location_series: Extract a time series of bioclimatic variables for one or...

In EvolEcolGroup/pastclim: Manipulate Time Series of Palaeoclimate Reconstructions

Extract a time series of bioclimatic variables for one or more locations.

Description

This function extract a time series of local climate for a set of locations. Note that this function does not apply any interpolation (as opposed to location_slice()). If you have a coastal location that just falls into the water for the reconstructions, you will have to amend the coordinates to put it more firmly on land.

Usage

location_series(
  x,
  time_bp = NULL,
  time_ce = NULL,
  coords = NULL,
  bio_variables,
  dataset,
  path_to_nc = NULL,
  nn_interpol = FALSE,
  buffer = FALSE,
  directions = 8
)

Arguments

x	a data.frame with columns of x and y coordinates (and an optional name column), or a vector of cell numbers. See coords for standard coordinate names, or how to use custom ones.
time_bp	time slices in years before present (negative values represent time before present, positive values time in the future). This parameter can be a vector of times (the slices need to exist in the dataset), a list with a min and max element setting the range of values, or left to NULL to retrieve all time steps. To check which slices are available, you can use get_time_bp_steps().
time_ce	time slice in years CE (see time_bp for options). For available time slices in years CE, use get_time_ce_steps(). Only one of time_bp or time_ce should be used.
coords	a vector of length two giving the names of the "x" and "y" coordinates, as found in data. If left to NULL, the function will try to guess the columns based on standard names c("x", "y"), c("X","Y"), c("longitude", "latitude"), or c("lon", "lat")
bio_variables	vector of names of variables to be extracted.
dataset	string defining the dataset to use. If set to "custom", then a single nc file is used from "path_to_nc"
path_to_nc	the path to the custom nc file containing the palaeoclimate reconstructions. All the variables of interest need to be included in this file.
nn_interpol	boolean determining whether nearest neighbour interpolation is used to estimate climate for cells that lack such information (i.e. they are under water or ice). By default, interpolation is only performed from the first ring of nearest neighbours; if climate is not available, NA will be returned for that location. The number of neighbours can be changed with the argument directions. nn_interpol defaults to FALSE (this is DIFFERENT from location_slice().
buffer	boolean determining whether the variable will be returned as the mean of a buffer around the focal cell. If set to TRUE, it overrides nn_interpol (which provides the same estimates as buffer but only for locations that are in cells with an NA). The buffer size is determined by the argument directions. buffer defaults to FALSE.
directions	character or matrix to indicate the directions in which cells are considered connected when using nn_interpol or buffer. The following character values are allowed: "rook" or "4" for the horizontal and vertical neighbours; "bishop" to get the diagonal neighbours; "queen" or "8" to get the vertical, horizontal and diagonal neighbours; or "16" for knight and one-cell queen move neighbours. If directions is a matrix it should have odd dimensions and have logical (or 0, 1) values.

Value

a data.frame with the climatic variables of interest

EvolEcolGroup/pastclim documentation built on Nov. 8, 2024, 5:21 a.m.