rubak / spatialeco

R package for spatial analysis and modelling of ecological systems

spatialEco (CRAN 1.3-7, developement 1.3-8)

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 1.3-8

spatialEco Function	Description
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
	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 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 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	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)
knn	returns ids, rownames and distance of nearest neighbors in two (or single) spatial
	objects. Optional radius distance constraint. Added optional covariates (weights)
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) 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 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 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 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.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, 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 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 [email protected].

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")