This package is considered a duplicate. The official version of this package is found at:https://adeverse.r-universe.dev/adespatial

Package: adespatial 0.3-29

Aurélie Siberchicot

adespatial: Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Authors:Stéphane Dray [aut], David Bauman [ctb], Guillaume Blanchet [ctb], Daniel Borcard [ctb], Sylvie Clappe [ctb], Guillaume Guenard [ctb], Thibaut Jombart [ctb], Guillaume Larocque [ctb], Pierre Legendre [ctb], Naima Madi [ctb], Hélène H Wagner [ctb], Aurélie Siberchicot [ctb, cre], John Chambers [ctb]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
adespatial/json (API)

# Install 'adespatial' in R:

install.packages('adespatial', repos = c('https://thioulouse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeverse/adespatial/issues

Pkgdown/docs site:https://adeverse.github.io

Uses libs:

openblas– Optimized BLAS

Datasets:

bacProdxy - Bacterial production data set
mastigouche - Mastigouche Lake network data set
ScotchWhiskey - Scotch Whiskey Data Set
Tiahura - Tiahura Transect Fish Data Set
trichoptera - Trichoptera data set

On CRAN:

openblas

11.05 score 42 stars 2 packages 756 scripts 7.4k downloads 36 mentions 50 exports 107 dependencies

Last updated from:309fa87017. Checks:13 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	274
linux-devel-x86_64	OK	312
source / vignettes	OK	343
linux-release-arm64	OK	280
linux-release-x86_64	OK	300
macos-release-arm64	OK	167
macos-release-x86_64	OK	379
macos-oldrel-arm64	OK	193
macos-oldrel-x86_64	OK	391
windows-devel	OK	275
windows-release	OK	240
windows-oldrel	OK	202
wasm-release	OK	240

Exports:aem aem.build.binary aem.time aem.weight.edges aem.weight.time beta.div beta.div.comp chooseCN constr.hclust Cperiodogram create.dbMEM.model dbmem directional.response dist.ldc envspace.test forward.sel forward.sel.par geoDist geoXY give.thresh global.rtest LCBD.comp listw.candidates listw.explore listw.select local.rtest mem mem.select mfpa moran.bounds moran.randtest moranNP.randtest mspa msr mst.nb multispati ortho.AIC orthobasis.listw orthobasis.poly quicksti rotation scalogram scores.listw stimodels TBI test.W tpaired.krandtest tpaired.randtest variogmultiv WRperiodogram

Dependencies:ade4 adegenet adegraphics adephylo ape askpass base64enc boot bslib cachem class classInt cli cluster commonmark cpp11 crayon curl DBI deldir digest dplyr e1071 farver fastmap fontawesome fs generics ggplot2 glue gtable hms htmltools httpuv httr igraph interp isoband jpeg jquerylib jsonlite KernSmooth labeling later lattice latticeExtra lifecycle magrittr MASS Matrix memoise mgcv mime nlme openssl otel permute phylobase pillar pixmap pkgconfig plyr png prettyunits progress promises proxy purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang rncl RNeXML s2 S7 sass scales segmented seqinr sf shiny sourcetools sp spData spdep stringi stringr sys tibble tidyr tidyselect units utf8 uuid vctrs vegan viridisLite withr wk XML xml2 xtable

Moran's Eigenvector Maps and related methods for the spatial multiscale analysis of ecological data

Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2023-10-04
Started: 2016-12-05

Help page	Topics
Construct asymmetric eigenvector maps (AEM)	aem
Construct a site-by-edge binary matrix	aem.build.binary
AEM for time series	aem.time
Weight edges when constructing AEM variables	aem.weight.edges aem.weight.time
Bacterial production data set	bacProdxy
Beta diversity computed as Var(Y)	beta.div
Decompose D in replacement and richness difference components	beta.div.comp
Function to choose a connection network	chooseCN
Space- And Time-Constrained Clustering	constr.hclust
Class For Constrained Hiereachical Clustering	constr.hclust-class
Contingency periodogram	Cperiodogram
Combine dbMEM matrices corresponding to groups of sites	create.dbMEM.model
dbMEM spatial eigenfunctions	dbmem
Directional indices of community change	directional.response
Dissimilarity matrices for community composition data	dist.ldc
Perform a test of the shared space-environment fraction of a variation partitioning using torus-translation (TT) or Moran Spectral Randomisation (MSR)	envspace.test
Forward selection with multivariate Y using permutation under reducel model	forward.sel
Parametric forward selection of explanatory variables in regression and RDA	forward.sel.par
Geodetic Distances from Latitude and Longitude	geoDist
Geodetic Coordinates from Latitude and Longitude	geoXY
Compute the maximum distance of the minimum spanning tree based on a distance matrix	give.thresh
Global and local tests	global.rtest local.rtest
Compute LCBD from any D matrix	LCBD.comp
Function to create a list of spatial weighting matrices	listw.candidates
Interactive tool to generate R code that creates a spatial weighting matrix	listw.explore
Function to optimize the selection of a spatial weighting matrix and select the best subset of eigenvectors (MEM, Moran's Eigenvector Maps)	listw.select
Mastigouche Lake network data set	mastigouche
Selection of the best subset of spatial eigenvectors (MEM, Moran's Eigenvector Maps)	mem.select
Multi-frequential periodogram analysis	mfpa plot.mfpa print.mfpa
Function to compute extreme values of Moran's I	moran.bounds
Function to compute Moran's index of spatial autocorrelation	moran.randtest
Function to compute positive and negative parts of Moran's index of spatial autocorrelation	moranNP.randtest
Multi-Scale Pattern Analysis	mspa print.mspa scatter.mspa
Moran spectral randomization	msr msr.default
Moran spectral randomization for fourth-corner analysis	msr.4thcorner
Moran spectral randomization for Mantel test	msr.mantelrtest
Moran spectral randomization for variation partitioning	msr.varipart
Function to compute neighborhood based on the minimum spanning tree	mst.nb
Multivariate spatial analysis	multispati plot.multispati print.multispati summary.multispati
Compute AIC for models with orthonormal explanatory variables	ortho.AIC
Function to compute polynomial of geographical coordinates	orthobasis.poly
Plotting Method For Space- And Time-Constrained Clustering	plot.constr.hclust
Function to display Moran's Eigenvector Maps (MEM) and other spatial orthogonal bases	plot.orthobasisSp
Plots of the outputs of a temporal beta diversity analysis	plot.TBI
Rotate a set of point by a certain angle	rotation
Function to compute a scalogram	plot.scalogram scalogram
Function to compute and manage Moran's Eigenvector Maps (MEM) of a listw object	mem orthobasis.listw scores.listw [.orthobasisSp
Scotch Whiskey Data Set	ScotchWhiskey
Space-time interaction in ANOVA without replication	quicksti stimodels
TBI: Difference between multivariate observations at T1 and T2	TBI
Function to compute and test eigenvectors of spatial weighting matrices	test.W
Tiahura Transect Fish Data Set	Tiahura
Paired t-tests of differences between T1 and T2 for each species	tpaired.krandtest
Permutational paired t-test	tpaired.randtest
Trichoptera data set	trichoptera
Function to compute multivariate empirical variogram	variogmultiv
Whittaker-Robinson periodogram	plot.WRperio WRperiodogram

Package: adespatial 0.3-29

adespatial: Multivariate Multiscale Spatial Analysis

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