Package: spEDM 1.13

Wenbo Lyu

spEDM: Spatial Empirical Dynamic Modeling

Inferring causation from spatial cross-sectional data through empirical dynamic modeling (EDM), with methodological extensions including geographical convergent cross mapping from Gao et al. (2023) <doi:10.1038/s41467-023-41619-6>, geographical cross mapping cardinality as introduced by Lyu et al. (2026) <doi:10.1080/13658816.2026.2687121>, as well as the spatial causality test following the approach of Herrera et al. (2016) <doi:10.1111/pirs.12144>, together with geographical pattern causality proposed in Zhang & Wang (2025) <doi:10.1080/13658816.2025.2581207>.

Authors:Wenbo Lyu [aut, cre, cph]

spEDM_1.13.tar.gz
spEDM_1.13.zip(r-4.7)spEDM_1.13.zip(r-4.6)spEDM_1.13.zip(r-4.5)
spEDM_1.13.tgz(r-4.6-x86_64)spEDM_1.13.tgz(r-4.6-arm64)spEDM_1.13.tgz(r-4.5-arm64)spEDM_1.13.tgz(r-4.5-x86_64)
spEDM_1.13.tar.gz(r-4.7-arm64)spEDM_1.13.tar.gz(r-4.7-x86_64)spEDM_1.13.tar.gz(r-4.6-arm64)spEDM_1.13.tar.gz(r-4.6-x86_64)
spEDM_1.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spEDM/json (API)

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

Bug tracker:https://github.com/stscl/spedm/issues

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

causal-analysiscausal-discoverycausal-inferencecausal-influencecausal-interactionscausal-networkscppempirical-dynamic-modelinggeoinformaticsgeospatial-causalityspatial-analysisspatial-data-analysisspatial-data-sciencespatial-statisticsopenblascppopenmp

8.60 score 71 stars 38 scripts 743 downloads 14 exports 51 dependencies

Last updated from:3334805fdd. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK333
linux-devel-x86_64OK325
source / vignettesOK511
linux-release-arm64OK332
linux-release-x86_64OK357
macos-release-arm64OK226
macos-release-x86_64OK350
macos-oldrel-arm64OK161
macos-oldrel-x86_64FAIL265
windows-develOK290
windows-releaseOK289
windows-oldrelOK286
wasm-releaseOK349

Exports:detectThreadsembeddedfnngccmgcmcgpcicmultiviewpcsc.testscpcmsimplexslmsmap

Dependencies:bootclassclassIntclicpp11DBIdeldirdigestdplyre1071farvergenericsgeosphereggplot2gluegtableisobandKernSmoothlabelinglatticelifecyclemagrittrMASSpanderpillarpkgconfigproxypurrrR6RColorBrewerRcppRcppArmadilloRcppThreadrlangs2S7scalessdsfunsfspspDataspdepterratibbletidyselectunitsutf8vctrsviridisLitewithrwk

Introduction to the spEDM package
Overview | Installation | Data | Columbus OH spatial analysis dataset | County-level population density in mainland China | Farmland NPP and related variables in mainland China | Usage | References
Rendered frommain1_pkgintro.Rmdusingknitr::rmarkdown

Last update: 2026-06-16
Started: 2025-12-01

Geographical Cross Mapping Cardinality
Methodological Background | Usage examples | Example of spatial vector data | Example of spatial raster data
Rendered frommain5_gcmc.Rmdusingknitr::rmarkdown

Last update: 2026-06-14
Started: 2025-12-01

State Space Reconstruction
Methodological Background | Usage examples | Example of spatial vector data | Example of spatial raster data
Rendered frommain2_ssr.Rmdusingknitr::rmarkdown

Last update: 2026-04-05
Started: 2025-12-01

Spatial Logistic Map
Methodological Background | Usage examples
Rendered fromsi1_slm.Rmdusingknitr::rmarkdown

Last update: 2026-04-05
Started: 2025-12-01

Spatial Causality Test
Methodological Background | Usage examples | Example of spatial vector data | Example of spatial raster data
Rendered fromsi2_sct.Rmdusingknitr::rmarkdown

Last update: 2026-04-05
Started: 2025-12-01

Geographical Convergent Cross Mapping
Methodological Background | Usage examples | Example of spatial vector data | Example of spatial raster data
Rendered frommain3_gccm.Rmdusingknitr::rmarkdown

Last update: 2026-04-04
Started: 2025-12-01

Geographical Pattern Causality
Methodological Background | Usage examples | Example of spatial vector data | Example of spatial raster data
Rendered frommain4_gpc.Rmdusingknitr::rmarkdown

Last update: 2026-04-04
Started: 2025-12-01

Spatially Convergent Partial Cross Mapping
Model principles | Usage examples | Example of spatial vector data | Example of spatial raster data
Rendered frommain6_scpcm.Rmdusingknitr::rmarkdown

Last update: 2026-04-04
Started: 2026-01-23

Readme and manuals

Help Manual

Help pageTopics
detect the number of available threadsdetectThreads
embedding spatial cross sectional dataembedded embedded,sf-method embedded,SpatRaster-method
false nearest neighboursfnn fnn,sf-method fnn,SpatRaster-method
geographical convergent cross mappinggccm gccm,sf-method gccm,SpatRaster-method
geographical cross mapping cardinalitygcmc gcmc,sf-method gcmc,SpatRaster-method
geographical pattern causalitygpc gpc,sf-method gpc,SpatRaster-method
optimal parameter search for intersectional cardinalityic ic,sf-method ic,SpatRaster-method
multiview embedding forecastmultiview multiview,sf-method multiview,SpatRaster-method
optimal parameter search for pattern causalitypc pc,sf-method pc,SpatRaster-method
spatial causality testsc.test sc.test,sf-method sc.test,SpatRaster-method
spatially convergent partial cross mappingscpcm scpcm,sf-method scpcm,SpatRaster-method
optimal parameter search for simplex projectionsimplex simplex,sf-method simplex,SpatRaster-method
spatial logistic mapslm slm,sf-method slm,SpatRaster-method
optimal parameter search for s-mappingsmap smap,sf-method smap,SpatRaster-method