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#' @aliases dupfilter_exact
#' @title Filter temporally and spatially exact duplicates
#' @description Function to filter temporally and spatially exact locations in tracking data.
#' @param sdata A data frame containing columns with the following headers: "id", "DateTime", "lat", "lon", "qi".
#' See the data \code{\link{turtle}} for an example.
#' The function filters the input data by a unique "id" (e.g. transmitter number, identifier for each animal).
#' "DateTime" is the GMT date & time of each location in class \code{\link[base:DateTimeClasses]{POSIXct}} or \code{\link[base]{character}} with the following format "2012-06-03 01:33:46".
#' "lat" and "lon" are the latitude and longitude of each location in decimal degrees.
#' "qi" is the quality index associated with each location fix.
#' The input values can be either the number of GPS satellites or Argos Location Classes.
#' Argos Location Classes will be converted to numerical values, where "A", "B", "Z" will be replaced with "-1", "-2", "-3" respectively.
#' The greater number indicates a higher accuracy.
#' @importFrom dplyr distinct
#' @export
#' @details This is a partial component of \code{\link{dupfilter}}, although works as a stand-alone function.
#' It looks for temporally and spatially exact locations and retains only a single fix (latitude/longitude pair) per time and location.
#' @return The input data frame is returned with temporally and spatially exact duplicates removed.
#' @author Takahiro Shimada
#' @references Shimada T, Limpus C, Jones R, Hazel J, Groom R, Hamann M (2016)
#' Sea turtles return home after intentional displacement from coastal foraging areas.
#' \emph{Marine Biology} 163:1-14 \doi{10.1007/s00227-015-2771-0}
#' @seealso \code{\link{dupfilter}}, \code{\link{dupfilter_qi}}, \code{\link{dupfilter_time}}, \code{\link{dupfilter_space}}
dupfilter_exact <- function(sdata){
## Original sample size
OriginalSS <- nrow(sdata)
## qi format
if(!is.numeric(sdata$qi)){
sdata <- within(sdata, {
qi[qi %in% "A"] <- "-1"
qi[qi %in% "B"] <- "-2"
qi[qi %in% "Z"] <- "-3"
qi <- as.numeric(as.character(qi))
})
}
## Date & time
if(!any(class(sdata$DateTime) %in% "POSIXct")){
sdata$DateTime <- with(sdata, as.POSIXct(DateTime, format = "%Y-%m-%d %H:%M:%S", tz = "GMT"))
}
#### Filter temporally and spatially exact duplicates
sdata <- dplyr::distinct(sdata, .data$id, .data$DateTime, .data$lat, .data$lon, .data$qi, .keep_all = TRUE)
#### Report the summary of filtering
## Filtered data
FilteredSS <- nrow(sdata)
RemovedSamplesN <- OriginalSS-FilteredSS
## Print report
cat("dupfilter_exact removed", RemovedSamplesN, "of", OriginalSS, "locations", fill = TRUE)
#### return the output
return(sdata)
}
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