spatialEco R package with utilities to support spatial data manipulation, query, sampling and modeling. Functions include models for species population density, qudrat-based analysis and sampling, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, polygon and point-distance structural metrics, auto-logistic model, sampling models, cluster optimization and statistical exploratory tools.
In version 2.0-3
Fixed bug in aspline.downscale where, grid.search = TRUE option was producing an error
Fixed bug in sf.kde where error was returned when specifying ref argument
Fixed bug in raster.kendall where, other than the default, the method argument was not being reconized
Depreciated cgls.url due to digest files no longer reliable
Depreciated oli.aws due to AWS Registry of Open Data changing to the AWS Data Exchange
As of version 2.0-2 I completley depreciated several functions (they no longer have aliasis) and cleaned up documentation. Other changes are;
Added suggest for the lwgeom package after sf dropped as Imports dependency
Added function to derive LAI (leaf area index) from NDVI
Fixed bug in sf.kde where bandwidth was not being reconized as argument
Reverted sf.kde to use modification of MASS 2dkde as, ks methods are somewhat
questionable with spatial data.
In version 2.0-1
Fixed bug in sf.kde (thanks to Dirk Pflugmacher for pointing out rotation issue)
Added function sf_dissolve for dissolving polygon features
Added function squareBuffer for creating square buffers
Fixed bug in raster.downsample where plot returned error when scatter=TRUE with one covariate
Added function aspline.downscale for downscaling rasters using multivariate adaptive
regression splines (thanks to discussion with Felipe Benavides)
Fixed a bug in breeding.density (thanks to Eric Newkirk) where st_distance was resulting
in a units class object and crashing the function.
Feature request (Alessandro Mondanaro), added an argument/option in sf_kde for using ks or the modified MASS kde2d function that
facilitates weights. The MASS kde2d was the KDE function in the sp.kde function.
Fixed a bug in curvature (thanks to Rachel Wright) where type="mcnab" was returning source raster values
Updated knn function to use sf class objects
Fixed bug in wt.centroid when sf object is tibble (thanks to Andrew Gustar for drawing my attention to the bug)
Fixed bug in stratified.random where if there are no replicates with replace = FALSE no results returned
Enhancement added support for prewhiting of autocorrelated time-series in kendall function
I jumped to a major release and pushed the version to 2.0-0. All spatial functions are now using the sf and terra packages due to sp, rgeos, rgdal, maptools and raster being retired. Sorry but, for the most part I removed backwards compatibility with these deprecated object classes so, you will need to make sure that you are using modern spatial object classes. In terra, there is now only one class type for multi or single band raster objects "SpatRaster" which can be read or coerced using terra::rast. For coercing sp class vector objects to sf you can use sf::st_as:sf or as(x, "sf") and, going from sf to sp you use as(x, "Spatial")
spatialEco Function Description all_pairwise Creates a list of all pairwise combinations of a vector annulus.matrix Creates a 0,1 matrix based on defined annulus parameters, can be used as a window matrix in a raster focal function aspline.downscale Downscale raster to a higher resolution using multivariate adaptive regression splines (MARS) background Creates a point sample that can be used as a NULL for SDM's and other modeling approaches (see pseudo.absence for alternate approach). bbox_extent Creates a bounding box polygon representing the extent of a feature or raster bearing.distance Calculate new point based on bearing/distance breeding.density Calculates n-th percent breeding density areas base on a kernel density estimate of population counts. built.index remote sensing built-up index cgls_urls Deprecated Based on query, provide URL's for Copernicus Global Land Service datasets chae The Canine-Human Age Equivalent (for fun) class.comparison Deprecated, with migration to terra, I collapsed into raster.change classBreaks for finding class breaks in a distribution collinear Test for linear or nonlinear collinearity/correlation in data combine Combines multiple rasters into an "all possible combinations" raster emulation the ESRI combine function concordance Performs a concordance/disconcordance (C-statistic) test on binomial models. conf.interval Calculates confidence interval for the mean or median of a distribution with with unknown population variance convexHull Derives a convex hull of points using the alpha hull approach with adjustable tension. Please note that due to licensing reasons, this function is only available in the GitHub development version and not on CRAN. You must call the function from the package namespace using spatialEco:::convexHull correlogram Calculates and plots a correlogram (spatially lagged correlations, "pearson", "kendall" or "spearman") cross.tab Cross tabulate two rasters, labels outputs crossCorrelation Calculates the partial spatial cross-correlation function csi Calculates cosine similarity and angular similarity on two vectors or a matrix curvature Zevenbergen & Thorne, McNab's or Bolstad's surface (raster) curvature dahi Calculates the DAHI (Diurnal Anisotropic Heat Index) date_seq Creates date sequence, given defined start and stop dates, with options for day, week, month, quarter, year or, minute. daymet.point Downloads DAYMET climate variables for specified point and timeperiod daymet.tiles Returns a vector of DAYMET tile id's within a specified extent dispersion Calculates the dispersion ("rarity") of targets associated with planning units dissection Evans (1972) Martonne's modified dissection divergence Kullback-Leibler Divergence (Cross-entropy) download.daymet Deprecated download.hansen Deprecated download.prism Deprecated effect.size Cohen's-d effect size with pooled sd for a control and experimental group erase.points Erases points inside or outside a polygon feature class explode Deprecated due to redundancy with sf::st_cast extract.vertices extracts (x,y) vertices coordinates from polygons and linesa fuzzySum Calculates the fuzzy sum of a vector gaussian.kernel Creates a Gaussian Kernel of specified size and sigma geo.buffer Buffers data in geographic coordinate space using a temporary projection group.pdf Creates a probability density plot of y for each group of x hexagons Create hexagon polygon “fishnet” of defined size and extent. hli.pt Heat Load Index for tabular "point" data with slope and aspect hli Heat Load Index, now with support for southern hemisphere data hsp Hierarchical Slope Position hybrid.kmeans Clustering using hierarchical clustering to define cluster-centers in k-means idw.smoothing Distance weighted smoothing (IDW) of a variable in a spatial point object. The function is a smoothing interpolator at the point observation(s) level using a distance-weighted mean. impute.loess Imputes NA's or smooths data (or both) for a vector, intended mostly for time-series or serial data. insert Inserts a row or column into a data.frame insert.values Inserts new values into a vector at specified positions is.empty Method, evaluates if vector is empty is.whole Deprecated after R release of base::is.whole in 4.1.0 kendall Kendall tau trend with continuity correction for time-series kl.divergence Calculates the Kullback-Leibler divergence (relative entropy) between unweighted theoretical component distributions. Divergence is calculated as: int[f(x) (log f(x) knn returns ids, rownames and distance of nearest neighbors in two (or single) spatial objects. Optional radius distance constraint. Added optional covariates (weights) lai Calculates two versions of Leaf Area Index local.min.max Calculates the local minimums and maximums in a numeric vector, indicating inflection points in the distribution. loess.boot Bootstrap of a Local Polynomial Regression (loess) loess.ci Calculates a local polynomial regression fit with associated confidence intervals logistic.regression Performs a logistic (binomial) and autologistic (spatially lagged binomial) regression using maximum likelihood estimation or penalized maximum likelihood estimation. max_extent Returns the maximum extent of multiple spatial inputs mean_angle Returns the mean of a vector of angles. Intended for focal and zonal functions on slope or aspect moments Calculate statistical moments of a distribution including percentiles, arithmetic-geometric-harmonic means, coefficient of variation, median absolute deviation, skewness, kurtosis, mode and number of modes. morans.plot Autocorrelation plot nni Calculates the nearest neighbor index (NNI) measure of clustering or dispersal nth.vlaue Returns the Nth (smallest/largest) values in a numeric vector oli.aws Deprecated Download Landsat 8 OLI from AWS. o.ring Calculates inhomogeneous O-ring point pattern statistic (Wiegand & Maloney 2004) optimal.k Find optimal k of k-Medoid partitions using silhouette widths optimized.sample.variance Draws an optimal sample that minimizes or maximizes the sample variance outliers Identify outliers using modified Z-score overlap For comparing the similarity of two niche estimates using Warren's-I parea.sample Creates a systematic or random point sample of polygons where n is based on percent area of each polygon parse.bits Based on integer value, pulls value(s) of specified bit(s) parial.cor Partial and Semi-partial correlation plot.effect.size Plot generic for effect size plot.loess.boot Plot generic for loess boot point.in.poly Deprecated because function is redundant with sf::st_intersection polygon_extract Deprecated because of migration to terra. Required package only supports raster class polyPerimeter Calculates the perimeter length(s) for a polygon object poly.regression smoothing data in time-series and imputing missing (NA) values using polynomial regression poly_trend Derives Nth order polynomial trend with confidence intervals pp.subsample Generates random subsample based on point process intensity function of the observed data. This is a spatially informed data thinning model that can be used to reduce pseudo-replication or autocorrelation. proximity.index Proximity index for a set of polygons pseudo.absence Generates pseudo-absence samples based on the spatial intensity function of known species locations. This is akin to distance constrained but is informed by the spatial process of the observed data and is drawn from a probabilistic sample following the intensity function. quadrats Quadrat sampling or analysis, variable size and angle options random.raster creates random raster/stack of defined dimensions and statistical distributions raster.change Compares two categorical rasters with a variety of statistical options raster.deviation Local deviation from the raster based on specified global statistic or a polynomial trend. rasterDistance This replicates the raster distanceFromPoints function but uses the Arya & Mount Approximate Near Neighbor (ANN) C++ library for calculating distances. Which results in a notable increase in performance. It is not memory safe and does not use the GeographicLib (Karney, 2013) spheroid distance method for geographic data raster.downscale Downscale raster to a higher resolution raster using robust regression raster.entropy Calculates entropy on integer raster (i.e., 8 bit 0-255) raster.gaussian.smooth Applies a Gaussian smoothing kernel to smooth raster.h raster.invert Inverts value of a raster raster.kendall Calculates Kendall's tau trend with continuity correction for raster time-series raster.mds Multidimensional scaling of raster values within an N x N focal window raster.modified.ttest Bivariate moving window correlation using Dutilleul's modified t-test raster.moments Calculates focal statistical moments of a raster raster.transformation Applies specified statistical transformation to a raster raster.vol Calculates a percent volume on a raster or based on the entire raster or a systematic sample raster.Zscore Calculates the modified z-score for all cells in a raster rasterCorrelation Performs a simple moving window correlation between two rasters remove_duplicates Removes duplicate duplicate feature geometries remove.holes Removes all holes (null geometry) in polygon sf class objects rm.ext Removes file extentions from text string rotate.polygon Rotates a polygon by specified angle sa.trans Trigonometric transformation of a slope and aspect interaction sample.annulus Creates sample points based on annulus with defined inner and outer radius sample.line Deprecated because sf::st_sample can aggregate samples by feature sample.poly Deprecated because sf::st_sample can aggregate samples by feature sampleTransect Creates random transects from points, generates sample points along each transect separability Calculates variety of univariate separability metrics for nominal class samples sf_dissolve Dissolves polygon geometry using attribute, globally or overlap sg.smooth Smoothing time-series data using a Savitzky-Golay filter shannons Calculates Shannon's Diversity Index and Shannon's Evenness Index shift Shifts a vector by n lags without changing its length, can specify fill values sieve Creates a minimum mapping unit by removing pixel clusters < specified area similarity Uses row imputation to identify "k" ecological similar observations smooth.time.series Smoothing and imputing missing (NA) of pixel-level data in raster time-series using (local polynomial) LOESS regression sobal Applies an isotropic image gradient operator (Sobel-Feldman) using a 3x3 window spatial.select Performs a spatial select (feature subset) similar to ArcGIS spectral.separability Calculates class-wise multivariate spectral separability sf.kde A weighted or un-weighted kernel density estimate (previously sp.kde now as alias) sp.na.omit Deprecated as only relevant to sp class objects, for sf use base na.omit squareBuffer Creates a square buffer of feature class srr Surface Relief Ratio stratified.random Creates a stratified random sample of an sp class object using a factor. subsample.distance Minimum, and optional maximum, distance constrained sub-sampling swvi Senescence weighted MSAVI or MTVI time_to_event Returns the time (sum to position) to a specified value topo.distance Calculates topographic corrected distance for a SpatialLinesDataFrame object tpi Calculates topographic position using mean deviations within specified window trasp Solar-radiation Aspect Index trend.line Calculated specified (linear, exponential, logarithmic, polynomial) trend line of x,y and plots results. tri Implementation of the Riley et al (1999) Terrain Ruggedness Index vrm Implementation of the Sappington et al., (2007) vector ruggedness measure winsorize Removes extreme outliers using a winsorization transformation wt.centroid Creates centroid of [x,y] coordinates, of a random field, based on a weights field in a point sample. zonal.stats Deprecated in leu of exactextractr library
Bugs: Users are encouraged to report bugs here. Go to issues in the menu above, and press new issue to start a new bug report, documentation correction or feature request. You can direct questions to jeffrey_evans@tnc.org.
To install spatialEco in R use install.packages() to download current stable release from CRAN
for the development version, run the following (requires the remotes package): remotes::install_github("jeffreyevans/spatialEco")
You can also install from ROpenSci (R-Universe):
# Enable repository from jeffreyevans
options(repos = c(
jeffreyevans = 'https://jeffreyevans.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))
# Download and install spatialEco in R
install.packages('spatialEco')
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