a step closer to understanding the observers’ behavior.
#' The 'BIRDS' packages provides a workflow for reproducible data review, involving
#' three basic steps: organize, summarize, and review data.
#'
#' @import sf
#' @docType package
#' @name BIRDS
#' @examples
#' \donttest{
#' library(sf)
#' # Organise the data
#' OB <- organizeBirds(bombusObsShort, sppCol = "scientificName", simplifySppName = TRUE)
#'
#' OB2 <- organizeBirds(bryophytaObs, sppCol = "species", simplifySppName = FALSE,
#'       taxonRankCol = "taxonRank", taxonRank = c("SPECIES", "SUBSPECIES","VARIETY"))
#'
#' # Make a grid that can be used by summariseBirds()
#' # gotaland is a SpatialPolygonDataFrame provided as an example
#' grid <- makeGrid(gotaland, gridSize = 10)
#'
#' # Summarise the data (using the grid to overlay with the organised data)
#' SB <- summariseBirds(OB, grid=grid)

#' EBnObs <- exportBirds(SB, dimension = "temporal", timeRes = "yearly",
#' variable = "nObs", method = "sum")
#' EBnVis <- exportBirds(SB, dimension = "temporal", timeRes = "yearly",
#' variable = "nVis", method = "sum")

#' EB<-exportBirds(SB, "Spatial", "Month", "nYears", "sum")
#' palBW <- leaflet::colorNumeric(c("white", "navyblue"),
#'          c(0, max(st_drop_geometry(EB), na.rm = TRUE)), na.color = "transparent")
#' old.par <- par(no.readonly =TRUE)
#' par(mfrow=c(1,2), mar=c(1,1,1,1))
#' plot(EB, col=palBW(EB$Jul))
#' mtext("July", 3)
#' plot(EB, col=palBW(EB$Dec))
#' mtext("December", 3)
#' legend("bottomleft", legend=seq(0, max(st_drop_geometry(EB), na.rm = TRUE),length.out = 5),
#'        col = palBW(seq(0, max(st_drop_geometry(EB), na.rm = TRUE), length.out = 5)),
#'        title = "Number of years", pch = 15, bty="n")
#' par(old.par)
#' }
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