create.outer: create.outer function This function generates an '_.outer'...

In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics

create.outer function This function generates an '.outer' file needed by EEMS, given the '.coords' file also needed by EEMS.

Description

create.outer function

This function generates an '.outer' file needed by EEMS, given the '.coords' file also needed by EEMS.

Usage

create.outer(
  coords,
  method = 2,
  buffer.adj = 0,
  coords.radius = 0.01,
  max.fractal.dimension = 1.1,
  plot.outer = TRUE,
  ask.use = FALSE,
  counter.clockwise = TRUE,
  output.path = NULL,
  plot.output.path = NULL
)

Arguments

coords	Two column numeric matrix containing longitude and latitude of the samples in decimal degree format, or a character string with path to the input .coords file used for eems; the input file must be space separated and without a header.
method	A number (1, 2, or 3) determining how the output coordinates will be generated. If method=1 generates an alpha hull surrounding geographic regions geographic regions that intersect with input coordinates. This method tends to works best for island arichpelagos, but may be slow if input coordinates include large sampling gaps. In such cases increase the value of alpha.start. If method=2 (the default) is similar to method 1, except that the output coordinates are only determined from the input coordinates (and buffer setting), rather than from the regions of the base map (political geography from natural earth dataset) that intersect the input coordinates. Either method should be fine for EEMS, but method 1 tends to look nicer for island archipelagos. If method=3 is fast and uses the minimum convex polygon of input coodinates as a starting point.
buffer.adj	This argument is not yet implemented. A number between 0 and 1 that determines the size of the buffer region surrounding the points supplied by coords.
coords.radius	Number specifying the radius in degrees to use around input coordinates when determining spatial intersections (default 0.01). Increasing this value can be useful if coordinates are located offshore of regions outlined in the geography basemap.
max.fractal.dimension	Value between 1 and 2 contolling the shape complexity of the polygon with the output coordinates. Values near 1 have low complexity (e.g., circles, squares), and shape complexity increases as max.fractal.dimension approaches 2. The default value 1.1 seems to work well for most cases. Ignored if method=3.
plot.outer	Logical indicating if the points defining the output ".outer" table should be plotted. Default TRUE.
ask.use	Logical indicating if, after plotting, the user should be prompted to ask if the output should be saved. Default is FALSE. Ignored if output.path is NULL or if plot.outer is FALSE.
counter.clockwise	Should the output cooordinates be ordered counterclockwise. Default is TRUE and is the required format for EEMS.
output.path	Character string with path where to save coordinates. Default is NULL.
plot.output.path	Optional character string with path to save plot. Default is NULL, in which case the value is equal to appending '.pdf' to 'output.path'. Ignored if plot.outer is FALSE.

Value

A two column numerical matrix containing the longitude and latitude of the output polygon. The matrix written to output.path can be used as the ".outer" polygon used by EEMS. A map is plotted to visualize the results.

JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.