Package: adespatial 0.3-24

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]

adespatial_0.3-24.tar.gz
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adespatial.pdf |adespatial.html✨
adespatial/json (API)

# Install 'adespatial' in R:
install.packages('adespatial', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • openblas– Optimized BLAS
Datasets:

6.33 score 2 stars 2 packages 380 scripts 4.7k downloads 36 mentions 48 exports 108 dependencies

Last updated 3 months agofrom:5c840c6a05. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-linux-x86_64OKNov 07 2024

Exports:aemaem.build.binaryaem.timeaem.weight.edgesaem.weight.timebeta.divbeta.div.compchooseCNconstr.hclustCperiodogramcreate.dbMEM.modeldbmemdirectional.responsedist.ldcenvspace.testforward.selforward.sel.pargive.threshglobal.rtestLCBD.complistw.candidateslistw.explorelistw.selectlocal.rtestmemmem.selectmfpamoran.boundsmoran.randtestmoranNP.randtestmspamsrmst.nbmultispatiortho.AICorthobasis.listworthobasis.polyquickstirotationscalogramscores.listwstimodelsTBItest.Wtpaired.krandtesttpaired.randtestvariogmultivWRperiodogram

Dependencies:ade4adegenetadegraphicsadephyloapeaskpassbase64encbootbslibcachemclassclassIntcliclustercolorspacecommonmarkcpp11crayoncurlDBIdeldirdigestdplyre1071fansifarverfastmapfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvhttrigraphinterpisobandjpegjquerylibjsonliteKernSmoothlabelinglaterlatticelatticeExtralifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpermutephylobasepillarpixmappkgconfigplyrpngprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrnclRNeXMLs2sassscalessegmentedseqinrsfshinysourcetoolsspspDataspdepstringistringrsystibbletidyrtidyselectunitsutf8uuidvctrsveganviridisLitewithrwkXMLxml2xtable

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

Stéphane Dray

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2023-10-12
Started: 2016-12-13

Readme and manuals

Help Manual

Help pageTopics
Construct asymmetric eigenvector maps (AEM)aem
Construct a site-by-edge binary matrixaem.build.binary
AEM for time seriesaem.time
Weight edges when constructing AEM variablesaem.weight.edges aem.weight.time
Bacterial production data setbacProdxy
Beta diversity computed as Var(Y)beta.div
Decompose D in replacement and richness difference componentsbeta.div.comp
Function to choose a connection networkchooseCN
Space- And Time-Constrained Clusteringconstr.hclust
Class For Constrained Hiereachical Clusteringconstr.hclust-class
Contingency periodogramCperiodogram
Combine dbMEM matrices corresponding to groups of sitescreate.dbMEM.model
dbMEM spatial eigenfunctionsdbmem
Directional indices of community changedirectional.response
Dissimilarity matrices for community composition datadist.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 modelforward.sel
Parametric forward selection of explanatory variables in regression and RDAforward.sel.par
Compute the maximum distance of the minimum spanning tree based on a distance matrixgive.thresh
Global and local testsglobal.rtest local.rtest
Compute LCBD from any D matrixLCBD.comp
Function to create a list of spatial weighting matriceslistw.candidates
Interactive tool to generate R code that creates a spatial weighting matrixlistw.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 setmastigouche
Selection of the best subset of spatial eigenvectors (MEM, Moran's Eigenvector Maps)mem.select
Multi-frequential periodogram analysismfpa plot.mfpa print.mfpa
Function to compute extreme values of Moran's Imoran.bounds
Function to compute Moran's index of spatial autocorrelationmoran.randtest
Function to compute positive and negative parts of Moran's index of spatial autocorrelationmoranNP.randtest
Multi-Scale Pattern Analysismspa print.mspa scatter.mspa
Moran spectral randomizationmsr msr.default
Moran spectral randomization for fourth-corner analysismsr.4thcorner
Moran spectral randomization for Mantel testmsr.mantelrtest
Moran spectral randomization for variation partitioningmsr.varipart
Function to compute neighborhood based on the minimum spanning treemst.nb
Multivariate spatial analysismultispati plot.multispati print.multispati summary.multispati
Compute AIC for models with orthonormal explanatory variablesortho.AIC
Function to compute polynomial of geographical coordinatesorthobasis.poly
Plotting Method For Space- And Time-Constrained Clusteringplot.constr.hclust
Function to display Moran's Eigenvector Maps (MEM) and other spatial orthogonal basesplot.orthobasisSp
Plots of the outputs of a temporal beta diversity analysisplot.TBI
Rotate a set of point by a certain anglerotation
Function to compute a scalogramplot.scalogram scalogram
Function to compute and manage Moran's Eigenvector Maps (MEM) of a listw objectmem orthobasis.listw scores.listw [.orthobasisSp
Scotch Whiskey Data SetScotchWhiskey
Space-time interaction in ANOVA without replicationquicksti stimodels
TBI: Difference between multivariate observations at T1 and T2TBI
Function to compute and test eigenvectors of spatial weighting matricestest.W
Tiahura Transect Fish Data SetTiahura
Paired t-tests of differences between T1 and T2 for each speciestpaired.krandtest
Permutational paired t-testtpaired.randtest
Trichoptera data settrichoptera
Function to compute multivariate empirical variogramvariogmultiv
Whittaker-Robinson periodogramplot.WRperio WRperiodogram