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R package for spatial analysis and modelling of ecological systems

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spatialEco (dev 2.0-3)

R-CMD-check CRAN status CRAN RStudio mirror downloads

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.

News

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 depreciated 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")

Available functions in development version of spatialEco 2.0-2

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 Depreciated Based on query, provide URL's for Copernicus Global Land Service datasets
chae The Canine-Human Age Equivalent (for fun)
class.comparison Depreciated, 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 Depreciated
download.hansen Depreciated
download.prism Depreciated
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 Depreciated 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 Depreciated 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 Depreciated 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 Depreciated because function is redundant with sf::st_intersection
polygon_extract Depreciated 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 Depreciated because sf::st_sample can aggregate samples by feature
sample.poly Depreciated 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 Depreciated 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 Depreciated 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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