R/distcalc.r

In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity

#' distcalc
#' 
#' Calculates pairwise geographic distance between locations on earth. Just a
#' convenient wrapper for fields::rdist.earth().
#' 
#' @author John L. Darcy
#' 
#' @param lat Numeric vector. Latitudes in decimal degree format.
#' @param lng Numeric vector. Longitudes in decimal degree format.
#' @param sampIDs Character vector. Sample identifiers. Only required
#'   if output dist should have names associated.
#' 
#' @return matrix containing all pairwise geographic distances in km. 
#' 
#' @examples
#' # library(specificity)
#' # attach(endophyte)
#' # geo_dists <- distcalc(metadata$Lat, metadata$Lon, metadata$SampleID)
#' # all(rownames(geo_dists) == metadata$SampleID)
#' 
#' @export
distcalc <- function(lat, lng, sampIDs=NULL){
	if(requireNamespace("fields", quietly=TRUE)){
		longlats <- data.frame(lng, lat)
		if(!is.null(sampIDs)){
			rownames(longlats) <- sampIDs
		}
		distmat=fields::rdist.earth(as.matrix(longlats), miles=FALSE, R=NULL) 
		return((distmat))	
	}else{
		stop("Package 'fields' is required for distcalc. Please install it and try again.")
	}
}