spatialEco R package with utilities to support spatial data manipulation, query, sampling and modeling. Functions include models for species population density, download utilities for climate and global deforestation spatial products, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, polygon and point-distance landscape metrics, auto-logistic model, sampling models, cluster optimization and statistical exploratory tools.
Available functions in spatialEco 1.3-7 are:
annulus.matrix - Creates a 0,1 matrix based on defined annulus parameters, can be used as a window
matrix in a raster focal function
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).
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 - Based on query, provide URL's for Copernicus Global Land Service datasets
chae - The Canine-Human Age Equivalent (for fun)
classBreaks - for finding class breaks in a distribution
class.comparison - Compares two nominal rasters
colinear - Test for linear or nonlinear collinearity/correlation in data
correlogram - Calculates and plots a correlogram (spatially lagged correlations, "pearson",
"kendall" or "spearman")
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 unknown
population variance
combine - Combines multiple rasters into an "all possible combinations" raster
emulation the ESRI combine function, ratifies the output and includes
a summary table of combinations and attributes that relates back to
the raster values
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
crossCorrelation - Calculates the partial spatial cross-correlation function
cross.tab - Cross tabulate two rasters, labels outputs
csi - Calculates the 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 - Batch download of daily gridded DAYMET climate data
download.hansen - Download of Hansen Global Forest Change 2000-2013
download.prism - Batch download of monthly gridded PRISM climate data
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 - Explodes multi-part to single-part feature geometry
extract.vertices - extracts (x,y) vertices coordinates from polygons and lines
focal.lmetrics (depreciated, moved to landmetrics package) - Landscape metrics using a focal window
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 - 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 - Method, evaluates if numeric vector is whole or float
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) - log g(x)) dx]
for distributions with densities f() and g().
knn - returns ids, rownames and distance of nearest neighbors in two (or single) spatial objects.
Optional radius distance constraint. Added optional covariates (weights).
land.metrics (depreciated, moved to landmetrics package) - Calculates a variety of landscape metrics, on binary rasters, for polygons or points with a buffer
distance. This is similar to the moving window in Fragstats but, uses either a buffer for each
point or a zonal approach with polygons, to derive local metrics.
libraries - Checks package(s) install, optionally installs and adds to namespace environment
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
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) as a measure of clustering or dispersal
nth.vlaue - Returns the Nth (smallest/largest) values in a numeric vector
oli.aws - Download Landsat 8 - OLI from AWS.
o.ring - Calculates the 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 - Intersects point and polygon feature classes and adds polygon attributes to the points
polygon_extract - Fast method for extracting raster values to polygons
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
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 rasters or stacks 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. Where this
results in a notable increase in performance it is not memory safe, needing to read
in the entire raster 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.
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.holes - Removes all holes (null geometry) in polygon sp class objects
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 - Creates a systematic or random point sample of an sp SpatialLinesDataFrame object based on
distance spacing, fixed size or proportional size
sample.poly - Creates an equal sample of n for each polygon in an sp Polygon class object
sampleTransect - Creates random transects from points and generates sample points along each transect
separability - Calculates variety of univariate separability metrics for nominal class samples
spectral.separability - Calculates univariate or multivariate separability for nominal class samples
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
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
sp.kde - A weighted or un-weighted kernel density estimate
sp.na.omit - Removes row or column NA's in sp object. The standard R na.omit function will not propagate through
all slots of an sp class object. This function removes the spatial objects, in all slots, corresponding
to NA's in the @data data.frame object.
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 - Polygon "zonal" statistics of a raster. Function can accept custom “vectorized” function. 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
or, for the development version, run the following (requires the remotes package): remotes::install_github("jeffreyevans/spatialEco")
