pleistodist_centroid: Calculate inter-island centroid-to-centroid distance over...

In g33k5p34k/PleistoDistR: Calculating Island Geomorphologies Over Pleistocene Time

Calculate inter-island centroid-to-centroid distance over time

Description

This function calculates the centroid-to-centroid distance between island landmasses over Pleistocene time. For each pairwise combination of source points provided by the user, this function selects the landmasses that correspond to each point, and calculates the distance between the centroids of the selected landmasses for each time/sea level interval. If both points lie on the same landmass, a distance value of 0 is returned. If one or both islands is/are underwater, then a value of NA is returned. After calculating the pairwise island distances for each interval, this function calculates the time-weighted average centroid-to-centroid distance between each island pair.

Usage

pleistodist_centroid(points, epsg, intervalfile, mapdir, outdir)

Arguments

points	A user-generated multi-point shapefile (.shp) containing at least two points. If the shapefile attribute table contains a column labelled 'Name', the output distance matrix will use the identifiers in this column to label each pairwise comparison. Otherwise, the output distance matrix will use the attribute FID values instead.
epsg	The projected coordinate system in EPSG code format. Because of the curvature of the Earth's surface, we need to apply a map projection to accurately calculate straight-line distances between points instead of using the default WGS84 geographical coordinate system. Users should specify a projected coordinate system appropriate to the geographic region being analysed using the projection's associated EPSG code (https://epsg.org/home). Geographic coordinate system projections are not recommended as those will result in distance matrices calculated in decimal degrees rather than in distance units.
intervalfile	This is the master control file generated using either the getintervals_time() or getintervals_sealvl() functions, or custom generated by the user, that defines the number of intervals, the sea level at each interval, and the duration of each interval.
mapdir	The directory containing map outputs from the makemaps() function (i.e. the directory containing the raster_flat, raster_topo, and shapefile folders).
outdir	Output directory for the inter-island centroid-to-centroid distance matrix file. If the specified output directory doesn't already exist, PleistoDist will create the output directory.

Value

This function outputs a pairwise distance matrix of pairwise inter-island centroid-to-centroid distances in long format, with one column per interval. This function also generates a file of pairwise relative island widths, which is used for calculating the net inter-island migration ratio.

Examples

#create temp directory
path <- file.path(tempdir())
#create points shapefile
points <- sf::st_multipoint(rbind(c(179.41256,-17.79426), c(179.27600,-17.97850)))
#convert points to feature geometry
points <- sf::st_sfc(points)
points <- sf::st_cast(points, "POINT")
#set default projection (WGS84)
sf::st_crs(points) <- 4326
#save shapefile
sf::write_sf(points,paste0(path,"/points.shp"))
#load bathymetry file
fiji <- system.file("extdata","FJ.asc",package="PleistoDist")
#generate interval file for 2 intervals and 20 kya cutoff time, binning by time
getintervals_time(time=20,intervals=2,outdir=path)
#generate maps based on interval file, projecting map using EPSG:3141
makemaps(inputraster=fiji,epsg=3141,intervalfile=paste0(path,"/intervals.csv"),outdir=path)
#calculate inter-island centroid-to-centroid distances, projecting points using EPSG:3141
pleistodist_centroid(points=paste0(path,"/points.shp"),epsg=3141,
    intervalfile=paste0(path,"/intervals.csv"), mapdir=path,outdir=path)

g33k5p34k/PleistoDistR documentation built on Oct. 9, 2022, 5:27 a.m.