From 00e3cc08e5e5f0a36ff50c948afef7394dba23bd Mon Sep 17 00:00:00 2001 From: Ornrakorn Mekchaiporn Date: Mon, 31 Jul 2023 22:51:24 +0700 Subject: [PATCH 1/7] Initial commit --- .Rbuildignore | 2 + .gitignore | 11 +- DESCRIPTION | 31 + NAMESPACE | 1 + R/STEHealthApp.R | 9 + R/rfunctions.R | 6 + STEHealthApp.Rproj | 20 + inst/STEHealthApp/.gitignore | 11 + .../STEHealthApp/runShinyApp.R | 0 .../sample data}/gadm40_THA_1.dbf | Bin .../sample data}/gadm40_THA_1.prj | 0 .../sample data}/gadm40_THA_1.shp | Bin .../sample data}/gadm40_THA_1.shx | Bin .../sample data}/suicide_th_data_sample.csv | 0 .../suicide_th_data_sample_have_e_value.csv | 0 {shiny => inst/STEHealthApp/shiny}/Manual.md | 0 .../STEHealthApp/shiny}/about_webapp.md | 0 {shiny => inst/STEHealthApp/shiny}/help.md | 0 .../STEHealthApp/shiny}/releases.md | 0 inst/STEHealthApp/shiny/server.R | 2943 +++++++++++++ inst/STEHealthApp/shiny/ui.R | 849 ++++ .../STEHealthApp/shiny}/www/Rectangle.svg | 0 .../www/STEHealth_Application_Manual.pdf | Bin .../shiny}/www/STEHealth_logo1.png | Bin .../shiny}/www/STEHealth_logo2.png | Bin .../shiny}/www/STEHealth_logo_0.ico | Bin .../STEHealthApp/shiny}/www/close.png | Bin .../STEHealthApp/shiny}/www/cluster.png | Bin .../STEHealthApp/shiny}/www/home.png | Bin .../STEHealthApp/shiny}/www/info.png | Bin .../STEHealthApp/shiny}/www/js/index.js | 0 .../STEHealthApp/shiny}/www/mapdis.png | Bin .../STEHealthApp/shiny}/www/nodata.png | Bin .../STEHealthApp/shiny}/www/risk.png | Bin .../STEHealthApp/shiny}/www/style.css | 0 .../STEHealthApp/shiny}/www/th_csv.jpg | Bin .../STEHealthApp/shiny}/www/th_shapfile.jpg | Bin .../shiny}/www/undraw_adventure_re.svg | 0 .../shiny}/www/undraw_file_searching.svg | 0 .../shiny}/www/undraw_location_search_re.svg | 0 .../shiny}/www/undraw_programming.svg | 0 .../shiny}/www/undraw_world_re.svg | 0 .../STEHealthApp/shiny}/www/warning.png | Bin shiny/STEHealth.R | 3714 ----------------- 44 files changed, 3874 insertions(+), 3723 deletions(-) create mode 100644 .Rbuildignore create mode 100644 DESCRIPTION create mode 100644 NAMESPACE create mode 100644 R/STEHealthApp.R create mode 100644 R/rfunctions.R create mode 100644 STEHealthApp.Rproj create mode 100644 inst/STEHealthApp/.gitignore rename runShinyApp.R => inst/STEHealthApp/runShinyApp.R (100%) rename {sample data => inst/STEHealthApp/sample data}/gadm40_THA_1.dbf (100%) rename {sample data => inst/STEHealthApp/sample data}/gadm40_THA_1.prj (100%) rename {sample data => inst/STEHealthApp/sample data}/gadm40_THA_1.shp (100%) rename {sample data => inst/STEHealthApp/sample data}/gadm40_THA_1.shx (100%) rename {sample data => inst/STEHealthApp/sample data}/suicide_th_data_sample.csv (100%) rename {sample data => inst/STEHealthApp/sample data}/suicide_th_data_sample_have_e_value.csv (100%) rename {shiny => inst/STEHealthApp/shiny}/Manual.md (100%) rename {shiny => inst/STEHealthApp/shiny}/about_webapp.md (100%) rename {shiny => inst/STEHealthApp/shiny}/help.md (100%) rename {shiny => inst/STEHealthApp/shiny}/releases.md (100%) create mode 100644 inst/STEHealthApp/shiny/server.R create mode 100644 inst/STEHealthApp/shiny/ui.R rename {shiny => inst/STEHealthApp/shiny}/www/Rectangle.svg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/STEHealth_Application_Manual.pdf (100%) rename {shiny => inst/STEHealthApp/shiny}/www/STEHealth_logo1.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/STEHealth_logo2.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/STEHealth_logo_0.ico (100%) rename {shiny => inst/STEHealthApp/shiny}/www/close.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/cluster.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/home.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/info.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/js/index.js (100%) rename {shiny => inst/STEHealthApp/shiny}/www/mapdis.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/nodata.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/risk.png (100%) rename {shiny => inst/STEHealthApp/shiny}/www/style.css (100%) rename {shiny => inst/STEHealthApp/shiny}/www/th_csv.jpg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/th_shapfile.jpg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/undraw_adventure_re.svg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/undraw_file_searching.svg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/undraw_location_search_re.svg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/undraw_programming.svg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/undraw_world_re.svg (100%) rename {shiny => inst/STEHealthApp/shiny}/www/warning.png (100%) delete mode 100644 shiny/STEHealth.R diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..91114bf --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.gitignore b/.gitignore index f0ab31c..5b6a065 100644 --- a/.gitignore +++ b/.gitignore @@ -1,11 +1,4 @@ - +.Rproj.user .Rhistory .RData -note for update.txt -note for app update.txt -note for manual update.txt -sample data/suicide_th_data_sampl_1.csv -sample data/suicide_th_data_sample - Copy.csv -test cal col.R -sample data/suicide_th_data_sample - อันเดิม.csv -pic for manual +.Ruserdata diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..e479740 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,31 @@ +Package: STEHealthApp +Type: Package +Title: An application for analyzing space-time pattern and association with risk factors of suicide and other health outcomes +Version: 1.2 +Author: Ornrakorn Mekchaiporn, Papin Thanutchapat, Chiraphat Phoncharoenwirote +Maintainer: Ornrakorn Mekchaiporn +Description: Allows users to import their own data, analyze, visualize, and export result. +Imports: + shiny, + shinydashboard, + shinyjs, + shinyBS, + leaflet, + dplyr, + ggplot2, + RColorBrewer, + rgdal, + shinyWidgets, + shinydashboardPlus, + spdep, + leaflet.extras, + bsplus, + remotes +Suggests: + INLA, + capture +Additional_repositories: https://inla.r-inla-download.org/R/stable +URL: https://github.com/mill-ornrakorn/STEHealth-Application +License: ? +Encoding: UTF-8 +LazyData: true diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..d75f824 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1 @@ +exportPattern("^[[:alpha:]]+") diff --git a/R/STEHealthApp.R b/R/STEHealthApp.R new file mode 100644 index 0000000..4c1d36f --- /dev/null +++ b/R/STEHealthApp.R @@ -0,0 +1,9 @@ +#' STEHealthApp: a shiny application for analyzing space-time pattern, cluster detection, and association with risk factors of health outcomes +#' +#' +#' @docType package +#' @name STEHealthApp +NULL + + + diff --git a/R/rfunctions.R b/R/rfunctions.R new file mode 100644 index 0000000..5f571ad --- /dev/null +++ b/R/rfunctions.R @@ -0,0 +1,6 @@ +#' Runs the Shiny web application. +#' @export +run_app <- function() { + shiny::runApp(system.file('STEHealthApp', package='STEHealthApp')) +} + diff --git a/STEHealthApp.Rproj b/STEHealthApp.Rproj new file mode 100644 index 0000000..497f8bf --- /dev/null +++ b/STEHealthApp.Rproj @@ -0,0 +1,20 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/inst/STEHealthApp/.gitignore b/inst/STEHealthApp/.gitignore new file mode 100644 index 0000000..f0ab31c --- /dev/null +++ b/inst/STEHealthApp/.gitignore @@ -0,0 +1,11 @@ + +.Rhistory +.RData +note for update.txt +note for app update.txt +note for manual update.txt +sample data/suicide_th_data_sampl_1.csv +sample data/suicide_th_data_sample - Copy.csv +test cal col.R +sample data/suicide_th_data_sample - อันเดิม.csv +pic for manual diff --git a/runShinyApp.R b/inst/STEHealthApp/runShinyApp.R similarity index 100% rename from runShinyApp.R rename to inst/STEHealthApp/runShinyApp.R diff --git a/sample data/gadm40_THA_1.dbf b/inst/STEHealthApp/sample data/gadm40_THA_1.dbf similarity index 100% rename from sample data/gadm40_THA_1.dbf rename to inst/STEHealthApp/sample data/gadm40_THA_1.dbf diff --git a/sample data/gadm40_THA_1.prj b/inst/STEHealthApp/sample data/gadm40_THA_1.prj similarity index 100% rename from sample data/gadm40_THA_1.prj rename to inst/STEHealthApp/sample data/gadm40_THA_1.prj diff --git a/sample data/gadm40_THA_1.shp b/inst/STEHealthApp/sample data/gadm40_THA_1.shp similarity index 100% rename from sample data/gadm40_THA_1.shp rename to inst/STEHealthApp/sample data/gadm40_THA_1.shp diff --git a/sample data/gadm40_THA_1.shx b/inst/STEHealthApp/sample data/gadm40_THA_1.shx similarity index 100% rename from sample data/gadm40_THA_1.shx rename to inst/STEHealthApp/sample data/gadm40_THA_1.shx diff --git a/sample data/suicide_th_data_sample.csv b/inst/STEHealthApp/sample data/suicide_th_data_sample.csv similarity index 100% rename from sample data/suicide_th_data_sample.csv rename to inst/STEHealthApp/sample data/suicide_th_data_sample.csv diff --git a/sample data/suicide_th_data_sample_have_e_value.csv b/inst/STEHealthApp/sample data/suicide_th_data_sample_have_e_value.csv similarity index 100% rename from sample data/suicide_th_data_sample_have_e_value.csv rename to inst/STEHealthApp/sample data/suicide_th_data_sample_have_e_value.csv diff --git a/shiny/Manual.md b/inst/STEHealthApp/shiny/Manual.md similarity index 100% rename from shiny/Manual.md rename to inst/STEHealthApp/shiny/Manual.md diff --git a/shiny/about_webapp.md b/inst/STEHealthApp/shiny/about_webapp.md similarity index 100% rename from shiny/about_webapp.md rename to inst/STEHealthApp/shiny/about_webapp.md diff --git a/shiny/help.md b/inst/STEHealthApp/shiny/help.md similarity index 100% rename from shiny/help.md rename to inst/STEHealthApp/shiny/help.md diff --git a/shiny/releases.md b/inst/STEHealthApp/shiny/releases.md similarity index 100% rename from shiny/releases.md rename to inst/STEHealthApp/shiny/releases.md diff --git a/inst/STEHealthApp/shiny/server.R b/inst/STEHealthApp/shiny/server.R new file mode 100644 index 0000000..68d2107 --- /dev/null +++ b/inst/STEHealthApp/shiny/server.R @@ -0,0 +1,2943 @@ +# ==================================== Check packages ==================================== + +list.of.packages <- c("shiny", "shinydashboard", "shinyjs", "shinyBS" , "leaflet" , + "dplyr", "ggplot2" ,"RColorBrewer" , "rgdal" ,"shinyWidgets", + "shinydashboardPlus","spdep", "leaflet.extras", "bsplus" ,"remotes") +new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])] +if(length(new.packages)) install.packages(new.packages) + + +if(!require(INLA)){ + # ต้องใช้ R 4.2.2 ถึงจะลงได้ ลองใช้ 4.3.1 แล้วลงไม่ได้ + install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE) + library(INLA) +} + + +if(!require(capture)){ + remotes::install_github("dreamRs/capture") + library(capture) +} + + +# ==================================== import packages ==================================== + +library(shiny) +library(shinydashboard) +library(shinyjs) +library(shinyBS) +library(leaflet) +library(dplyr) +library(ggplot2) +library(RColorBrewer) +library(rgdal) +library(shinyWidgets) +library(shinydashboardPlus) + +library(INLA) +inla.setOption(scale.model.default = TRUE) +library(spdep) # อันนี้ใช้ nb2mat + +library(capture) # ลงโดยใช้ remotes::install_github("dreamRs/capture") +library(leaflet.extras) +library(bsplus) + +# install.packages("sf") +# ถ้าลง sf ไม่ได้ให้พิมพ์คำสั่งด้านล่างนี้ก่อน +# options("install.lock"= FALSE) + + +# By default the file size limit is 5MB. Here limit is 70MB. +options(shiny.maxRequestSize = 70*1024^2) + +# options(scipen=999) + + + +# server = function(input, output, session) { +# +# # IMPORTANT! +# # this is needed to terminate the R process when the +# # shiny app session ends. Otherwise, you end up with a zombie process +# session$onSessionEnded(function() { +# stopApp() +# }) +# +# dataset = reactive({ +# switch( +# input$dataset, +# "rock" = rock, +# "pressure" = pressure, +# "cars" = cars, +# "iris" = iris) +# }) +# +# output$commandArgs = renderPrint({ +# commandArgs() +# }) +# +# output$dataSummary = renderPrint({ +# summary(dataset()) +# }) +# +# output$dataView = renderTable({ +# head(dataset(), n = input$obs) +# }) +# } + + + + +############################################################### +# +# server +# +############################################################### + +server <- function(input, output, session) { + + #observe(print(input$columnexpvalueindata)) + + # message menu + + output$messageMenu <- renderMenu({ + dropdownMenu(type = "messages", + messageItem( + from = "Project in Github", + message = "Documentation, Source, Citation", + icon = icon("github", style = 'color: #5c5c68;'), + href = "https://github.com/mill-ornrakorn/STEHealth-Application"), + + badgeStatus = NULL, + icon = tags$i(tags$img(src='info.png', height='16', width='16')), + #icon = icon("circle-info", style = 'color: #5c5c68;'), + headerText = "App Information" + ) + }) + + + + # แบบรูปไม่ position:absolute + output$status_map <- renderUI({ + if (is.null(input$filemap)) { + HTML("

+ nodata") + + } + }) + + # แบบ text + # output$status_csv <- renderPrint({ + # if (is.null(input$file1)) { + # return(HTML('Please upload "csv file" to preview data.')) + # } + # }) + + + output$status_csv <- renderUI({ + if (is.null(input$file1)) { + HTML("

+ nodata") + + } + }) + + # แบบ text + # output$status_map_dis <- renderPrint({ + # if (is.null(input$filemap) & is.null(input$file1)) { + # return(HTML('Please upload data in "Upload Data" page to display map distribution.')) + # } + # + # }) + + output$status_map_dis <- renderUI({ + if (is.null(input$filemap) & is.null(input$file1)) { + HTML("

+ ") + + } + }) + + + # แบบ text + # output$status_cluster <- renderPrint({ + # if (is.null(input$filemap) & is.null(input$file1)) { + # return(HTML('Please upload data in "Upload Data" page to display cluster detection.')) + # } + # + # }) + + output$status_cluster <- renderUI({ + if (is.null(input$filemap) & is.null(input$file1)) { + HTML("

+ ") + + } + }) + + # แบบรูป position:absolute + # output$status_cluster <- renderUI({ + # if (is.null(input$filemap) & is.null(input$file1)) { + # #HTML("

+ # HTML("

+ # ") + # + # } + # }) + + # แบบ text + # output$status_risk_fac <- renderPrint({ + # if (is.null(input$filemap) & is.null(input$file1)) { + # return(HTML('Please upload data in "Upload Data" page to display association with risk factors.')) + # } + # + # }) + + + output$status_risk_fac <- renderUI({ + if (is.null(input$filemap) & is.null(input$file1)) { + HTML("

+ ") + + } + }) + + # ==================================== write error messages ==================================== + + + output$status_risk_fac_nocova <- renderPrint({ + x1 <- input$columncov1indata + x2 <- input$columncov2indata + x3 <- input$columncov3indata + x4 <- input$columncov4indata + x5 <- input$columncov5indata + x6 <- input$columncov6indata + x7 <- input$columncov7indata + + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + return(HTML('📌 There are no covariates have been selected ❗')) + } + + + }) + + + output$messageCheckData_1<-renderText( + paste(rv$messageCheckDataText_1) + ) + + #observeEvent(input$Preview_Map_Distribution | input$tabs == "Map_Distribution", { + observeEvent(input$Preview_Map_Distribution , { + + if (is.null(rv$map) & is.null(rv$datosOriginal) ){ + rv$messageCheckDataText_1<-"📌 Error: There are no data (shapefile and csv file) have been uploaded ❗" + return(NULL) + } + + + else if (is.null(rv$map) & (!is.null(rv$datosOriginal))){ + rv$messageCheckDataText_1<-"📌 Error: There are no shapefile have been uploaded ❗" + return(NULL) + } + + + else if (!is.null(rv$map) & is.null(rv$datosOriginal)){ + rv$messageCheckDataText_1<-"📌 Error: There is no csv file have been uploaded ❗" + return(NULL) + } + + else if (!is.null(rv$map) & (!is.null(rv$datosOriginal))){ + rv$messageCheckDataText_1<-NULL + return(NULL) + } + + + }) + + + output$messageCheckData_2<-renderText( + paste(rv$messageCheckDataText_2) + ) + + output$messageCheckData_3<-renderText( + paste(rv$messageCheckDataText_3) + ) + + #observeEvent(input$nextpage | input$tabs == "Analysis", { + observeEvent(input$nextpage , { + + if (is.null(rv$map) & is.null(rv$datosOriginal) ){ + rv$messageCheckDataText_2<-"📌 Error: There are no data (shapefile and csv file) have been uploaded ❗" + rv$messageCheckDataText_3<-"📌 Error: There are no data (shapefile and csv file) have been uploaded ❗" + + return(NULL) + } + + + else if (is.null(rv$map) & (!is.null(rv$datosOriginal))){ + rv$messageCheckDataText_2<-"📌 Error: There are no shapefile have been uploaded ❗" + rv$messageCheckDataText_3<-"📌 Error: There are no shapefile have been uploaded ❗" + + return(NULL) + } + + + else if (!is.null(rv$map) & is.null(rv$datosOriginal)){ + rv$messageCheckDataText_2<-"📌 Error: There is no csv file have been uploaded ❗" + rv$messageCheckDataText_3<-"📌 Error: There is no csv file have been uploaded ❗" + + return(NULL) + } + + else if (!is.null(rv$map) & (!is.null(rv$datosOriginal))){ + rv$messageCheckDataText_2<-NULL + rv$messageCheckDataText_3<-NULL + + return(NULL) + } + + + }) + + + + + + + + # ======================================================================== + + + observe({ + if (is.null(names(rv$datosOriginal))) + xd <- character(0) + + xd<-names(rv$datosOriginal) + + if (is.null(xd)) + xd <- character(0) + + xd2<- c("-", xd) + + # Can also set the label and select items + #label = paste("Select input label", length(x)), + updateSelectInput(session, "columnidareaindata", choices = xd, selected = head(xd, 1)) + updateSelectInput(session, "columnidareanamedata", choices = xd, selected = head(xd, 1)) + updateSelectInput(session, "columndateindata", choices = xd, selected = head(xd, 1)) + updateSelectInput(session, "columnexpvalueindata", choices = xd, selected = head(xd, 1)) + updateSelectInput(session, "columncasesindata", choices = xd, selected = head(xd, 1)) + updateSelectInput(session, "columnpopindata", choices = xd, selected = head(xd, 1)) + + + #columncov1indata + updateSelectInput(session, "columncov1indata", choices = xd, selected = "-") + updateSelectInput(session, "columncov2indata", choices = xd, selected = "-") + updateSelectInput(session, "columncov3indata", choices = xd, selected = "-") + updateSelectInput(session, "columncov4indata", choices = xd, selected = "-") + updateSelectInput(session, "columncov5indata", choices = xd, selected = "-") + updateSelectInput(session, "columncov6indata", choices = xd, selected = "-") + updateSelectInput(session, "columncov7indata", choices = xd, selected = "-") + #updateSelectInput(session, "columncov5indata", choices = xd, selected = "-") + + }) + + + + observe({ + x <- names(rv$map) + xd<-c("-",x) + # Can use character(0) to remove all choices + if (is.null(x)){ + x <- character(0) + xd<-x + } + + updateSelectInput(session, "columnidareainmap", choices = x, selected = head(x, 1)) + #updateSelectInput(session, "columnnameareainmap", choices = x, selected = head(x, 1)) + #updateSelectInput(session, "columnnamesuperareainmap", choices = xd, selected = head(xd, 1)) + + }) + + + rv <- reactiveValues( + columnidareainmap=NULL, columnnameareainmap=NULL, #columnnamesuperareainmap=NULL, + idpolyhighlighted = NULL, posinmapFilteredIdpolyhighlighted=NULL, colores=NULL, + minrisk=0, maxrisk=1, + vblePintar="Risk", textareareactive="NULL",messageCheckDataText_1="", messageCheckDataText_2="", messageCheckDataText_3="", + map=NULL,datosOriginal=NULL, + datoswithvaluesforeachidandtime=NULL, + datossatscan=NULL, + lastselectstage=NULL, + usedcovs=NULL, + usedarealcovs=NULL, + selectstage='stageuploaddata') + + + + + + # output$uploadmapmap <- renderPlot({ + # if (is.null(rv$map)) + # return(NULL) + # plot(rv$map) + # }) + + output$uploadmapmap <- renderPlot({ + if (!is.null(rv$map)) + plot(rv$map) + }) + + output$uploadmapsummary <- renderPrint({ + if (!is.null(rv$map)){ + print(summary(rv$map@data)) + } + }) + + output$uploaddatasummary <- renderPrint({ + if (!is.null(rv$datosOriginal)){ + print(summary(rv$datosOriginal)) + } + }) + + # output$uploadmaptable <- renderDataTable({ + # if (is.null(rv$map)) + # return(NULL) + # rv$map@data + # + # } , options = list(scrollX=TRUE, # แถบเลื่อนแนวแกน x + # pageLength = 5)) + # + + output$uploadmaptable <- renderDataTable({ + if (!is.null(rv$map)) + rv$map@data + + } , options = list(scrollX=TRUE, # แถบเลื่อนแนวแกน x + pageLength = 5)) + + output$uploaddatatable <- renderDataTable({ + if (is.null(rv$datosOriginal)) + return(NULL) + rv$datosOriginal + + } , options = list(scrollX=TRUE, # แถบเลื่อนแนวแกน x + pageLength = 5)) + + + + # Upload shapefile + observe({ + + shpdf <- input$filemap + if(is.null(shpdf)){ + return() + } + previouswd <- getwd() + uploaddirectory <- dirname(shpdf$datapath[1]) + setwd(uploaddirectory) + for(i in 1:nrow(shpdf)){ + file.rename(shpdf$datapath[i], shpdf$name[i]) + } + setwd(previouswd) + + #map <- readShapePoly(paste(uploaddirectory, shpdf$name[grep(pattern="*.shp", shpdf$name)], sep="/"), delete_null_obj=TRUE) + #reads the file that finishes with .shp using $ at the end: grep(pattern="*.shp$", shpdf$name) + map <- readOGR(paste(uploaddirectory, shpdf$name[grep(pattern="*.shp$", shpdf$name)], sep="/"), encoding = "UTF-8")#, delete_null_obj=TRUE) + map <- spTransform(map, CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")) + + rv$map<-map + + + + + }) + + # Upload data + observe({ + inFile <- input$file1 + if (is.null(inFile)) + return(invisible()) + rv$datosOriginal<-read.csv(inFile$datapath) + + }) + + + # ==================================== ปุ่ม preview map dis ==================================== + + #observeEvent(input$Preview_Map_Distribution | input$tabs == "Map_Distribution" , { + observeEvent(input$Preview_Map_Distribution , { + if (is.null(rv$datosOriginal)| is.null(rv$map)) + return(NULL) + + #print(input$tabs) + if(input$tabs == "Map_Distribution"){ + data <- rv$datosOriginal + + #updateSelectInput(session, "columnidareainmap", choices = x, selected = head(x, 1)) + updateSelectInput(session, "time_point_filter", choices = data[,input$columndateindata], selected = head(data[,input$columndateindata], 1)) + #min = min(data[,input$columndateindata]), max = max(data[,input$columndateindata]) ) + # print(min(data[,input$columndateindata])) + # print(max(data[,input$columndateindata])) + # print(range(data[,input$columndateindata])) + + updateSelectInput(session, "time_point_filter_cluster", choices = data[,input$columndateindata], selected = head(data[,input$columndateindata], 1)) + + } + + }) + + + + + + + + + # ==================================== ปุ่ม action input$nextpage ==================================== + #observeEvent(input$nextpage | input$tabs == "Analysis", { + observeEvent(input$nextpage , { + + if (is.null(rv$datosOriginal) | is.null(rv$map)) + return(NULL) + + + if(input$tabs == "Analysis"){ + data <- rv$datosOriginal + + #updateSliderInput(session, "time_point_filter_cluster", min = min(data[,input$columndateindata]), max = max(data[,input$columndateindata]) ) + + + + ######################### คำนวณ cluster ################################### + map <- rv$map + #data <- rv$datosOriginal + + + + # y (case) + data[,input$columncasesindata] <- as.numeric(data[,input$columncasesindata]) + + + ########################## --- คำนวน expected value ---- ######################### + + # # ของเก่า: ค่า E ที่ให้ user ใส่มาเอง + # data[,input$columnexpvalueindata] <- as.numeric(data[,input$columnexpvalueindata]) + + + + + if(input$Expected_Value_from_csv == "yes" ){ + if(input$columnexpvalueindata != "" ){ + print("Check: ...this csv have expected value...") + data['expected_value'] <- as.numeric(data[,input$columnexpvalueindata]) + + } + + }else if (input$Expected_Value_from_csv == "no" ){ + print("Check: ...this csv doesn't have expected value...") + + # คิด (sum(case) / (pop))*population + # sum case กับ pop ทั้งหมด เอามาหารกัน แล้วคูณด้วย pop ของจังหวัด,ปี นั้นๆ + sum_case <- sum(data[,input$columncasesindata]) + sum_pop <- sum(data[,input$columnpopindata]) + + divide_case_pop <- sum_case / sum_pop + + + expected_value <- data[,input$columnpopindata] * divide_case_pop + + + # Add a Column to a Data Frame + data['expected_value'] <- expected_value + + } + + + + # --------------------------- + + # area id (data$province) + data[,input$columnidareaindata] <- as.numeric(data[,input$columnidareaindata]) # id of province 1-77 + + # # year data$year + data[,input$columndateindata] <- as.numeric(data[,input$columndateindata]) # id of year 1-11 (?) + + # # data$province_year <- seq(1, 1064) # id of province-year interaction + data$province_year <- seq(1, nrow(data)) # id of year 1-11 (?) + + # # interaction id + province_int <- data[,input$columnidareaindata] + year_int <- data[,input$columndateindata] + + + + + if(input$shapefile_from_thailand == "yes" ){ + + # build adj matrix from shape file + tha_adj <- nb2mat( + poly2nb(map), + style = "B", + zero.policy = TRUE) + + # add path between Phuket and Pang nga (?) + tha_adj[38, 47] <- 1 + tha_adj[47, 38] <- 1 + + }else if (input$shapefile_from_thailand == "no" ){ + + # build adj matrix from shape file + tha_adj <- nb2mat( + poly2nb(map), + style = "B", + zero.policy = TRUE) + + } + + # อันใหม่เด้อ + # formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + # f(data$x1_id, x1, model = "iid") + + # f(data$x2_id, x2, model = "iid") + + # f(data$x3_id, x3, model = "iid") + + # f(data$x4_id, x4, model = "iid") + + # f(data$x5_id, x5, model = "iid") + + # f(data$x6_id, x6, model = "iid") + + # f(data$x7_id, x7, model = "iid") + + # f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + # f(data[,input$columndateindata], model = "rw1") + + # f(province_int, model = "iid") + + + #################### Cluter #################### + + + + formula_1_bym_rw1_Cluter <- data[,input$columncasesindata] ~ 1 + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model_Cluter <- inla( + formula_1_bym_rw1_Cluter, + family = "poisson", + data = data, + #E = data[,input$columnexpvalueindata], + E = data[, 'expected_value'], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + exceedance_prob <- sapply( + model_Cluter$marginals.fitted.values, + FUN = function(marg) { + 1 - inla.pmarginal(q = 1, marginal = marg) }) + + data[, "label"] <- exceedance_prob > 0.95 + data[, "label"] <- ifelse(exceedance_prob > 0.95, + "hotspot", "non-hotspot") + + rv$data <- data + + + rv$model_Cluter <- model_Cluter + + + # model2 <- rv$model + + + #################################################### + + + + #################### asso #################### + + x1 <- input$columncov1indata + x2 <- input$columncov2indata + x3 <- input$columncov3indata + x4 <- input$columncov4indata + x5 <- input$columncov5indata + x6 <- input$columncov6indata + x7 <- input$columncov7indata + + + + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + print("Check: ...all null...") + + + + + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + + print("Check: ...1 not null...") + x1 <- data[,input$columncov1indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + + rv$data <- data + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)) + ) -1 )*100 + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep="")) + + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + + #rv$association_wsf_df <- association_wsf_df + + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + rv$association_wsf_df <- association_wsf_df + + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + + print("Check: ...1,2 not null...") + x1 <- data[,input$columncov1indata] + x2 <- data[,input$columncov2indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + data$x2_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data$x2_id, x2, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)) + ) -1 )*100 + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_percent_increase", sep="")) + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + + # x2 + association_wsf_df[, paste( input$columncov2indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] + association_wsf_df[, paste( input$columncov2indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,6] + + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] > 0 + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x2_id`[,4] > 0 | model2$summary.random$`data|S|x2_id`[,6] < 0, "significant", "not significant") + + + rv$association_wsf_df <- association_wsf_df + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + + print("Check: ...1,2,3 not null...") + x1 <- data[,input$columncov1indata] + x2 <- data[,input$columncov2indata] + x3 <- data[,input$columncov3indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + data$x2_id <- data[,input$columnidareaindata] + data$x3_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data$x2_id, x2, model = "iid") + + f(data$x3_id, x3, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)), + c(exp(model2$summary.random$`data|S|x3_id`$mean)) + ) -1 )*100 + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_percent_increase", sep="")) + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + + # x2 + association_wsf_df[, paste( input$columncov2indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] + association_wsf_df[, paste( input$columncov2indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,6] + + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] > 0 + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x2_id`[,4] > 0 | model2$summary.random$`data|S|x2_id`[,6] < 0, "significant", "not significant") + + # x3 + association_wsf_df[, paste( input$columncov3indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] + association_wsf_df[, paste( input$columncov3indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,6] + + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] > 0 + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x3_id`[,4] > 0 | model2$summary.random$`data|S|x3_id`[,6] < 0, "significant", "not significant") + + + rv$association_wsf_df <- association_wsf_df + + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + + print("Check: ...1,2,3,4 not null...") + x1 <- data[,input$columncov1indata] + x2 <- data[,input$columncov2indata] + x3 <- data[,input$columncov3indata] + x4 <- data[,input$columncov4indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + data$x2_id <- data[,input$columnidareaindata] + data$x3_id <- data[,input$columnidareaindata] + data$x4_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data$x2_id, x2, model = "iid") + + f(data$x3_id, x3, model = "iid") + + f(data$x4_id, x4, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)), + c(exp(model2$summary.random$`data|S|x3_id`$mean)), + c(exp(model2$summary.random$`data|S|x4_id`$mean)) + ) -1 )*100 + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_percent_increase", sep="")) + + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + + # x2 + association_wsf_df[, paste( input$columncov2indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] + association_wsf_df[, paste( input$columncov2indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,6] + + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] > 0 + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x2_id`[,4] > 0 | model2$summary.random$`data|S|x2_id`[,6] < 0, "significant", "not significant") + + # x3 + association_wsf_df[, paste( input$columncov3indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] + association_wsf_df[, paste( input$columncov3indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,6] + + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] > 0 + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x3_id`[,4] > 0 | model2$summary.random$`data|S|x3_id`[,6] < 0, "significant", "not significant") + + # x4 + association_wsf_df[, paste( input$columncov4indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] + association_wsf_df[, paste( input$columncov4indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,6] + + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] > 0 + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x4_id`[,4] > 0 | model2$summary.random$`data|S|x4_id`[,6] < 0, "significant", "not significant") + + rv$association_wsf_df <- association_wsf_df + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + print("Check: ...1,2,3,4,5 not null...") + x1 <- data[,input$columncov1indata] + x2 <- data[,input$columncov2indata] + x3 <- data[,input$columncov3indata] + x4 <- data[,input$columncov4indata] + x5 <- data[,input$columncov5indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + data$x2_id <- data[,input$columnidareaindata] + data$x3_id <- data[,input$columnidareaindata] + data$x4_id <- data[,input$columnidareaindata] + data$x5_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data$x2_id, x2, model = "iid") + + f(data$x3_id, x3, model = "iid") + + f(data$x4_id, x4, model = "iid") + + f(data$x5_id, x5, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)), + c(exp(model2$summary.random$`data|S|x3_id`$mean)), + c(exp(model2$summary.random$`data|S|x4_id`$mean)), + c(exp(model2$summary.random$`data|S|x5_id`$mean)) + ) -1 )*100 + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_percent_increase", sep="")) + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + + # x2 + association_wsf_df[, paste( input$columncov2indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] + association_wsf_df[, paste( input$columncov2indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,6] + + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] > 0 + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x2_id`[,4] > 0 | model2$summary.random$`data|S|x2_id`[,6] < 0, "significant", "not significant") + + # x3 + association_wsf_df[, paste( input$columncov3indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] + association_wsf_df[, paste( input$columncov3indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,6] + + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] > 0 + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x3_id`[,4] > 0 | model2$summary.random$`data|S|x3_id`[,6] < 0, "significant", "not significant") + + # x4 + association_wsf_df[, paste( input$columncov4indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] + association_wsf_df[, paste( input$columncov4indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,6] + + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] > 0 + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x4_id`[,4] > 0 | model2$summary.random$`data|S|x4_id`[,6] < 0, "significant", "not significant") + + # x5 + association_wsf_df[, paste( input$columncov5indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x5_id`[,4] + association_wsf_df[, paste( input$columncov5indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x5_id`[,6] + + association_wsf_df[, paste( input$columncov5indata,"_significance", sep="")] <- model2$summary.random$`data|S|x5_id`[,4] > 0 + association_wsf_df[, paste( input$columncov5indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x5_id`[,4] > 0 | model2$summary.random$`data|S|x5_id`[,6] < 0, "significant", "not significant") + + rv$association_wsf_df <- association_wsf_df + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + print("Check: ...1,2,3,4,5,6 not null...") + x1 <- data[,input$columncov1indata] + x2 <- data[,input$columncov2indata] + x3 <- data[,input$columncov3indata] + x4 <- data[,input$columncov4indata] + x5 <- data[,input$columncov5indata] + x6 <- data[,input$columncov6indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + data$x2_id <- data[,input$columnidareaindata] + data$x3_id <- data[,input$columnidareaindata] + data$x4_id <- data[,input$columnidareaindata] + data$x5_id <- data[,input$columnidareaindata] + data$x6_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data$x2_id, x2, model = "iid") + + f(data$x3_id, x3, model = "iid") + + f(data$x4_id, x4, model = "iid") + + f(data$x5_id, x5, model = "iid") + + f(data$x6_id, x6, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)), + c(exp(model2$summary.random$`data|S|x3_id`$mean)), + c(exp(model2$summary.random$`data|S|x4_id`$mean)), + c(exp(model2$summary.random$`data|S|x5_id`$mean)), + c(exp(model2$summary.random$`data|S|x6_id`$mean)) + ) -1 )*100 + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_percent_increase", sep="")) + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + + # x2 + association_wsf_df[, paste( input$columncov2indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] + association_wsf_df[, paste( input$columncov2indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,6] + + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] > 0 + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x2_id`[,4] > 0 | model2$summary.random$`data|S|x2_id`[,6] < 0, "significant", "not significant") + + # x3 + association_wsf_df[, paste( input$columncov3indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] + association_wsf_df[, paste( input$columncov3indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,6] + + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] > 0 + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x3_id`[,4] > 0 | model2$summary.random$`data|S|x3_id`[,6] < 0, "significant", "not significant") + + # x4 + association_wsf_df[, paste( input$columncov4indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] + association_wsf_df[, paste( input$columncov4indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,6] + + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] > 0 + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x4_id`[,4] > 0 | model2$summary.random$`data|S|x4_id`[,6] < 0, "significant", "not significant") + + # x5 + association_wsf_df[, paste( input$columncov5indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x5_id`[,4] + association_wsf_df[, paste( input$columncov5indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x5_id`[,6] + + association_wsf_df[, paste( input$columncov5indata,"_significance", sep="")] <- model2$summary.random$`data|S|x5_id`[,4] > 0 + association_wsf_df[, paste( input$columncov5indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x5_id`[,4] > 0 | model2$summary.random$`data|S|x5_id`[,6] < 0, "significant", "not significant") + + # x6 + association_wsf_df[, paste( input$columncov6indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x6_id`[,4] + association_wsf_df[, paste( input$columncov6indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x6_id`[,6] + + association_wsf_df[, paste( input$columncov6indata,"_significance", sep="")] <- model2$summary.random$`data|S|x6_id`[,4] > 0 + association_wsf_df[, paste( input$columncov6indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x6_id`[,4] > 0 | model2$summary.random$`data|S|x6_id`[,6] < 0, "significant", "not significant") + + rv$association_wsf_df <- association_wsf_df + + + + }else { + print("Check: ...all not null...") + x1 <- data[,input$columncov1indata] + x2 <- data[,input$columncov2indata] + x3 <- data[,input$columncov3indata] + x4 <- data[,input$columncov4indata] + x5 <- data[,input$columncov5indata] + x6 <- data[,input$columncov6indata] + x7 <- data[,input$columncov7indata] + + + + # id for association each province + data$x1_id <- data[,input$columnidareaindata] + data$x2_id <- data[,input$columnidareaindata] + data$x3_id <- data[,input$columnidareaindata] + data$x4_id <- data[,input$columnidareaindata] + data$x5_id <- data[,input$columnidareaindata] + data$x6_id <- data[,input$columnidareaindata] + data$x7_id <- data[,input$columnidareaindata] + + + formula_1_bym_rw1 <- data[,input$columncasesindata] ~ 1 + + f(data$x1_id, x1, model = "iid") + + f(data$x2_id, x2, model = "iid") + + f(data$x3_id, x3, model = "iid") + + f(data$x4_id, x4, model = "iid") + + f(data$x5_id, x5, model = "iid") + + f(data$x6_id, x6, model = "iid") + + f(data$x7_id, x7, model = "iid") + + f(data[,input$columnidareaindata], model = "bym", graph = tha_adj) + + f(data[,input$columndateindata], model = "rw1") + + f(province_int, model = "iid") + + # computing part + model <- inla( + formula_1_bym_rw1, + family = "poisson", + data = data, + E = data[,input$columnpopindata], + control.predictor = list(compute = TRUE), + control.compute = list( + dic = TRUE, + waic = TRUE, + cpo = TRUE, + return.marginals.predictor = TRUE)) + + + + rv$model <- model + + + model2 <- rv$model + + association_df <- (data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)), + c(exp(model2$summary.random$`data|S|x3_id`$mean)), + c(exp(model2$summary.random$`data|S|x4_id`$mean)), + c(exp(model2$summary.random$`data|S|x5_id`$mean)), + c(exp(model2$summary.random$`data|S|x6_id`$mean)), + c(exp(model2$summary.random$`data|S|x7_id`$mean)) + ) -1 )*100 + + + + colnames(association_df) <- c(paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_percent_increase", sep="")) + + + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + + # rv$association_wsf_df <- association_wsf_df + + ad <- names(association_df) + updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + # ค่า sig + # x1 + association_wsf_df[, paste( input$columncov1indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] + association_wsf_df[, paste( input$columncov1indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x1_id`[,6] + + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- model2$summary.random$`data|S|x1_id`[,4] > 0 + association_wsf_df[, paste( input$columncov1indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x1_id`[,4] > 0 | model2$summary.random$`data|S|x1_id`[,6] < 0, "significant", "not significant") + + + # x2 + association_wsf_df[, paste( input$columncov2indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] + association_wsf_df[, paste( input$columncov2indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x2_id`[,6] + + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- model2$summary.random$`data|S|x2_id`[,4] > 0 + association_wsf_df[, paste( input$columncov2indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x2_id`[,4] > 0 | model2$summary.random$`data|S|x2_id`[,6] < 0, "significant", "not significant") + + # x3 + association_wsf_df[, paste( input$columncov3indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] + association_wsf_df[, paste( input$columncov3indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x3_id`[,6] + + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- model2$summary.random$`data|S|x3_id`[,4] > 0 + association_wsf_df[, paste( input$columncov3indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x3_id`[,4] > 0 | model2$summary.random$`data|S|x3_id`[,6] < 0, "significant", "not significant") + + # x4 + association_wsf_df[, paste( input$columncov4indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] + association_wsf_df[, paste( input$columncov4indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x4_id`[,6] + + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- model2$summary.random$`data|S|x4_id`[,4] > 0 + association_wsf_df[, paste( input$columncov4indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x4_id`[,4] > 0 | model2$summary.random$`data|S|x4_id`[,6] < 0, "significant", "not significant") + + # x5 + association_wsf_df[, paste( input$columncov5indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x5_id`[,4] + association_wsf_df[, paste( input$columncov5indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x5_id`[,6] + + association_wsf_df[, paste( input$columncov5indata,"_significance", sep="")] <- model2$summary.random$`data|S|x5_id`[,4] > 0 + association_wsf_df[, paste( input$columncov5indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x5_id`[,4] > 0 | model2$summary.random$`data|S|x5_id`[,6] < 0, "significant", "not significant") + + # x6 + association_wsf_df[, paste( input$columncov6indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x6_id`[,4] + association_wsf_df[, paste( input$columncov6indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x6_id`[,6] + + association_wsf_df[, paste( input$columncov6indata,"_significance", sep="")] <- model2$summary.random$`data|S|x6_id`[,4] > 0 + association_wsf_df[, paste( input$columncov6indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x6_id`[,4] > 0 | model2$summary.random$`data|S|x6_id`[,6] < 0, "significant", "not significant") + + # x7 + association_wsf_df[, paste( input$columncov7indata,"_lowerbound", sep="")] <- model2$summary.random$`data|S|x7_id`[,4] + association_wsf_df[, paste( input$columncov7indata,"_upperbound", sep="")] <- model2$summary.random$`data|S|x7_id`[,6] + + association_wsf_df[, paste( input$columncov7indata,"_significance", sep="")] <- model2$summary.random$`data|S|x7_id`[,4] > 0 + association_wsf_df[, paste( input$columncov7indata,"_significance", sep="")] <- ifelse(model2$summary.random$`data|S|x7_id`[,4] > 0 | model2$summary.random$`data|S|x7_id`[,6] < 0, "significant", "not significant") + + + rv$association_wsf_df <- association_wsf_df + + + + + } # จบ else + + + #################################################### + + # computing part + # model <- inla( + # # formula_2_bym_rw1, + # formula_1_bym_rw1, + # family = "poisson", + # data = data, + # E = data[,input$columnexpvalueindata], + # control.predictor = list(compute = TRUE), + # control.compute = list( + # dic = TRUE, + # waic = TRUE, + # cpo = TRUE, + # return.marginals.predictor = TRUE)) + + + + + # exceedance_prob <- sapply( + # model$marginals.fitted.values, + # FUN = function(marg) { + # 1 - inla.pmarginal(q = 1, marginal = marg) }) + # + # data[, "label"] <- exceedance_prob > 0.95 + # data[, "label"] <- ifelse(exceedance_prob > 0.95, + # "hotspot", "non-hotspot") + # + # rv$data <- data + + + ######################### คำนวณ asso risk fac ################################### + + # rv$model <- model + # + # + # model2 <- rv$model + # + # association_df <- (data.frame( + # c(exp(model2$summary.random$`data|S|x1_id`$mean)), + # c(exp(model2$summary.random$`data|S|x2_id`$mean)), + # c(exp(model2$summary.random$`data|S|x3_id`$mean)), + # c(exp(model2$summary.random$`data|S|x4_id`$mean)), + # c(exp(model2$summary.random$`data|S|x5_id`$mean)), + # c(exp(model2$summary.random$`data|S|x6_id`$mean)), + # c(exp(model2$summary.random$`data|S|x7_id`$mean)) + # ) -1 )*100 + # + # colnames(association_df) <- c(paste("percent_increase_",input$columncov1indata, sep=""), + # paste("percent_increase_",input$columncov2indata, sep=""), + # paste("percent_increase_",input$columncov3indata, sep=""), + # paste("percent_increase_",input$columncov4indata, sep=""), + # paste("percent_increase_",input$columncov5indata, sep=""), + # paste("percent_increase_",input$columncov6indata, sep=""), + # paste("percent_increase_",input$columncov7indata, sep="")) + + + # ========================= ที่ทำcbind ====================== + + # association_wsf <- cbind(map, association_df) + # + # association_wsf_df <- data.frame(association_wsf) + # + # + # rv$association_wsf_df <- association_wsf_df + + # ============================================================== + + + # ad <- names(association_df) + # updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + } + }) + + # ===================================================== + + + + + # ==================================== map_distribution ==================================== + output$map_distribution <- renderLeaflet({ + + if (is.null(rv$datosOriginal)| is.null(rv$map)) + return(NULL) + + print("Plot: ...map distribution...") + + map <- rv$map + data <- rv$datosOriginal + + + data <- data %>% + filter( + data[,input$columndateindata] %in% input$time_point_filter + + ) + + + + #datafiltered <- data[which(data[,input$columndateindata] == input$time_point_filter), ] + datafiltered <- data + ordercounties <- match(map@data[, input$columnidareainmap], datafiltered[, input$columnidareanamedata]) + map@data <- datafiltered[ordercounties, ] + + # Create leaflet + l <- leaflet(map) %>% addTiles() + pal <- colorNumeric(palette = input$color, domain = map@data[, input$columncasesindata]) + labels <- sprintf(" %s
%s : %s ", + map@data[, input$columnidareanamedata] , input$columncasesindata, map@data[, input$columncasesindata] + ) %>% + lapply(htmltools::HTML) + + l %>% + addProviderTiles(providers$OpenStreetMap.Mapnik, group = "Open Street Map") %>% + addProviderTiles(providers$Esri.WorldImagery, group = "ESRI World Imagery") %>% + addProviderTiles(providers$Esri.NatGeoWorldMap, group = "ESRI National Geographic World Map") %>% + addProviderTiles(providers$CartoDB.Positron, group = "CartoDB Positron") %>% + #addProviderTiles(providers$Stamen.Watercolor, group = "Stamen Watercolor") %>% + #addProviderTiles(providers$Stamen.Toner, group = "Stamen Toner") %>% + + addPolygons( + color = "grey", weight = 1, + fillColor = ~ pal(map@data[, input$columncasesindata]), fillOpacity = 0.7, + highlightOptions = highlightOptions(weight = 4), + label = labels, + labelOptions = labelOptions( + style = list( + "font-weight" = "normal", + padding = "3px 8px" + ), + textsize = "15px", direction = "auto" + ) + ) %>% + addLegend( + pal = pal, values = ~map@data[, input$columncasesindata], opacity = 0.7, + title = input$columncasesindata, position = "bottomright" + ) %>% + addLayersControl(baseGroups = c("Open Street Map", "ESRI World Imagery", "ESRI National Geographic World Map", "CartoDB Positron" + #"Stamen Watercolor", "Stamen Toner" + ), + position = c("topleft"), + options = layersControlOptions(collapsed = TRUE) + ) %>% + addFullscreenControl() + + + + }) + + + # ==================================== cluster_dec ver ลองplot ==================================== + + output$map_cluster <- #renderPrint({ + renderLeaflet({ + + if (is.null(rv$datosOriginal) | is.null(rv$map)) + return(NULL) + + print("Plot: ...map cluster...") + #print(rv$data) # ได้แน้วออกเป็นlabelเรย + + data2 <- rv$data + map <- rv$map + + # plot + data2 <- data2 %>% + filter( + data2[,input$columndateindata] %in% input$time_point_filter_cluster + + ) + + + datafiltered <- data2 + ordercounties <- match(map@data[, input$columnidareainmap], datafiltered[, input$columnidareanamedata]) + map@data <- datafiltered[ordercounties, ] + + # print(map@data[, "label"]) + + # Create leaflet c("red", "blue") + l <- leaflet(map) %>% addTiles() + pal <- colorFactor(palette = input$color_cluster, domain = map@data[, "label"], + levels = c("hotspot", "non-hotspot")) + labels <- sprintf(" %s
label : %s ", + map@data[, input$columnidareanamedata] , map@data[, "label"] + ) %>% + lapply(htmltools::HTML) + + l %>% + addProviderTiles(providers$OpenStreetMap.Mapnik, group = "Open Street Map") %>% + addProviderTiles(providers$Esri.WorldImagery, group = "ESRI World Imagery") %>% + addProviderTiles(providers$Esri.NatGeoWorldMap, group = "ESRI National Geographic World Map") %>% + addProviderTiles(providers$CartoDB.Positron, group = "CartoDB Positron") %>% + #addProviderTiles(providers$Stamen.Watercolor, group = "Stamen Watercolor") %>% + #addProviderTiles(providers$Stamen.Toner, group = "Stamen Toner") %>% + + addPolygons( + color = "grey", weight = 1, + fillColor = ~ pal(map@data[, "label"]), fillOpacity = 0.7, + highlightOptions = highlightOptions(weight = 4), + label = labels, + labelOptions = labelOptions( + style = list( + "font-weight" = "normal", + padding = "3px 8px" + ), + textsize = "15px", direction = "auto" + ) + ) %>% + addLegend( + pal = pal, values = ~map@data[, "label"] , opacity = 0.7, + title = "label", position = "bottomright" + )%>% + addLayersControl(baseGroups = c("Open Street Map", "ESRI World Imagery", "ESRI National Geographic World Map", "CartoDB Positron" + #"Stamen Watercolor", "Stamen Toner" + ), + position = c("topleft"), + options = layersControlOptions(collapsed = TRUE) + )%>% + addFullscreenControl() + + #labels = c("hotspot", "non-hotspot") + + + }) + + + + # ==================================== risk_fac ==================================== + + output$risk_fac_text <- renderPrint({ + #rv$model + model2 <- rv$model + map <- rv$map + + # model2 # ออกมาเยอะ + # model2$summary.random # ออกมาเยอะจัด ๆ + # model2$summary.random[, data$x1_id$mean] # Error in $: object of type 'closure' is not subsettable + + # model2$summary.random[, data2$x1_id$mean] + + # model2$summary.random$x1_id$mean # ขึ้น NULL + # model2$summary.random$x1_id # ขึ้น NULL + + # model2$summary.random$`data|S|x1_id` # ขึ้นแล้วจ้า + + # model2$summary.random$`data|S|x1_id`$mean # ได้สักที + + association_df <- data.frame( + c(exp(model2$summary.random$`data|S|x1_id`$mean)), + c(exp(model2$summary.random$`data|S|x2_id`$mean)), + c(exp(model2$summary.random$`data|S|x3_id`$mean)), + c(exp(model2$summary.random$`data|S|x4_id`$mean)), + c(exp(model2$summary.random$`data|S|x5_id`$mean)), + c(exp(model2$summary.random$`data|S|x6_id`$mean)), + c(exp(model2$summary.random$`data|S|x7_id`$mean)) + ) + + + + + colnames(association_df) <- c('exp_x1', + 'exp_x2', + 'exp_x3', + 'exp_x4', + 'exp_x5', + 'exp_x6', + 'exp_x7' + ) + + + + association_wsf <- cbind(map, association_df) + + association_wsf_df <- data.frame(association_wsf) + + # association_wsf_df[, "exp_x1"] # ออกมาแน้ว + + # ad <- names(association_df) + # updateSelectInput(session, "risk_factor_filter", choices = ad, selected = head(ad, 1)) + + + }) + + + + output$risk_fac_text2 <- renderPrint({ + + # association_wsf_df <- rv$association_wsf_df + # + # # association_wsf_df[, "exp_x1"] # ค่าออกนะ + # + # # association_wsf_df[, input$columnidareanamedata] # error จ้า + # + # association_wsf_df[, input$columnidareainmap] # ค่าออกนะ + + map <- rv$map + + association_wsf_df <- rv$association_wsf_df + + datafiltered <- association_wsf_df + ordercounties <- match(map@data[, input$columnidareainmap], datafiltered[, input$columnidareainmap]) + map@data <- datafiltered[ordercounties, ] + + map@data + + + + }) + + + output$map_risk_fac <- renderLeaflet({ + + if (is.null(rv$datosOriginal) | is.null(rv$map)) + return(NULL) + + print("Plot: ...map risk factor...") + + map <- rv$map + + association_wsf_df <- rv$association_wsf_df + + datafiltered <- association_wsf_df + ordercounties <- match(map@data[, input$columnidareainmap], datafiltered[, input$columnidareainmap]) + map@data <- datafiltered[ordercounties, ] + + + if (input$risk_factor_filter == paste(input$columncov1indata,"_percent_increase", sep="")){ + sig_col <- map@data[, paste(input$columncov1indata,"_significance", sep="")] + + } else if (input$risk_factor_filter == paste(input$columncov2indata,"_percent_increase", sep="")) { + sig_col <- map@data[, paste(input$columncov2indata,"_significance", sep="")] + + } else if (input$risk_factor_filter == paste(input$columncov3indata,"_percent_increase", sep="")) { + sig_col <- map@data[, paste(input$columncov3indata,"_significance", sep="")] + + } else if (input$risk_factor_filter == paste(input$columncov4indata,"_percent_increase", sep="")) { + sig_col <- map@data[, paste(input$columncov4indata,"_significance", sep="")] + + } else if (input$risk_factor_filter == paste(input$columncov5indata,"_percent_increase", sep="")) { + sig_col <- map@data[, paste(input$columncov5indata,"_significance", sep="")] + + } else if (input$risk_factor_filter == paste(input$columncov6indata,"_percent_increase", sep="")) { + sig_col <- map@data[, paste(input$columncov6indata,"_significance", sep="")] + + } else if (input$risk_factor_filter == paste(input$columncov7indata,"_percent_increase",sep="")) { + sig_col <- map@data[, paste(input$columncov7indata,"_significance", sep="")] + + } + + + # Create leaflet + l <- leaflet(map) %>% addTiles() + pal <- colorNumeric(palette = input$color_asso, domain = map@data[, input$risk_factor_filter]) + labels <- sprintf(" %s
%s : %s
Significance: %s", + map@data[, input$columnidareainmap] , input$risk_factor_filter, map@data[, input$risk_factor_filter] , sig_col #paste(input$columncov1indata,"_significance", sep="") + ) %>% + lapply(htmltools::HTML) + + l %>% + addProviderTiles(providers$OpenStreetMap.Mapnik, group = "Open Street Map") %>% + addProviderTiles(providers$Esri.WorldImagery, group = "ESRI World Imagery") %>% + addProviderTiles(providers$Esri.NatGeoWorldMap, group = "ESRI National Geographic World Map") %>% + addProviderTiles(providers$CartoDB.Positron, group = "CartoDB Positron") %>% + #addProviderTiles(providers$Stamen.Watercolor, group = "Stamen Watercolor") %>% + #addProviderTiles(providers$Stamen.Toner, group = "Stamen Toner") %>% + + addPolygons( + color = "grey", weight = 1, + fillColor = ~ pal(map@data[, input$risk_factor_filter]), fillOpacity = 0.7, + highlightOptions = highlightOptions(weight = 4), + label = labels, + labelOptions = labelOptions( + style = list( + "font-weight" = "normal", + padding = "3px 8px" + ), + textsize = "15px", direction = "auto" + ) + ) %>% + addLegend( + pal = pal, values = ~map@data[, input$risk_factor_filter], opacity = 0.7, + title = input$risk_factor_filter, position = "bottomright" + ) %>% + addLayersControl(baseGroups = c("Open Street Map", "ESRI World Imagery", "ESRI National Geographic World Map", "CartoDB Positron" + #"Stamen Watercolor", "Stamen Toner" + ), + position = c("topleft"), + options = layersControlOptions(collapsed = TRUE) + )%>% + addFullscreenControl() + + + }) + + + # ==================================== ปุุ่ม downloadData ==================================== + + dataresult_cluster <- reactive({ + # data <- rv$data + + if(input$Expected_Value_from_csv == "yes" ){ + if(input$columnexpvalueindata != "" ){ + print("download data: ...this csv have expected value...") + + # Remove Columns in List + data <- rv$data[,!names(rv$data) %in% c("province_year", "x1_id", "x2_id", "x3_id", "x4_id", "x5_id", "x6_id", "x7_id","expected_value")] + + + } + + }else if (input$Expected_Value_from_csv == "no" ){ + print("download data: ...this csv doesn't have expected value...") + + # Remove Columns in List + data <- rv$data[,!names(rv$data) %in% c("province_year", "x1_id", "x2_id", "x3_id", "x4_id", "x5_id", "x6_id", "x7_id")] + + + } + + }) + + + + output$downloadData_cluster <- downloadHandler( + filename = function() { + paste("result-cluster-detection-", Sys.Date(), ".csv", sep="") + }, + content = function(file) { + write.csv(dataresult_cluster(), file) + } + ) + + + dataresult_asso_risk <- reactive({ + + x1 <- input$columncov1indata + x2 <- input$columncov2indata + x3 <- input$columncov3indata + x4 <- input$columncov4indata + x5 <- input$columncov5indata + x6 <- input$columncov6indata + x7 <- input$columncov7indata + + + asso_select_column <- paste(input$asso_select_column, collapse = ",") + + + + if (asso_select_column != ""){ + + if (asso_select_column == "lowerbound,upperbound,significance"){ + + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + paste(input$columncov5indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + paste(input$columncov6indata,"_upperbound", sep=""), + paste(input$columncov6indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + paste(input$columncov6indata,"_upperbound", sep=""), + paste(input$columncov6indata,"_significance", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_lowerbound", sep=""), + paste(input$columncov7indata,"_upperbound", sep=""), + paste(input$columncov7indata,"_significance", sep="")) + + } + + } # จบ if (asso_select_column == "lowerbound,upperbound,significance"){ + else if (asso_select_column == "lowerbound,upperbound"){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_upperbound", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + paste(input$columncov6indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + paste(input$columncov6indata,"_upperbound", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_lowerbound", sep=""), + paste(input$columncov7indata,"_upperbound", sep="")) + + } + + + }else if (asso_select_column == "upperbound,significance"){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + paste(input$columncov5indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_upperbound", sep=""), + paste(input$columncov6indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_upperbound", sep=""), + paste(input$columncov6indata,"_significance", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_upperbound", sep=""), + paste(input$columncov7indata,"_significance", sep="")) + + } + + }else if (asso_select_column == "lowerbound,significance"){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + paste(input$columncov6indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + paste(input$columncov6indata,"_significance", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_lowerbound", sep=""), + paste(input$columncov7indata,"_significance", sep="")) + + } + + }else if (asso_select_column == "lowerbound"){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_lowerbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_lowerbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_lowerbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_lowerbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_lowerbound", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_lowerbound", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_lowerbound", sep="")) + + } + + + }else if (asso_select_column == "upperbound"){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_upperbound", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_upperbound", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_upperbound", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_upperbound", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_upperbound", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_upperbound", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_upperbound", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_upperbound", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_upperbound", sep="")) + + } + + + }else if (asso_select_column == "significance"){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_significance", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_significance", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + paste(input$columncov1indata,"_significance", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + paste(input$columncov2indata,"_significance", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + paste(input$columncov3indata,"_significance", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + paste(input$columncov4indata,"_significance", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + paste(input$columncov5indata,"_significance", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + paste(input$columncov6indata,"_significance", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep=""), + paste(input$columncov7indata,"_significance", sep="")) + + } + } + + + + } # จบ if (asso_select_column != ""){ + else if (asso_select_column == ""){ + if(x1 == ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ){ + + # print("all null") + + }else if (x1 != ""& x2== ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep="")) + + + }else if (x1 != ""& x2!= ""& x3== ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4== ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5== ""& x6== "" & x7== "" ) { + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep="")) + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6== "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7== "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep="")) + + + + }else if (x1 != ""& x2!= ""& x3!= ""& x4!= ""& x5!= ""& x6!= "" & x7!= "" ) { + + col_order <- c(input$columnidareainmap, + paste(input$columncov1indata,"_percent_increase", sep=""), + + paste(input$columncov2indata,"_percent_increase", sep=""), + + paste(input$columncov3indata,"_percent_increase", sep=""), + + paste(input$columncov4indata,"_percent_increase", sep=""), + + paste(input$columncov5indata,"_percent_increase", sep=""), + + paste(input$columncov6indata,"_percent_increase", sep=""), + + paste(input$columncov7indata,"_percent_increase", sep="")) + + } + + + + } # จบ else if (is.null(asso_select_column)){ + + + + df2 <- rv$association_wsf_df[,col_order] + + + + }) + + + + output$downloadData_asso_risk <- downloadHandler( + filename = function() { + paste("result-association-risk-factor-", Sys.Date(), ".csv", sep="") + }, + content = function(file) { + write.csv(dataresult_asso_risk(), file) + } + ) + + + # ---------------------------- portable App ------------------------------ + + + + # session$onSessionEnded(function() { + # stopApp() + # }) + + + # ------------------------------------------------------------------------ + +} # end shinyApp + + +##------------------------------Run Shiny App--------------------------------## + +#shinyApp(ui = ui, server = server) + diff --git a/inst/STEHealthApp/shiny/ui.R b/inst/STEHealthApp/shiny/ui.R new file mode 100644 index 0000000..a6d3064 --- /dev/null +++ b/inst/STEHealthApp/shiny/ui.R @@ -0,0 +1,849 @@ +# ==================================== Check packages ==================================== + +list.of.packages <- c("shiny", "shinydashboard", "shinyjs", "shinyBS" , "leaflet" , + "dplyr", "ggplot2" ,"RColorBrewer" , "rgdal" ,"shinyWidgets", + "shinydashboardPlus","spdep", "leaflet.extras", "bsplus" ,"remotes") +new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])] +if(length(new.packages)) install.packages(new.packages) + + +if(!require(INLA)){ + # ต้องใช้ R 4.2.2 ถึงจะลงได้ ลองใช้ 4.3.1 แล้วลงไม่ได้ + install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE) + library(INLA) +} + + +if(!require(capture)){ + remotes::install_github("dreamRs/capture") + library(capture) +} + + +# ==================================== import packages ==================================== + +library(shiny) +library(shinydashboard) +library(shinyjs) +library(shinyBS) +library(leaflet) +library(dplyr) +library(ggplot2) +library(RColorBrewer) +library(rgdal) +library(shinyWidgets) +library(shinydashboardPlus) + +library(INLA) +inla.setOption(scale.model.default = TRUE) +library(spdep) # อันนี้ใช้ nb2mat + +library(capture) # ลงโดยใช้ remotes::install_github("dreamRs/capture") +library(leaflet.extras) +library(bsplus) + +# install.packages("sf") +# ถ้าลง sf ไม่ได้ให้พิมพ์คำสั่งด้านล่างนี้ก่อน +# options("install.lock"= FALSE) + + +# By default the file size limit is 5MB. Here limit is 70MB. +options(shiny.maxRequestSize = 70*1024^2) + +# options(scipen=999) + + +# ==================================== header ========================================== + + +header <- dashboardHeader(title = 'STEHealth', + + # tags$li(class = "dropdown", + # tags$div( + # + # )), + dropdownMenuOutput("messageMenu")) + +header$children[[2]]$children <- tags$img(src='STEHealth_logo1.png',width='180', style = "margin-left: -10px; ") + + +# ==================================== menuItem ==================================== + +sidebar <- dashboardSidebar( + sidebarMenu(id="tabs", + menuItem(HTML(" Home"), tabName = "Home", icon = icon("house")), + menuItem(HTML(" Upload Data"), tabName = "Upload_data", icon = icon("folder-open")), + menuItem(HTML(" Map Distribution"), tabName = "Map_Distribution", icon = icon("map")), + menuItem(HTML(" Spatiotemporal
   Epidemiology Analysis"), tabName="Analysis", icon=icon("globe")), + menuItem(HTML(" About Application"), tabName = "About", icon = icon("file")), + menuItem(HTML(" Manual"), tabName = "Manual", icon = icon("book")), + menuItem(HTML(" Help"), tabName = "Help", icon=icon("question")), + menuItem(HTML(" Releases"), tabName = "Releases", icon=icon("tasks")) + + ) +) + + +body <- dashboardBody( + tags$script("document.title = 'STEHealth | Spatiotemporal Epidemiological Analysis'"), + tags$head(tags$link(rel="icon", + href="STEHealth_logo_0.ico") + ), + + tags$head( + tags$meta(charset="utf-8"), + tags$link(rel = "stylesheet", type = "text/css", href = "style.css"), # import css file + tags$script(src="js/index.js") # เป็นตัวช่วยในการลิงก์ tag a ไปยัง tap อื่น ๆ + + + ), + + # font + HTML(""), + + #HTML(''), + + + fluidRow( + tabItems( + # ==================================== Home ==================================== + + tabItem(tabName = "Home", + + HTML(' +

+
+
+ STEHealth_logo +

+ Spatiotemporal Epidemiological Analysis +

+

+ This is an application for analyzing space-time pattern and + association with risk factors of suicide and other health outcomes, + which allows users to import their own data, analyze, and visualize.

+ +
+ + ← Get Started + + + + + How to use? + + +
+
+ +
+ homepage + +
+ +
+
+ ') + + + ),# tabItem 1 : tabName = "Home" + + + # ==================================== Upload_data ==================================== + tabItem(tabName = "Upload_data", + + HTML("
+

Upload Data

+
"), + # fluidRow(column(3, div(class = 'heading_container', HTML("

Upload Data

") )), + # column(2, offset=6, actionButton("Preview_Map_Distribution", + # strong("Preview Map Distribution"), + # onclick = "$('li:eq(7) a').tab('show');", + # class = 'btn-primary', + # style='color: #FFFFFF; margin-top: 30px;' + # )) + # + # ), + + div(style = "margin-bottom: 30px;"), + + HTML("

Input Data

"), + + sidebarLayout( + + sidebarPanel( + style = "height: 80vh; overflow-y: auto;", + + + #width = 8, + tags$style(".well {background-color:#FFFFFF;}"), + #div(style = "background-color: #FFFFFF;" ), + #HTML("

Input Data

"), + #HTML("

Upload map (shapefile)

"), + + + # ==================================== Upload map (shapefile) ==================================== + # ปุ่ม ? แต่ติดปัญหาตรงที่มันไม่บรรทัดเดียวกัน แม้จะใส่ inline-block แล้ว + div(style="display: inline-block;", + HTML('

1. + Upload shapefile

+ '), + + # เลยต้องแก้แบบนี้แทน + div(style = "margin-left: 280px; margin-top: -45px;", + bsButton("question_shapefile", label = "", icon = icon("question"), style = "Question"), + + bsPopover(id = "question_shapefile", title = "Shapefile", + content = paste0(strong("What is a shapefile? "),br(), + "A shapefile is a simple, nontopological format for storing the geometric location and attribute information of geographic features. ", + a("(5)", + href = "https://desktop.arcgis.com/en/arcmap/latest/manage-data/shapefiles/what-is-a-shapefile.htm", + target="_blank"), + + br(),br(), + strong("Examples of shapefiles"),br(), + "This examples shapefiles include shp, dbf, shx, prj. ", + a("click here to downloads shapefiles", + href = "https://drive.google.com/drive/folders/1vheBturgr3gclBq7kqp5dWouPf_C0VbQ?usp=share_link", + target="_blank") + ), + placement = "right", + trigger = "click", + options = list(container = "body") + )) + ), + + hr(), + #width = 7, + HTML("Upload 4 shapefile at once: shp, dbf, shx and prj."), + fileInput("filemap", "", accept=c('.shp','.dbf','.sbn','.sbx','.shx',".prj"), multiple=TRUE), + + helpText("Select column area name in the map."), + fluidRow(column(12, selectInput("columnidareainmap", label = "area name", choices = c(""), selected = "")%>% + shinyInput_label_embed( + icon("info") %>% + bs_embed_tooltip(title = '"area name" in the shapefile must be matched to "area name" in the csv file') + ) + ), + #column(6, selectInput("columnnameareainmap", label = "area name", choices = c(""), selected = "")) + ), + + + HTML("
"), + + radioButtons("shapefile_from_thailand", "Are these shapefiles from Thailand and do they include all 77 provinces, representing provincial boundaries (Level 1)? ", inline=TRUE, c("Yes" = "yes", "No" = "no"), selected="no"), + + + + # ==================================== Upload data (.csv file) ==================================== + # ปุ่ม ? แต่ติดปัญหาตรงที่มันไม่บรรทัดเดียวกัน แม้จะใส่ inline-block แล้ว + div(style="display: inline-block;", + HTML('

2. + Upload csv file

'), + + # เลยต้องแก้แบบนี้แทน + div(style = "margin-left: 240px; margin-top: -45px;", + bsButton("question_csvfile", label = "", icon = icon("question"), style = "Question"), + + bsPopover(id = "question_csvfile", title = "csv file", + content = paste0(strong("The csv file "),br(), + ".csv file needs to have columns: ", + strong("