version 1.0.4

cran · May 25, 2023 · 7913dd3 · 7913dd3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: HDSpatialScan
 Type: Package
 Title: Multivariate and Functional Spatial Scan Statistics
-Version: 1.0.3
+Version: 1.0.4
 Authors@R: c(person("Camille", "FREVENT", role = c("aut", "cre", "cph"), email = "camille.frevent@univ-lille.fr"), person("Mohamed-Salem", "AHMED", role = "aut"), person("Julien", "SOULA", role = "aut"), person("Zaineb", "SMIDA", role = "aut"), person("Lionel", "CUCALA", role = "aut"), person("Sophie", "DABO-NIANG", role = "aut"), person("Michaël", "GENIN", role = "aut"))
-Description: 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>, Zaineb SMIDA and Lionel CUCALA and Ali GANNOUN (2020) <https://hal.archives-ouvertes.fr/hal-02908496>, Camille FREVENT and Mohamed-Salem AHMED and Matthieu MARBAC and Michael GENIN (2021) <arXiv:2011.03482>, Camille FREVENT and Mohamed-Salem AHMED and Sophie DABO-NIANG and Michael GENIN (2021) <arXiv:2103.14401>.
+Description: 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>.
 Depends: R (>= 3.5.0)
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Imports: Rcpp, parallel, pbapply, purrr, matrixStats, SpatialNP, sp,
-        sf, DT, TeachingDemos, plotrix, fmsb, swfscMisc, rgeos,
+        sf, DT, TeachingDemos, plotrix, fmsb, swfscMisc, raster,
         graphics, stats, grDevices, methods
 LinkingTo: RcppArmadillo, Rcpp
 Collate: 'documentation_page.R' 'clusters.R' 'permutations.R'
@@ -27,7 +27,7 @@ Collate: 'documentation_page.R' 'clusters.R' 'permutations.R'
 RoxygenNote: 7.1.1
 Suggests: knitr, rmarkdown
 NeedsCompilation: yes
-Packaged: 2022-07-26 08:20:30 UTC; cfrevent
+Packaged: 2023-05-24 10:35:54 UTC; cfrevent
 Author: Camille FREVENT [aut, cre, cph],
   Mohamed-Salem AHMED [aut],
   Julien SOULA [aut],
@@ -37,4 +37,4 @@ Author: Camille FREVENT [aut, cre, cph],
   Michaël GENIN [aut]
 Maintainer: Camille FREVENT <camille.frevent@univ-lille.fr>
 Repository: CRAN
-Date/Publication: 2022-08-05 12:00:06 UTC
+Date/Publication: 2023-05-25 07:30:05 UTC
diff --git a/MD5 b/MD5
@@ -1,5 +1,5 @@
-263ba967acda3c806c446cadf4b27677 *DESCRIPTION
-5ff94e7d8cca78704e4ec0c187f65c24 *NAMESPACE
+8744be4d76f997d83f71fbf7209194d2 *DESCRIPTION
+7791224441460b4f622eca3d16a163f8 *NAMESPACE
 3a73ab13fc61fa6fee9c7f9abe1bac2b *R/HDSpatialScan_Classes.R
 9661a37365824b4229cc9a5ae4d42feb *R/HDSpatialScan_plot.R
 8d8f7cca26af515becd8f5b9130a1a77 *R/HDSpatialScan_plotCurves.R
@@ -16,17 +16,17 @@ c44a609f1309ee2ddc9baa73ab7b8b8c *R/data_map_sites.R
 b8e404c4feb262614563324956b7d7da *R/data_multi_data.R
 0a0456aea93cff88c21f81911a281169 *R/dfree.R
 cf4c1bbab9b4345a16ac35ba5fdd282f *R/dfree_index_multi.R
-b257032c31e4e14b4d8108ab946c1aa4 *R/documentation_page.R
+11b52227f1bbfe9c5bb6672e82dbce03 *R/documentation_page.R
 a3d3d0d09a6b03000306f50b99ddd5ac *R/finalizing_scan_procedure.R
 5c8581d4c78c35d30d907b2cf5c4a12a *R/gaussian_multi.R
 da13ee3ed62bcbfc1a7abff9868f0ab4 *R/non_overlap.R
 5f7be2c6ce3c78be0810f96b25d847f8 *R/permutations.R
-edd762fbcd3b706abec3b61ea233fccc *R/plot_map.R
+542c0999523de6a09292bfa94167ca15 *R/plot_map.R
 c18b49594b1ed4ef437304de55a4d002 *R/pointwise_dfree.R
 f7432b40663793c9b6f0369a438ef0d9 *R/pointwise_wmw_multi.R
 831a4f802e486ad6dba2eef2824e29f3 *R/pointwise_wmw_uni.R
 1a05ac201c1d35c7c6ac554633c200b9 *R/posteriori_filtering.R
-03997230918e4ab71328b7ca2f870f0c *R/scan_fonc.R
+4ead6f7a61ef5ee55116d61b66069546 *R/scan_fonc.R
 2f4b10dab1256fa4e461446cafc6bf54 *R/scan_multi.R
 66787cb0af160e129887b8b677fd9762 *R/scan_uni.R
 5ff4784a9ed68f136c046d3b23213fc4 *R/transform_data.R
@@ -37,17 +37,17 @@ e74bc633bf103ba80bc508f41f72f73a *R/wmw_uni.R
 53ce6afbe200471b3656394b6c9e6be9 *data/funi_data.rda
 da66be1514a6e035f819ca1d5dae36f2 *data/map_sites.rda
 8906380baee8bb329eafcedab9bc06a4 *data/multi_data.rda
-010505f6bf697594e0e219df38e41e82 *man/DFFSS.Rd
+7be0f5c8e6a898076bcf2a28d2c7d3df *man/DFFSS.Rd
 4281f626b30924d6446f0f490fb124fc *man/FinScan.Rd
-5ac08abbf5e3a890846856821f91e9db *man/HDSpatialScan-package.Rd
+09f5b854fa53ebe1b96e07034eb8aae7 *man/HDSpatialScan-package.Rd
 a987636e1bb962d82b4e6668c4efc0ba *man/InitScan.Rd
-a828b9e0e90c4932763e088f2b9bc374 *man/MDFFSS.Rd
+b8a250701f09efbee487f2483b1aa26b *man/MDFFSS.Rd
 a4fb6d5867d55340588b0087065a97c8 *man/MG.Rd
 0a99a7f503cc3db80a839d5b9ac5a75a *man/MNP.Rd
-88f04302abafdeab7d10c6374101df24 *man/MPFSS.Rd
-fb2f003de1ba8c0dd8aa6eb7afdd5a30 *man/MRBFSS.Rd
-0d5c56a1c9fcfcacd86040072f89537d *man/NPFSS.Rd
-5fa66a40de5e35ec789b99d4f4da41a6 *man/PFSS.Rd
+4c21bf46dd43c332261fd8728c4fbdf0 *man/MPFSS.Rd
+1701187b767bc3ac9dce6b65c8cd632e *man/MRBFSS.Rd
+1ac5b5070fbc7d2ebe6f77ae9d0defa0 *man/NPFSS.Rd
+21557afa5e5eba9097a2b3bc0a1cce66 *man/PFSS.Rd
 cb9fa7efe3d6de41b7a7bd8b8edcf6ae *man/ResScanOutput.Rd
 66e24e3fb1bf07adcd9cfaa672ad530d *man/ResScanOutputMulti.Rd
 71f4158e8f3ccbc0ed3dca53def4a78b *man/ResScanOutputMultiFunct.Rd

diff --git a/NAMESPACE b/NAMESPACE
@@ -33,7 +33,7 @@ importFrom(graphics,lines)
 importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(methods,is)
-importFrom(rgeos,gUnaryUnion)
+importFrom(raster,aggregate)
 importFrom(stats,quantile)
 importFrom(stats,sd)
 useDynLib(HDSpatialScan)
diff --git a/R/documentation_page.R b/R/documentation_page.R
@@ -5,8 +5,8 @@
 ##' \tabular{ll}{
 ##' Package: \tab HDSpatialScan\cr
 ##' Type: \tab Package\cr
-##' Version: \tab 1.0.3\cr
-##' Date: \tab 2022-07-26\cr
+##' Version: \tab 1.0.4\cr
+##' Date: \tab 2023-05-24\cr
 ##' License: \tab GPL-3\cr
 ##' LazyLoad: \tab yes\cr
 ##' }
@@ -29,7 +29,7 @@
 ##' @import sf
 ##' @import fmsb
 ##' @import swfscMisc
-##' @importFrom rgeos gUnaryUnion
+##' @importFrom raster aggregate
 ##' @importFrom graphics legend lines par points
 ##' @importFrom stats quantile sd
 ##' @importFrom grDevices adjustcolor
@@ -48,11 +48,11 @@
 ##'
 ##' Lionel Cucala and Michaël Genin and Florent Occelli and Julien Soula (2019). A Multivariate Nonparametric Scan Statistic for Spatial Data. Spatial statistics, 29, 1-14.
 ##'
-##' Zaineb Smida and Lionel Cucala and Ali Gannoun. A Nonparametric Spatial Scan Statistic for Functional Data. Pre-print.
+##' Camille Frévent and Mohamed-Salem Ahmed and Matthieu Marbac and Michaël Genin (2021). Detecting Spatial Clusters in Functional Data: New Scan Statistic Approaches. Spatial Statistics, 46.
 ##'
-##' Camille Frévent and Mohamed-Salem Ahmed and Matthieu Marbac and Michaël Genin. Detecting Spatial Clusters in Functional Data: New Scan Statistic Approaches. Pre-print.
+##' Zaineb Smida and Lionel Cucala and Ali Gannoun and Ghislain Durif (2022). A Wilcoxon-Mann-Whitney spatial scan statistic for functional data. Computational Statistics & Data Analysis, 167.
 ##'
-##' Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin. Investigating Spatial Scan Statistics for Multivariate Functional Data. Pre-print.
+##' Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin (2023). Investigating Spatial Scan Statistics for Multivariate Functional Data. Journal of the Royal Statistical Society Series C: Applied Statistics, 72(2), 450-475.
 ##'
 ##'
 ##'

diff --git a/R/plot_map.R b/R/plot_map.R
@@ -191,7 +191,7 @@ plot_map2 <- function(spobject, sites_coord, output_clusters, system, colors = "
     }
 
     if(length(colors)==1){
-      c_union <- suppressWarnings(gUnaryUnion(spobject[indices_sites,]))
+      c_union <- suppressWarnings(raster::aggregate(spobject[indices_sites,]))
       adj_color <- adjustcolor(colors, alpha.f = 0.6)
       plot(c_union, add = TRUE, col = adj_color)
 
@@ -204,7 +204,7 @@ plot_map2 <- function(spobject, sites_coord, output_clusters, system, colors = "
         stop("There must be one color or the same number of colors than the number of clusters to be plotted")
       }
 
-      c_union <- suppressWarnings(gUnaryUnion(spobject[indices_sites,]))
+      c_union <- suppressWarnings(raster::aggregate(spobject[indices_sites,]))
       adj_color <- adjustcolor(colors[cl], alpha.f = 0.6)
 
       plot(c_union, add = TRUE, col = adj_color)

diff --git a/R/scan_fonc.R b/R/scan_fonc.R
@@ -15,7 +15,7 @@
 ##'
 ##' @return An object of class ResScanOutputUniFunct or ResScanOutputMultiFunct depending on the data
 ##'
-##' @references Zaineb Smida and Lionel Cucala and Ali Gannoun. A Nonparametric Spatial Scan Statistic for Functional Data. Pre-print <https://hal.archives-ouvertes.fr/hal-02908496>.
+##' @references Zaineb Smida and Lionel Cucala and Ali Gannoun and Ghislain Durif (2022). A Wilcoxon-Mann-Whitney spatial scan statistic for functional data. Computational Statistics & Data Analysis, 167.
 ##'
 ##'
 NPFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, variable_names = NULL, times = NULL, initialization, permutations){
@@ -190,7 +190,7 @@ NPFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, variable_names = NULL
 ##'
 ##' @return An object of class ResScanOutputUniFunct.
 ##'
-##' @references Camille Frévent and Mohamed-Salem Ahmed and Matthieu Marbac and Michaël Genin. Detecting Spatial Clusters in Functional Data: New Scan Statistic Approaches. Pre-print <arXiv:2011.03482>.
+##' @references Camille Frévent and Mohamed-Salem Ahmed and Matthieu Marbac and Michaël Genin (2021). Detecting Spatial Clusters in Functional Data: New Scan Statistic Approaches. Spatial Statistics, 46.
 ##'
 ##'
 PFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, times = NULL, initialization, permutations){
@@ -283,7 +283,7 @@ PFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, times = NULL, initiali
 ##'
 ##' @return List of objects of class ResScanOutputMultiFunct (one element by method)
 ##'
-##' @references Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin. Investigating Spatial Scan Statistics for Multivariate Functional Data. Pre-print <arXiv:2103.14401>.
+##' @references Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin (2023). Investigating Spatial Scan Statistics for Multivariate Functional Data. Journal of the Royal Statistical Society Series C: Applied Statistics, 72(2), 450-475.
 ##'
 ##'
 MPFSS <- function(data, MC = 999, typeI = 0.05, method = c("LH","W","P","R"), nbCPU = 1, variable_names = NULL, times = NULL, initialization, permutations){
@@ -466,7 +466,7 @@ MPFSS <- function(data, MC = 999, typeI = 0.05, method = c("LH","W","P","R"), nb
 ##'
 ##' @return An object of class ResScanOutputUniFunct.
 ##'
-##' @references Camille Frévent and Mohamed-Salem Ahmed and Matthieu Marbac and Michaël Genin. Detecting Spatial Clusters in Functional Data: New Scan Statistic Approaches. Pre-print <arXiv:2011.03482>.
+##' @references Camille Frévent and Mohamed-Salem Ahmed and Matthieu Marbac and Michaël Genin (2021). Detecting Spatial Clusters in Functional Data: New Scan Statistic Approaches. Spatial Statistics, 46.
 ##'
 ##'
 DFFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, times = NULL, initialization, permutations){
@@ -559,7 +559,7 @@ DFFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, times = NULL, initial
 ##'
 ##' @return An object of class ResScanOutputMultiFunct.
 ##'
-##' @references Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin. Investigating Spatial Scan Statistics for Multivariate Functional Data. Pre-print <arXiv:2103.14401>.
+##' @references  Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin (2023). Investigating Spatial Scan Statistics for Multivariate Functional Data. Journal of the Royal Statistical Society Series C: Applied Statistics, 72(2), 450-475.
 ##'
 ##'
 MDFFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, variable_names = NULL, times = NULL, initialization, permutations){
@@ -666,7 +666,7 @@ MDFFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, variable_names = NUL
 ##'
 ##' @return An object of class ResScanOutputMultiFunct
 ##'
-##' @references Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin. Investigating Spatial Scan Statistics for Multivariate Functional Data. Pre-print <arXiv:2103.14401>.
+##' @references Camille Frévent and Mohamed-Salem Ahmed and Sophie Dabo-Niang and Michaël Genin (2023). Investigating Spatial Scan Statistics for Multivariate Functional Data. Journal of the Royal Statistical Society Series C: Applied Statistics, 72(2), 450-475.
 ##'
 ##'
 MRBFSS <- function(data, MC = 999, typeI = 0.05, nbCPU = 1, variable_names = NULL, times = NULL, initialization, permutations){

diff --git a/man/DFFSS.Rd b/man/DFFSS.Rd
diff --git a/man/HDSpatialScan-package.Rd b/man/HDSpatialScan-package.Rd
diff --git a/man/MDFFSS.Rd b/man/MDFFSS.Rd
diff --git a/man/MPFSS.Rd b/man/MPFSS.Rd
diff --git a/man/MRBFSS.Rd b/man/MRBFSS.Rd
diff --git a/man/NPFSS.Rd b/man/NPFSS.Rd
diff --git a/man/PFSS.Rd b/man/PFSS.Rd