Package: HDSpatialScan 1.0.4

Camille FREVENT

HDSpatialScan: Multivariate and Functional Spatial Scan Statistics

Allows to detect spatial clusters of abnormal values on multivariate or functional data. Martin KULLDORFF and Lan HUANG and Kevin KONTY (2009) <doi:10.1186/1476-072X-8-58>, Inkyung JUNG and Ho Jin CHO (2015) <doi:10.1186/s12942-015-0024-6>, Lionel CUCALA and Michael GENIN and Caroline LANIER and Florent OCCELLI (2017) <doi:10.1016/j.spasta.2017.06.001>, Lionel CUCALA and Michael GENIN and Florent OCCELLI and Julien SOULA (2019) <doi:10.1016/j.spasta.2018.10.002>, Camille FREVENT and Mohamed-Salem AHMED and Matthieu MARBAC and Michael GENIN (2021) <doi:10.1016/j.spasta.2021.100550>, Zaineb SMIDA and Lionel CUCALA and Ali GANNOUN and Ghislain Durif (2022) <doi:10.1016/j.csda.2021.107378>, Camille FREVENT and Mohamed-Salem AHMED and Sophie DABO-NIANG and Michael GENIN (2023) <doi:10.1093/jrsssc/qlad017>.

Authors:Camille FREVENT [aut, cre, cph], Mohamed-Salem AHMED [aut], Julien SOULA [aut], Zaineb SMIDA [aut], Lionel CUCALA [aut], Sophie DABO-NIANG [aut], Michaël GENIN [aut]

HDSpatialScan_1.0.4.tar.gz
HDSpatialScan_1.0.4.tar.gz(r-4.5-noble)HDSpatialScan_1.0.4.tar.gz(r-4.4-noble)
HDSpatialScan_1.0.4.tgz(r-4.4-emscripten)HDSpatialScan_1.0.4.tgz(r-4.3-emscripten)
HDSpatialScan.pdf |HDSpatialScan.html✨
HDSpatialScan/json (API)

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
Datasets:
  • fmulti_data - Multivariate functional data
  • funi_data - Univariate functional data
  • map_sites - Spatial object corresponding to the sites of the data of the package HDSpatialScan
  • multi_data - Multivariate non-functional data

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascppjags

1.00 score 4 scripts 255 downloads 3 exports 112 dependencies

Last updated 2 years agofrom:7913dd3925. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-linux-x86_64OKDec 13 2024

Exports:plotCurvesplotSummarySpatialScan

Dependencies:abindbase64encbslibcachemclassclassIntcliclueclustercodacolorspacecpp11crosstalkDBIdeldirdigestdplyrDTe1071evaluatefansifarverfastmapfBasicsfmsbfontawesomefsgenericsggplot2ggrepelgluegssgtableHDIntervalhighrhtmltoolshtmlwidgetshttpuvigraphisobandjquerylibjsonliteKernSmoothkknnknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemodeestmunsellnlmepbapplypillarpkgconfigplotrixpolyclippromisesproxypurrrR6rappdirsrasterRColorBrewerRcppRcppArmadillorlangrmarkdownrmutilrpartrunjagss2sassscalessfspspatialSpatialNPspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstablestablediststatipstringistringrswfscMiscTeachingDemosterratibbletidyrtidyselecttimeDatetimeSeriestinytexunitsutf8vctrsviridisLitewithrwkxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Multivariate and Functional Spatial Scan StatisticsHDSpatialScan-package HDSpatialScan
Creation of the matrix of potential clustersclusters
DFFSS scan procedureDFFSS
Index for the UG scan proceduredfree
Index for the MDFFSS scan proceduredfree_index_multi
Finalization of the scan proceduresFinScan
Multivariate functional datafmulti_data
Univariate functional datafuni_data
Initalization of the scan procedures by creating the matrix of potential clustersInitScan
Spatial object corresponding to the sites of the data of the package HDSpatialScanmap_sites
MDFFSS scan procedureMDFFSS
MG scan procedureMG
MNP scan procedureMNP
MPFSS scan procedureMPFSS
MRBFSS scan procedureMRBFSS
Multivariate non-functional datamulti_data
Index for the NPFSS scan procedure (multivariate functional case)multi_fWMW
Index for the MG scan proceduremulti_gaussian
List of matrix of signs (multivariate functional data)multi_signs_matrix
Index for the MNP scan proceduremulti_WMW
Return only the detected clusters with no overlapping in their order of detectionnon_overlap
NPFSS scan procedure (univariate functional or multivariate functional)NPFSS
Permutates the datapermutate
PFSS scan procedurePFSS
Map of circular clustersplot_map
Map of the clustersplot_map2
Schema of the clustersplot_schema
Schema or map of the clustersplot.ResScanOutput
Generic function to plot curvesplotCurves
Plots the curves in the clusters detected by the multivariate functional scan functions (MPFSS, NPFSS, MDFFSS or MRBFSS)plotCurves.ResScanOutputMultiFunct
Plots the curves in the clusters detected by the univariate functional scan functions (PFSS, NPFSS, DFFSS or URBFSS)plotCurves.ResScanOutputUniFunct
Generic function to plot a summaryplotSummary
Plots the mean or median spider chart of the clusters detected by a multivariate scan function (MG or MNP)plotSummary.ResScanOutputMulti
Plots the mean or median curves in the clusters detected by a multivariate functional scan procedure (MPFSS, NPFSS, MDFFSS or MRBFSS)plotSummary.ResScanOutputMultiFunct
Plots the mean or median curves in the clusters detected by a univariate functional scan procedure (PFSS, NPFSS, DFFSS or URBFSS)plotSummary.ResScanOutputUniFunct
Index for the DFFSS scan procedurepointwise_dfree
Index for the MRBFSS scan procedurepointwise_wmw_multi
Index for the URBFSS scan procedurepointwise_wmw_uni
A posteriori filtering on the areapost_filt_area
A posteriori filtering on the number of sites/individualspost_filt_nb_sites
A posteriori filtering on the radiuspost_filt_radius
Prints a result of a scan procedureprint.ResScanOutput
Constructor function for objects of the ResScanOutput classResScanOutput
Constructor function for objects of the ResScanOutputMulti classResScanOutputMulti
Constructor function for objects of the ResScanOutputMultiFunct classResScanOutputMultiFunct
Constructor function for objects of the ResScanOutputUni classResScanOutputUni
Constructor function for objects of the ResScanOutputUniFunct classResScanOutputUniFunct
Spatial scan procedureSpatialScan
Summary of the clusters obtained with a multivariate scan function (MG or MNP).summary.ResScanOutputMulti
Summary of the clusters obtained with a multivariate functional scan function (MPFSS, NPFSS, MDFFSS or MRBFSS).summary.ResScanOutputMultiFunct
Summary of the clusters obtained with a univariate scan function (UG or UNP).summary.ResScanOutputUni
Summary of the clusters obtained with a univariate functional scan function (PFSS, NPFSS, DFFSS or URBFSS).summary.ResScanOutputUniFunct
Computation of the multivariate functional rankstransform_data
UG scan procedureUG
Index for the NPFSS scan procedure (univariate functional case)uni_fWMW
Computation of the matrix of signsuni_signs_matrix
UNP scan procedureUNP
URBFSS scan procedureURBFSS
Index for the UNP scan procedurewmw_uni