getTrend {ecotrends}R Documentation

Get trend

Description

This function uses terra::app() to apply the trend::sens.slope() function to each pixel of a multi-layer time series SpatRaster, testing for a monotonic (either increasing or decreasing) linear trend in the raster values, as well as the confidence interval of the slope.

Usage

getTrend(
  rasts,
  occs = NULL,
  alpha = 0.05,
  conf.level = 0.95,
  file = NULL,
  full = TRUE,
  verbosity = 2
)

Arguments

rasts

multi-layer SpatRaster with the output of getPredictions(), or another time series of values for which to detect a trend. Note that >3 non-NA values (i.e. more than 3 time steps) are required for a trend to be computed. If there are >1 replicates per year, their pixel-wise mean is computed prior to analysing the trend.

occs

SpatVector of species occurrence points, or their spatial coordinates (2 columns in this order: x, y or LONGitude, LATitude) in an object coercible to a data.frame (e.g. a data.frame, matrix, tibble, sf object), and in the same coordinate reference system as 'rasts'. If provided, output pixels that do not overlap these points will be NA

alpha

numeric value indicating the threshold significance level for Sen's slope. Default 0.05. Pixels with p-value above this will have NA value in the output.

conf.level

numeric value to pass to trend::sens.slope() indicating the confidence level for the slope of the trend. Default 0.95.

file

optional file name (including path, not including extension) if you want the outputs raster(s) to be imported from or saved to disk.

full

logical value indicating whether to output a multi-layer raster with the full results of the Mann-Kendall test (namely the Tau value, p-value, S, and variance of S) and the results of Sen's slope calculation (slope estimate, p-value, upper and lower confidence limit). If set to FALSE, a single-layer raster will be returned with the (significant) Sen's slope values.

verbosity

integer value indicating the amount of messages to display. The default is 2, for the maximum number of messages available.

Value

If full=FALSE, a single-layer SpatRaster where each pixel (or each pixel with occurrence points, if 'occs' is not NULL) has the value of Sen's slope (positive if increasing, negative if decreasing), or NA if the trend is non-significant (i.e., if the p-value is larger than the specified 'alpha'). If full=TRUE (the default), additional layers are produced with associated statistics, including the lower and upper bounds of Sen's slope (given the input 'conf.level').

Author(s)

A. Marcia Barbosa

See Also

trend::sens.slope(), trend::mk.test(), Kendall::MannKendall(), spatialEco::raster.kendall()

Examples

# Several data prep steps required.
# See https://github.com/AMBarbosa/ecotrends for a full worked example.

[Package ecotrends version 1.0 Index]