spatialEco (dev 2.0-3)

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 [email protected].

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')