costCalcMaster: This function takes a datafile of ocean currents, and uses it...

In rossholmberg/pkgButterfly: Functions to calculate relevant local oceanographic variables based on Afan et. al

Description

The process used is as per Af<c3><a1>n et al 2015

Usage

costCalcMaster(currents.file, lat.variableName = NA, lon.variableName = NA,
  depth.variableName = NA, time.variableName = NA,
  current.variableNames = NA, depth.touse = NULL, depth.dimension = NULL,
  dates.range = NA, buffer.days = 10L, output.folder, POI,
  foraging.distance, cell.size = 0.1, split.quant = 0.75,
  circuitscape.link = ifelse(Sys.info()["sysname"] == "Windows",
  "C:/\"Program Files\"/Circuitscape/cs_run.exe", "python2.7"), parallel)

Arguments

currents.file	complete link to .nc data file containing ocean currents data
lat.variableName	character name of latitude variable in .nc currents.file. Default "lat"
lon.variableName	character name of longitude variable in .nc currents.file. Default "lon"
depth.variableName	character name of depth variable in .nc currents.file. Default "depth"
time.variableName	character name of time variable in .nc currents.file. Default "time"
current.variableNames	character vector (length 2), names of current variables in .nc currents.file. Element 1 is for the zonal current values, element 2 is for the meridional current values. Default c( "ZonalCurrent", "MeridionalCurrent" )
depth.touse	numerical depth value. Which available depth dataset (if more than one) is to be analysed here?
depth.dimension	integer value specifying which dimension of the currents arrays in the .nc file represents "depth". This will be used to subset only the depth to be analysed here. depth.dimension is treated in the same way as a MARGIN value, for example a value of 3 represents x[,,i].
dates.range	range of dates to subset from input data. If NA, all dates in input file are used.
buffer.days	buffer around requested date to search for data
output.folder	complete link to a folder to use for temporary files during processing. A temporary folder will be created within this specified folder, and deleted when computation has completed.
POI	c( [longitude], [latitude] ) marking the central point (eg: colony)
foraging.distance	A distance in km to consider as the area of interest from the POI.
cell.size	Resolution (in degrees) to create for output. Note data will be interpolated from input.
split.quant	The point at which to split for areas of influence (0.75 takes the TOP 25% influence), as per Af<c3><a1>n et al 2015
circuitscape.link	complete link to executable file to be used for running Circuitscape. Under Windows, this can be a '.exe' file for Circuitscape itself. Under *nix systems, this can be a link to python, under which Circuitscape will be called.
parallel	FALSE will not use multi-threading, TRUE will guess at an optimal number of cores based on processor, integer value specifies a number of cores to use when multi-threading tasks.

rossholmberg/pkgButterfly documentation built on May 27, 2019, 11:36 p.m.