Package 'ecotrends'

output of getModels().

integer value (default 10; increase for more accurate but computationally intensive results) indicating the number of permutations for shuffling each variable.

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

logical value specifying whether to produce a line (spaghetti) plot of the mean importance of each variable along the periods. Note that this plot does not reflect the deviations around this mean, and that it may become hard to read if there are many variables or if their importances overlap.

argument to pass to hcl.colors() specifying the colours for the lines (if plot=TRUE). The default is "Dark2"; run hcl.pals() for other options.

additional arguments that can be passed to base::plot(), e.g. 'main', 'xlab', 'ylab' or 'las'.

species occurrence 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 or SpatVector of points), and in the same coordinate reference system as 'rasts'

(multi-layer) SpatRaster with a time series of variables to use in the models. The layers should be ordered chronologically, and their names should be in the form "varname [underscore] time", e.g. "tmin_1985" or "tmin_1" (with no more underscores than this), as in the output of getVariables(). Note that, if a variable has no spatial variation in a given time step or period, it is excluded (as it cannot have an effect) from that model, so in practice not all models will include the exact same set of variables. If verbosity > 1, messages will report which variables were excluded from each period.

optional SpatExtent or SpatVector polygon delimiting the region of 'rasts' within which to compute the models. The default is NULL, to use the entire extent of 'rasts' with pixel values. Note that 'region' should ideally include only reasonably surveyed areas that are accessible to the species, as pixels that don't overlap presence points are taken by Maxent as available and unoccupied.

integer value indicating the maximum number of background pixels to select randomly for use in the models. The default is 10,000, or the total number of non-NA pixels in 'rasts' if that's less.

optional integer value to pass to set.seed() specifying the random seed to use for sampling the background pixels (if 'nbg' is smaller than the number of pixels in 'rasts') and for extracting the test samples (if nreps > 0).

argument to pass to fuzzySim::selectAbsences() specifying if/how the selection of unoccupied background points should be biased to incorporate survey effort. Can be TRUE to make selection more likely towards the vicinity of occurrence points (which may indicate that those areas have been surveyed); or a SpatRaster of weights (bias layer), with the same coordinate reference system as 'occs' and 'rasts', with higher values where selection should be proportionally more likely, and zero or NA where points should not be placed. Default FALSE.

logical value indicating whether multicollinearity among the variables should be reduced prior to computing each model. The default is TRUE, in which case the collinear::collinear() function is used. Note that, if the collinearity structure varies among periods, the set of included variables may also vary. If verbosity > 1, messages will report which variables were excluded from each period.

numeric value to pass to collinear::collinear() (if collin = TRUE) indicating the maximum correlation allowed between any pair of predictor variables. The default is 0.75.

numeric value to pass to collinear::collinear() (if collin = TRUE) indicating the maximum VIF allowed for selected predictor variables. The default is 5.

character value to pass to maxnet::maxnet.formula() indicating the continuous feature classes desired. Can be "default" or any subset of "lqpht" (linear, quadratic, product, hinge, threshold) – for example, "lqh" for just linear, quadratic and hinge features. See References for guidance.

numeric value to pass to maxnet::maxnet() indicating the constant to adjust regularization. The default is 1. See References for guidance.

integer value indicating the number of train-test datasets for testing the models. The default is 10. With nreps = 0, there is no division of the dataset into train and test samples, so models are trained on the entire dataset for each period. If nreps > 0, presences are randomly assigned to the train and test sample in each replicate (in the proportion defined by the 'test' argument), while the background remains the same.

(if nreps > 0) numeric value indicating the proportion of presences to set aside for testing each model. The default is 0.2, i.e. 20%.

optional file name (including path, not including extension) if you want the output list of model objects to be saved on disk. If 'file' already exists in the working directory (meaning that models were already computed), models are imported from there.

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

SpatRasterDataset output of getPredictions(), or 'file' argument previously provided to getPredictions()

output of getModels()

character vector with the metrics to compute. Can be any subset of c("AUC", "TSS"), the latter computed at its optimal threshold. The default is both. Performance metrics are computed with presence against all background (using 'modEvA' package functions with pbg=TRUE), so they evaluate the capacity of distinguishing presence from random, rather than presence from absence pixels (Phillips et al., 2006).

logical value indicating whether plots should also be produced to illustrate the performance metrics for each model. The default is FALSE; TRUE can be slow for large datasets.

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

(multi-layer) SpatRaster containing the variables (with the same names) used in the models.

output of getModels().

optional SpatExtent or SpatVector polygon delimiting the region of 'rasts' within which to compute the predictions. The default is NULL, to use the entire extent of 'rasts'. Note that predictions may be unreliable outside the 'region' used for getModels(), as they are extrapolating beyond the analysed conditions.

character value to pass to predict() indicating the type of response to compute. Can be "cloglog" (the default and currently recommended), "logistic" (previously but no longer recommended) (Phillips et al., 2017), "exponential", or "link".

logical value to pass to predict() indicating whether predictors and features should be restricted to the range seen during model training. Default TRUE.

optional folder name (including path within the working directory) if you want the prediction rasters to be saved to disk. If 'file' already exists in the working directory (meaning that predictions were already computed), predictions are imported from there.

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

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.

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

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.

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

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

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.

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

source to import the raster variables from, e.g. "TerraClimate" (currently the only one implemented)

character vector of the names of the variables to be imported. Run varsAvailable() for options. The default is to download all available variables from the specified 'source'. Note that the download can take a long time, especially for many variables, long series of years, and/or large regions.

year range to get the variables from (e.g. 1979:2013). Note that the download can take a long time for long series of years.

optional length-four numeric vector (xmin, xmax, ymin, ymax geodetic coordinates in degrees), SpatExtent or SpatVector polygon delimiting the region of the world for which the variables should be downloaded. See ?getRegion for suggestions. The larger the region, the longer the download time.

optional file name (including the path, not including the filename extension) if you want the downloaded variable rasters to be saved on disk, in which case they are saved as a compressed multi-layer GeoTIFF. If 'file' already exists in the working directory, variables are imported from there.

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

SpatRaster for which to compute the pixel area

character value indicating whether the output value should be the "mean" (default) or "centroid" pixel area

numeric value indicating the units for the output value: either "m" (default) or "km" squared.

logical value (default TRUE) indicating whether to consider only the areas of non-NA pixels

logical value (default TRUE) indicating whether to also plot a map

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

the source database where to check available variables. By default (i.e. if left NULL), all implemented sources are used. Currently "TerraClimate" (https://www.climatologylab.org/terraclimate.html) is the only implemented source.