Nothing
#' Which cells are not empty
#'
#' This function returns the ID of those cells that have some data. It is used to
#' speed up other functions
#'
#' @param x A list.
#' @return The a \code{vector} with list elements IDs.
#' @export
whichNonEmpty <- function(x){
# res <- which( lengths(x) > 1)
# res <- unname(which(unlist(!is.null(lapply(x, nrow) > 0)))
res <- which(
unlist(
lapply(x,
function(y){
!all(is.na(y))
}
)
)
)
return(res)
}
#' Create spillover overlay for specific grid
#'
#' An internal function. Takes the resulting data.frame from the spatial overlay
#' for a specific grid cell and searches for spillover visits, i.e. visits that are split by grid cell boundaries.
#'
#' @param x A data.frame for a specific grid without spillover.
#' @param birdData An OrganizedBirds object, which is the input to the \code{\link{overlayBirds}}-function.
#' @param visitCol A character string specifying the columns that identify a visit.
#'
#' @return The overlay data.frame for a specific grid, including the spillover visits.
#' @keywords internal
createOverlayForGrid <- function(x, birdData, visitCol){
visitsInGrid <- unique(x[visitCol])
birdDF <- st_drop_geometry(birdData$spdf)
res <- birdDF[which(birdDF[,visitCol] %in% visitsInGrid[,1]),]
return(res)
}
#' Include spillover observations
#'
#' An internal function to include spillover observations to the gridcells.
#' This function duplicates observations across gridcells
#'
#' @param x An observationsInGrid list from \code{\link{overlayBirds}}. This
#' is also what will be modified and become the output.
#' @param birdData An OrganizedBirds object, which is the input to the \code{\link{overlayBirds}}-function.
#' @param visitCol A character string for specifying the columns that identify a visit.
#'
#' @return A modified observationsInGrid list
#' @keywords internal
includeSpillover <- function(x, birdData, visitCol){
res <- lapply(x, createOverlayForGrid, birdData, visitCol)
return(res)
}
#' Include unique spillover observations
#'
#' An internal function to include spillover observations to the gridcells.
#' This function moves spillover observations to the gridcells were the focal visit has the most observations (or at random if ties)
#'
#' @param birdData An OrganizedBirds object, which is the input to the \code{\link{overlayBirds}}-function.
#' @param grid A sf or SpatialPolygonsDataFrame object of the grid over the study area
#' @param visitCol A character string for specifying the columns that identify a visit.
#'
#' @return A ObservationsInGrid list
#' @importFrom nnet which.is.max
#' @keywords internal
includeUniqueSpillover <- function(birdData, grid, visitCol){
if(!any(class(birdData) %in% c("sf","OrganizedBirds","SpatialPointsDataFrame")))
stop("Data must be of class 'OrganizedBirds', 'sf' or 'SpatialPointsDataFrame'")
if(any(class(birdData)=="OrganizedBirds")) birdData <- birdData$spdf
if(any(class(birdData)=="SpatialPointsDataFrame")) birdData <- st_as_sf(birdData)
if(!identical(st_crs(birdData), st_crs(grid))){
stop("Organized data and grid do not share the same CRS")
}
if(any(class(grid)=="sfc")) grid <- st_as_sf(grid)
## create ids
if(length(grep("id", colnames(grid), ignore.case = TRUE)) ==0) {
grid$id <- seq(nrow(grid))
} else {
grid$id <- st_drop_geometry(grid[, grep("id", colnames(grid),
ignore.case = TRUE)[1]])
}
obs <- st_drop_geometry(
suppressWarnings(
suppressMessages(
st_intersection(birdData, grid)
)
)
)
wNA <- which(is.na(obs$id))
if(length(wNA)>0){
obs <- obs[-wNA,]
}
crossTab <- table("grid" = obs[,"id"],
"visits" = obs[,visitCol])
visits <- unique(obs[, visitCol])
visits <- cbind(visits, "grid" = NA)
for(v in dimnames(crossTab)$visits){
visits[visits[, "visits"] == as.integer(v), "grid"] <- as.integer(dimnames(crossTab)$grid[nnet::which.is.max(crossTab[,v])])
##nnet::which.is.max is good since if it's equal number it takes one on random.
}
wNAvis <- which(is.na(visits[,"grid"]))
if(length(wNAvis)>0){
visits <- visits[-wNAvis,]
}
colsExc <- which(colnames(obs) == "id")
res <- list()
for(g in seq(nrow(grid))){
res[[g]] <- obs[obs[, visitCol] %in% unique(visits[visits[, "grid"] == g, "visits"]), -colsExc]
}
return(res)
}
#' Overlay BIRDS object and grid
#'
#' Make an overlay for an OrganizedBirds object and a grid to identify which
#' observations that fall into which grid cell.
#'
#' This function takes an OrganizedBirds object, created by
#' \code{\link{organizeBirds}}, and a polygon grid-layer, which could be created
#' by \code{\link{makeGrid}} and splits the visits in the OrganizedBirds
#' (i.e. data belonging to identified visits) to each grid cell.
#'
#' If \code{spillOver = NULL} the splitting is done spatially according to the
#' overlay of observations and grid cells, without further consideration of
#' coherence for visits (visit UID). If \code{spillOver = c("unique", "duplicate")}
#' the splitting will be done spatially in a first step, and then:
#' if \code{(spillOver = "unique")} assigns (and moves) all observations with same visitUID
#' to the grid cell with most observations (or picks one grid cell at random if
#' there is a tie); or if \code{(spillOver = "duplicate")} duplicates all
#' observations with same visitUID across all grid cells containing at least one
#' observation with that visitUID.
#'
#' The later approach is useful when the amount of observations spilled over
#' neighbouring cells is minimal and information over the spatial extent of the
#' sampling effort is more important than sample independence.
#'
#' @param x An OrganizedBirds object
#' @param grid A sf or SpatialPolygonsDataFrame object of the grid over the study area
#' @param spillOver Specifies if the function should search for observations
#' with the same visitUID over several grid cell, and what to do with them.
#' It accepts \code{c(NULL, "unique", "duplicate")}. Default NULL.
#' @param cleanGrid logical. Whether to remove all data from the grid.
#'
#' @return The output is a OverlaidBirds-class object, which is a list
#' containing three objects;
#' \describe{
#' \item{\code{observationsInGrid}}{Is
#' basically the data in the OrganizedBirds object split by each grid cell
#' (\emph{n.b.} the use of \code{spillOver} discussed under "Usage")}
#' \item{\code{grid}}{The sf from the input, optionally cleared of data }
#' \item{\code{nonEmptyGridCells}}{An integer vector of which grid cells that have observations}
#' }
#' @export
#' @examples
#' \donttest{
#' ob <- organizeBirds(bombusObs)
#' grid <- makeGrid(gotaland, 10)
#' ovB <- overlayBirds(ob, grid)
#' }
overlayBirds <- function(x,
grid,
spillOver = NULL,
cleanGrid = TRUE){
if(!is.null(spillOver)){
### Bad spill over definition
if (!spillOver %in% c("unique", "duplicate") ) stop("Unknown definition of 'spillOver'")
} #else { stop("Unknown definition of 'spillOver'") }
UseMethod("overlayBirds")
}
##TODO make a overlayBirds.default
#' @export
#' @rdname overlayBirds
overlayBirds.OrganizedBirds <- function(x,
grid,
spillOver = NULL,
cleanGrid = TRUE){
spBird <- x$spdf
if(any(class(spBird) == "SpatialPointsDataFrame")){
spBird <- st_as_sf(spBird)
}
if(any(class(grid) %in% c("SpatialPolygonsDataFrame", "SpatialPolygons"))){
grid <- st_as_sf(grid)
}
if (cleanGrid){
grid <- st_geometry(grid) ##Removes unnecessary data from the input grid, if there is any
}
visitCol <- attr(x, "visitCol")
nVis <- length(unique(st_drop_geometry(spBird)[,visitCol]))
nObs <- nrow(spBird)
if(!identical(st_crs(spBird), st_crs(grid))){
grid <- st_transform(grid,
crs = st_crs(spBird))
}
#### Rename grid
if (any(duplicated(names(grid)))){
grid <- renameGrid(grid)
warning("There are duplicated cell names in your grid. We rename them internally to 'ID1'...'IDn'.
All results will use this nomenclature, but the order of the cells will remain unaltered.")
}
#### SPILL OVER
### Generic overlay
## overlay the data with the grid
listGrid <- suppressMessages(st_intersects(grid, spBird))
ObsInGridList <- list()
for(i in seq(length(listGrid))){
if(length(listGrid[[i]]) == 0){
ObsInGridList[[i]] <- NA
} else {
ObsInGridList[[i]] <- st_drop_geometry(spBird[listGrid[[i]],])
}
}
wNonEmpty <- whichNonEmpty(ObsInGridList)
if(length(wNonEmpty) == 0) stop("Observations don't overlap any grid cell.")
### Check nObs
nObsInGrid <- sum(unlist(lapply(ObsInGridList, nrow)))
if((nObs-nObsInGrid)>0){
message(paste((nObs-nObsInGrid), "observations did not overlap with the grid and will be discarded."))
}
visitsIDGrid <- lapply(ObsInGridList[wNonEmpty], function(x) unique(x[,visitCol]))
nSpill <- sum(duplicated(unlist(visitsIDGrid)))
if(nSpill>0){
porcSpill<-round(nSpill/nVis*100,3)
message(paste(porcSpill, "% of the visits spill over neighbouring grid cells."))
if (porcSpill >= 20) {
message("20% or more of the visits spill observations over other grid cells.
This may suggest that either your grid cell is too narrow or your definition of a 'visit' is not properly defined to match your grid cell size.
Please, consider using 'exploreVisits()' to double check your assumptions.")
}
}
if(!is.null(spillOver)){
# if (!spillOver %in% c("unique", "duplicate") ) stop("Unknown definition of 'spillOver'")
### Good definition
if(spillOver == "unique"){ ### UNIQUE SPILL OVER
ObsInGridList <- includeUniqueSpillover(spBird, grid, visitCol)
wNonEmpty <- whichNonEmpty(ObsInGridList)
}
if(spillOver == "duplicate"){ ### DUPLICATE SPILL OVER
ObsInGridList[wNonEmpty] <- includeSpillover(ObsInGridList[wNonEmpty], x, visitCol)
}
} #else {stop("Unknown definition of 'spillOver'")}
res <- list("observationsInGrid" = ObsInGridList,
"grid"= grid,
"nonEmptyGridCells" = wNonEmpty)
attr(res, "visitCol") <- visitCol ##An attribute to indicate which of the visits-column should be used in further analyses
attr(res, "spillOver") <- spillOver ##An attribute to indicate how spillover observations are included
return(res)
}
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