From 112d2afd08350da6b4357ecd139350d386d9dbb7 Mon Sep 17 00:00:00 2001 From: Maira Alejandra Moreno C Date: Thu, 16 May 2024 11:02:16 -0300 Subject: [PATCH] Add files via upload --- .Rbuildignore | 2 + .Rhistory | 512 +++++++++++++++++++++++++++++++++++++++++++ .gitignore | 1 + DESCRIPTION | 27 +++ NAMESPACE | 22 ++ webspatialscan.Rproj | 22 ++ 6 files changed, 586 insertions(+) create mode 100644 .Rbuildignore create mode 100644 .Rhistory create mode 100644 .gitignore create mode 100644 DESCRIPTION create mode 100644 NAMESPACE create mode 100644 webspatialscan.Rproj diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..025b8dc --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^webspatialscan\.Rproj$ +^\.Rproj\.user$ diff --git a/.Rhistory b/.Rhistory new file mode 100644 index 0000000..ae41c70 --- /dev/null +++ b/.Rhistory @@ -0,0 +1,512 @@ +# Load rsatscan package +library(rsatscan) +# Load csv files for cases, population and coordinates +MCRJ_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_OCPUtestes/arquivos_csv/2015-2016/mc15-16.csv" , sep = ";") +NVRJ_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_OCPUtestes/arquivos_csv/2015-2016/nv15-16.csv" , sep = ";") +RJ_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_OCPUtestes/arquivos_csv/2015-2016/rj.csv" , sep = ";") +# Create a temporary directory for storing writen files +td = tempdir() +# Write and store cases, population and coordinates satscan files +write.cas(MCRJ_data, td, "MCRJ") +write.pop(NVRJ_data, td, "MCRJ") +write.geo(RJ_data, td, "MCRJ") +# Resetting the parameter file +invisible(ss.options(reset=TRUE, version="10.1")) +# Create satscan parameter list +ss.options(list(CaseFile="MCRJ.cas", StartDate="2015/1/1",EndDate="2016/12/31", PopulationFile="MCRJ.pop", CoordinatesFile="MCRJ.geo", CoordinatesType=0, AnalysisType=3)) +ss.options(c("NonCompactnessPenalty=0", "ReportGiniClusters=n", "LogRunToHistoryFile=n" , "MaxSpatialSizeInPopulationAtRisk=25", "TimeAggregationUnits=1", "TimeAggregationLength=2")) +# Write satscan parameter file +write.ss.prm(td,"poissonmc") +# Run poisson analysis by calling the satscan function +poissonmc = satscan(td,"poissonmc", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +summary(poissonmc) +# Load rsatscan +library(rsatscan) +#Load data +MCBr16_data <-read.csv("C:/Users/Maira Alejandra/Desktop/dados_OCPUtestes/arquivos_csv/2016/MCBr_16.csv" , sep = ";") +NVBr16_data <-read.csv("C:/Users/Maira Alejandra/Desktop/dados_OCPUtestes/arquivos_csv/2016/NVBr_16.csv" , sep = ";") +GEOBr_data <-read.csv("C:/Users/Maira Alejandra/Desktop/dados_OCPUtestes/arquivos_csv/2016/GEOBr.csv" , sep = ";") +# Create a temporary directory for storing writen files +td = tempdir() +# Write and store cases, population and coordinates satscan files +write.cas(MCBr16_data, td, "MCBr") +write.pop(NVBr16_data, td, "MCBr") +write.geo(GEOBr_data, td, "MCBr") +# Resetting the parameter file +invisible(ss.options(reset=TRUE, version="10.1")) +# Create satscan parameter list +ss.options(list(CaseFile="MCBr.cas", StartDate="2016/1/1",EndDate="2016/12/31", PopulationFile="MCBr.pop", CoordinatesFile="MCBr.geo", CoordinatesType=0, AnalysisType=1)) +ss.options(c("NonCompactnessPenalty=0", "ReportGiniClusters=n", "LogRunToHistoryFile=n" , "MaxSpatialSizeInPopulationAtRisk=25")) +# Write satscan parameter file +write.ss.prm(td,"poissonmc") +# Run poisson analysis by calling the satscan function +poissonmc = satscan(td,"poissonmc", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +#Get results summary +summary(poissonmc) +# Visualizing col data +cluster_data <- subset(poissonmc$col) +View(cluster_data) +# Visualizing gis data +location_data <- subset(poissonmc$gis) +View(location_data) +# Creating multilayer map with scale +library(leaflet) +library(leaflet.extras) +leaflet(cluster_data) %>% +addTiles(group = "Mapa") %>% +addCircleMarkers( +~Y, +~X, +~RADIUS * 25, +fillColor = ~ifelse(P_VALUE < 0.05, "red", "blue"), +stroke = FALSE, fillOpacity = 0.2, +popup = ~paste("RESUMO DADOS CLUSTER ", "
", +"Cluster: ", CLUSTER, "
", +"Periodo analisado: ", START_DATE, END_DATE, "
", +"População: ", POPULATION, "
", +"Número de casos: ", OBSERVED, "
", +"Número de casos esperados: ", EXPECTED, "
", +"Número de casos / casos esperados: ", ODE, "
", +"Risco Relativo: ", REL_RISK, "
", +"P-Valor: " , P_VALUE +), +group = "Clusters detectados") %>% +addCircleMarkers( +data = location_data, +~LOC_Y, +~LOC_X, +radius = 2, +color = 'black', +stroke = FALSE, fillOpacity = 0.7, +popup = ~paste("Local: ", LOC_ID), +group = "Locais identificados") %>% +# Layers control +addLayersControl( +baseGroups = c("Mapa"), +overlayGroups = c("Clusters detectados", "Locais identificados"), +options = layersControlOptions(collapsed = FALSE) +) %>% +# Map leyed +addLegend(position = "bottomright", +colors = c("red", "blue"), +labels = c("Significativo (p < 0.05)" , "Não significativo (p > 0.05)"), +title = "Clusters Microcefalia Congênita", +opacity = 0.4) %>% +addScaleBar(position = "bottomleft") %>% +# Location search box +addSearchOSM(options = searchOptions(position = "topleft", autoCollapse = TRUE, hideMarkerOnCollapse = TRUE, zoom = 5)) +print(poissonmc) +library(DBI) +library(rsatscan) +library(leaflet) +library(leaflet.extras) +library(htmlwidgets) +spatial_scan <- function(harm_code, year, data_iniChar, data_fimChar, scan_areaStr, tamanho_cluStr) { + conn_db <- dbConnect(RPostgres::Postgres(), dbname="spatialscan_db", host="localhost", user="postgres", password="postgres") + query_db <- paste("SELECT * FROM acbr_data", +"WHERE agravo =", harm_code, sep = " ", +"AND ano =", year) + filter_data <- dbGetQuery(conn_db, query_db) + td = tempdir() + casos_data <- data.frame(locID_cas = filter_data$cod, +                           cases_cas = filter_data$casos, +                           year_cas = filter_data$ano) + View(casos_data) + pop_data <- data.frame(locID_pop = filter_data$cod, +                         year_pop = filter_data$ano, +                         population_pop = filter_data$pop) + View(pop_data) + geo_data <- data.frame(locID_geo = filter_data$cod, +                         lat_geo = filter_data$lat, +                         long_geo = filter_data$long) + View(geo_data) +   + local_data <- data.frame(loc_name = filter_data$nm_local, +                           harm_name = filter_data$nm_agravo) + View(local_data) + dbDisconnect(conn_db) +  + write.cas(casos_data, td, "SSCAN") +write.pop(pop_data, td, "SSCAN") +write.geo(geo_data, td, "SSCAN") + invisible(ss.options(reset=TRUE, version="10.1")) + ss.options(list(CaseFile="SSCAN.cas", StartDate=data_iniChar,EndDate=data_fimChar, PopulationFile="SSCAN.pop", CoordinatesFile="SSCAN.geo", CoordinatesType=0, AnalysisType=1)) + ss.options(c("NonCompactnessPenalty=0", "ReportGiniClusters=n", "LogRunToHistoryFile=n" , scan_areaStr, tamanho_cluStr)) + write.ss.prm(td,"sscanresult") + sink(file = "sscanresult_output.txt") + sscanresult = satscan(td,"sscanresult", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") + print(sscanresult) +sink(file = NULL) + cluster_data <- subset(sscanresult$col) + View(cluster_data) +location_data <- subset(sscanresult$gis) + View(location_data) +m <- leaflet(cluster_data) %>% +addTiles(group = "Mapa") %>% +addCircles( +lat = ~Y, +lng = ~X, +radius = ~RADIUS * 25, +fillColor = ~ifelse(P_VALUE < 0.05, "red", "blue"), +stroke = FALSE, fillOpacity = 0.2, +popup = ~paste("RESUMO DADOS CLUSTER ", "
", +"Cluster: ", CLUSTER, "
", +"Periodo analisado: ", START_DATE, END_DATE, "
", +"População: ", POPULATION, "
", +"Número de casos: ", OBSERVED, "
", +"Número de casos esperados: ", EXPECTED, "
", +"Número de casos / casos esperados: ", ODE, "
", +"Risco Relativo: ", REL_RISK, "
", +"P-Valor: " , P_VALUE +), +group = "Clusters detectados") %>% +addCircleMarkers( +data = location_data, +~LOC_Y, +~LOC_X, +radius = 2, +color = 'black', +stroke = FALSE, fillOpacity = 0.7, +      popup = ~paste("Local: ", LOC_ID), +group = "Locais identificados") %>% +addLayersControl( +baseGroups = c("Mapa"), +overlayGroups = c("Clusters detectados", "Locais identificados"), +options = layersControlOptions(collapsed = FALSE) +) %>% +addLegend(position = "bottomright", +colors = c("red", "blue"), +labels = c("Significativo (p < 0.05)" , "Não significativo (p > 0.05)"), +title = "Clusters Microcefalia Congênita", +opacity = 0.4) %>% +addScaleBar(position = "bottomleft") %>% +addSearchOSM(options = searchOptions(position = "topleft", autoCollapse = TRUE, hideMarkerOnCollapse = TRUE, zoom = 5)) +scan_map <- saveWidget(m, "sscanresult_map.html", selfcontained = FALSE) +} +year = 2020 +harm_code = 1 +data_iniVal <- as.Date("2020/1/1") +data_fimVal <- as.Date("2020/12/31") +scan_areaVal <- 1 +tamanho_cluVal <- 25 +data_iniChar <- format(data_iniVal, "%Y/%m/%d") +data_fimChar <- format(data_fimVal, "%Y/%m/%d") +scan_areaStr <- paste("ScanAreas=", scan_areaVal, sep = " ") +tamanho_cluStr <- paste("MaxSpatialSizeInPopulationAtRisk=", tamanho_cluVal, sep = " ") +spatial_scan(harm_code, year, data_iniChar, data_fimChar, scan_areaStr, tamanho_cluStr) +library(opencpu) +ocpu_start_server() +library(opencpu) +ocpu_start_server() +install.packages("webspatialscan_0.0.0.9000.tar.gz", repos = NULL, type = "source") +library(opencpu) +ocpu_start_server() +library(leaflet) +csv_data <- read.csv("C:/Users/Maira Alejandra/Desktop/geo_shapeBR-GF.csv", sep = ";") +View(csv_data) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lat, +~lng, +radius = 0.5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 0.5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +Leaflet(csv_data) %>% addTiles() %>% ++addCircleMarkers( +~lng, +~lat, +radius = 2, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 2, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +csv_data2 <- read.csv("C:/Users/Maira Alejandra/Desktop/geo_shapeBR-GF2.csv", sep = ";") +View(csv_data2) +leaflet(csv_data2) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data2) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 3, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +csv_data3 <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testeBR-GF.csv", sep = ";") +View(csv_data3) +leaflet(csv_data3) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data3) %>% addTiles() %>% +addCircleMarkers( +~X.lng., +~X.lat., +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +csv_data4 <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testeBR-GF2.csv", sep = ";") +View(csv_data4) +leaflet(csv_data4) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data4) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 3, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +library(rsatscan) +casos_data <- data.frame( +loc_id = csv_data4$id, +malaria_data = csv_data4$casos, +ano_data = csv_data4$ano +) +View(casos_data) +geo_data <- data.frame( +geo_id = csv_data4$id, +lati = csv_data4$lat, +long = csv_data4$lng +) +View(geo_data) +td = tempdir() +write.cas(casos_data, td, "BRGFmalaria") +write.geo(geo_data, td, "BRGFmalaria") +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="BRGFmalaria.cas", StartDate="2019/1/1",EndDate="2019/12/31", CoordinatesFile="BRGFmalaria.geo", CoordinatesType=0, AnalysisType=3, ModelType=2)) +ss.options(c("NonCompactnessPenalty=0", "ReportGiniClusters=n", "LogRunToHistoryFile=n" , "MaxSpatialSizeInPopulationAtRisk=50")) +write.ss.prm(td, "scan_BRGFmalaria") +scan_BRGFmalaria = satscan(td,"scan_BRGFmalaria", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +summary(scan_BRGFmalaria) +write.cas(casos_data, td, "scan_BRGF") +write.geo(geo_data, td, "scan_BRGF") +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="scan_BRGF.cas", PrecisionCaseTimes=1)) +ss.options(c("StartDate=2019/1/1","EndDate=2019/12/31")) +ss.options(list(CoordinatesFile="scan_BRGF.geo", AnalysisType=3, ModelType=2, TimeAggregationUnits=1)) +ss.options(list(UseDistanceFromCenterOption="n", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0)) +ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=1)) +ss.options(list(ReportGiniClusters="n", LogRunToHistoryFile="n")) +head(ss.options(),3) +write.ss.prm(td, "scan_malariaBRGF") +scan_malariaBRGF = satscan(td,"scan_malariaBRGF", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +summary(scan_malariaBRGF) +View(geo_data) +View(casos_data) +library(rsatscan) +csv_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testeBR-GF2.csv", sep = ";") +View(csv_data) +td = tempdir() +casos_data <- data.frame( +cas_id = csv_data$id, +cas_data = csv_data$casos, +cas_ano = csv_data$ano +) +View(casos_data) +geo_data <- data.frame( +geo_id = csv_data$id, +latitude = csv_data$lat, +longitude = csv_data$lng +) +View(geo_data) +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="scan_BRGF.cas", PrecisionCaseTimes=1)) +ss.options(c("StartDate=2019/1/1","EndDate=2019/12/21")) +ss.options(list(CoordinatesFile="scan_BRGF.geo", AnalysisType=3, ModelType=2, TimeAggregationUnits=1)) +ss.options(list(UseDistanceFromCenterOption="y", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0)) +ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=1)) +ss.options(list(ReportGiniClusters="n", LogRunToHistoryFile="n")) +ss.options(list(SaveSimLLRsDBase="y")) +head(ss.options(),3) +write.ss.prm(td, "malaria_BRGF") +write.cas(casos_data, td, "scan_BRGF") +write.geo(geo_data, td, "scan_BRGF") +malaria_BRGF = satscan(td,"malaria_BRGF", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +summary(malaria_BRGF) +library(rsatscan) +csv_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testeBR-GF2.csv", sep = ";") +View(csv_data) +casos_data <- data.frame( +cas_id = csv_data$id, +cas_data = csv_data$casos, +cas_ano = csv_data$ano +) +View(casos_data) +geo_data <- data.frame( +geo_id = csv_data$id, +geo_lat = csv_data$lat, +geo_lng = csv_data$lng +) +td = tempdir() +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="BRGF.cas", PrecisionCaseTimes=2)) +ss.options(c("StartDate=2019/1/1","EndDate=2019/12/31")) +ss.options(list(CoordinatesFile="BRGF.geo", AnalysisType=4, ModelType=2, TimeAggregationUnits=2)) +ss.options(list(UseDistanceFromCenterOption="y", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0)) +ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=7)) +ss.options(list(ProspectiveStartDate="2019/12/31", ReportGiniClusters="n", LogRunToHistoryFile="n")) +ss.options(list(SaveSimLLRsDBase="y")) +write.ss.prm(td, "scan_BRGF") +write.cas(casos_data, td, "BRGF") +write.geo(geo_data, td, "BRGF") +scan_BRGF = satscan(td,"scan_BRGF", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +summary(scan_BRGF) +library("rsatscan") +head(NYCfevercas) +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="NYCfever.cas", PrecisionCaseTimes=3)) +ss.options(c("StartDate=2001/11/1","EndDate=2001/11/24")) +ss.options(list(CoordinatesFile="NYCfever.geo", AnalysisType=4, ModelType=2, TimeAggregationUnits=3)) +ss.options(list(UseDistanceFromCenterOption="y", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0)) +ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=7)) +ss.options(list(ProspectiveStartDate="2001/11/24", ReportGiniClusters="n", LogRunToHistoryFile="n")) +ss.options(list(SaveSimLLRsDBase="y")) +td = tempdir() +write.ss.prm(td, "NYCfever") +write.cas(NYCfevercas, td, "NYCfever") +write.geo(NYCfevergeo, td, "NYCfever") +NYCfever = satscan(td, "NYCfever", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +install.packages(rgdal) +install.packages("rgdal") +summary(NYCfever) +summary.default(NYCfever) +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="NYCfever.cas", PrecisionCaseTimes=3)) +ss.options(c("StartDate=2001/11/1","EndDate=2001/11/24")) +ss.options(list(CoordinatesFile="NYCfever.geo", AnalysisType=3, ModelType=2, TimeAggregationUnits=3)) +ss.options(list(UseDistanceFromCenterOption="y", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0)) +ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=7)) +ss.options(list(ReportGiniClusters="n", LogRunToHistoryFile="n")) +ss.options(list(SaveSimLLRsDBase="y")) +NYCfever = satscan(td, "NYCfever", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +summary(NYCfever) +library(rsatscan) +invisible(ss.options(reset=TRUE, version="10.1")) +ss.options(list(CaseFile="NYCfever.cas", PrecisionCaseTimes=3)) +ss.options(c("StartDate=2001/11/1","EndDate=2001/11/24")) +ss.options(list(CoordinatesFile="NYCfever.geo", AnalysisType=3, ModelType=2, TimeAggregationUnits=3)) +ss.options(list(UseDistanceFromCenterOption="y", MaxSpatialSizeInDistanceFromCenter=3, NonCompactnessPenalty=0)) +ss.options(list(MaxTemporalSizeInterpretation=1, MaxTemporalSize=7)) +ss.options(list(ReportGiniClusters="n", LogRunToHistoryFile="n")) +ss.options(list(SaveSimLLRsDBase="y")) +td = tempdir() +write.ss.prm(td, "NYCfever") +write.cas(NYCfevercas, td, "NYCfever") +write.geo(NYCfevergeo, td, "NYCfever") +NYCfever = satscan(td, "NYCfever", sslocation="C:/Program Files/SaTScan", ssbatchfilename="SaTScanBatch64") +print(NYCfever) +summary(NYCfever) +library(opencpu) +ocpu_start_server() +library(leaflet) +csv_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testBRGF/xlsx/dados_testeBR-GF3.csv", sep = ";") +csv_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testBRGF/csv/dados_testeBR-GF3.csv", sep = ";") +View(csv_data) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +) +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5 +popup = ~nm_local +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5, +popup = ~nm_local +) +read(NYCfevercas) +NYCfevercas +head(NYCfevercas) +library(rsatscan) +NYCfevercas +library(leaflet) +csv_data <- read.csv("C:/Users/Maira Alejandra/Desktop/dados_testBRGF/csv/dados_testeBR-GF3.csv", sep = ";") +leaflet(csv_data) %>% addTiles() %>% +addCircleMarkers( +~lng, +~lat, +radius = 5, +color = "blue", +stroke = FALSE, fillOpacity = 0.5, +popup = ~nm_local +) +library(opencpu) +ocpu_start_server() +install.packages("webspatialscan_0.0.0.9000.tar.gz", repos = NULL, type = "source") +library(opencpu) +ocpu_start_server() +library(opencpu) +ocpu_start_server() +library(opencpu) +ocpu_start_server() +install.packages("webspatialscan_0.0.0.9000.tar.gz", repos = NULL, type = "source") +library(opencpu) +ocpu_start_server() +library(opencpu) +ocpu_start_server() +install.packages("webspatialscan_0.0.0.9000.tar.gz", repos = NULL, type = "source") +library(opencpu) +ocpu_start_server() +install.packages("webspatialscan_0.0.0.9000.tar.gz", repos = NULL, type = "source") +library(opencpu) +ocpu_start_server() diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..cd67eac --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.Rproj.user diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..9819546 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,27 @@ +Package: webspatialscan +Title: an R package to enable Spatial Scan Statistics on WebGIS applications +Version: 0.0.0.9000 +Authors@R: + person(given = "Maira Alejandra", + family = "Moreno C.", + email = "mairamorenoc26@gmail.com", + role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-2910-2970")) +Description: Interfacing SatScan desktop software with a web application via OpenCPU and rsatscan, to allows users to run scan statistics and visualize results on the web. +License: MIT + file LICENSE +Encoding: UTF-8 +LazyData: true +Depends: + rsatscan +Imports: + leaflet, + leaflet.extras, + magrittr, + htmlwidgets +Suggests: + knitr, + sf, + rmarkdown, + roxygen2 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.2.3 diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..deeb8e0 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,22 @@ +# Generated by roxygen2: do not edit by hand + +export(spatial_scanUp) +importFrom(htmlwidgets,saveWidget) +importFrom(leaflet,addCircleMarkers) +importFrom(leaflet,addCircles) +importFrom(leaflet,addLayersControl) +importFrom(leaflet,addLegend) +importFrom(leaflet,addScaleBar) +importFrom(leaflet,addTiles) +importFrom(leaflet,layersControlOptions) +importFrom(leaflet,leaflet) +importFrom(leaflet.extras,addSearchOSM) +importFrom(leaflet.extras,searchOptions) +importFrom(magrittr,"%>%") +importFrom(rsatscan,satscan) +importFrom(rsatscan,ss.options) +importFrom(rsatscan,write.cas) +importFrom(rsatscan,write.geo) +importFrom(rsatscan,write.pop) +importFrom(rsatscan,write.ss.prm) +importFrom(utils,read.csv) diff --git a/webspatialscan.Rproj b/webspatialscan.Rproj new file mode 100644 index 0000000..38b9011 --- /dev/null +++ b/webspatialscan.Rproj @@ -0,0 +1,22 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes +LineEndingConversion: Posix + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace