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.
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")