Wip, using now the R6 class CitizenAir in the webapp

citizenair/DESCRIPTION

@@ -9,4 +9,19 @@ Authors@R: c(
 Description: Utilities for the Citizen Air application. 
 License: CC BY-SA 4.0
 RoxygenNote: 6.0.1
-Imports: readxl, cellranger, data.table, fasttime, rmarkdown, tools, utils, sensorweb4R, httr, methods, sp, lubridate, R6
+Imports: 
+    tools, 
+    utils, 
+    methods, 
+    R6, 
+    data.table, 
+    sp, 
+    readxl, 
+    cellranger, 
+    fasttime, 
+    rmarkdown, 
+    sensorweb4R, 
+    httr, 
+    lubridate, 
+    rgeos
+Suggests: BelgiumMaps.StatBel

citizenair/NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.frame,citizenair_userdata)
+S3method(error_message,default)
 export(CitizenAir)
+export(error_message)
 export(read_citizenair)
 export(read_stations)
 export(run_app)
@@ -21,6 +23,7 @@ importFrom(httr,content)
 importFrom(lubridate,as.interval)
 importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)
+importFrom(rgeos,gIntersects)
 importFrom(rmarkdown,run)
 importFrom(sensorweb4R,Station)
 importFrom(sensorweb4R,as.Endpoint)

citizenair/R/appdata.R

@@ -25,11 +25,13 @@ citizenair_userdata_empty <- function(){
 #' @field endpoint object of class \code{Endpoint} as returned by \code{as.Endpoint}
 #' @field stations object of class \code{citizenair_stations} as returned by \code{\link{read_stations}}
 #' @field data object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}
+#' @field closest_station a character string with the id of the closest station.
 #' @format The CitizenAir object is an R6Class
 #' @section Methods:
 #' \describe{
 #'   \item{\code{fetch_timeseries(id = "123", time_span)}}{Get timeseries for Station with \code{id} and a certain time_span The argument \code{timespan.} Passed on to \code{sensorweb4R::getData}}
 #'   \item{\code{getStations()}}{Get a SpatialPointsDataFrame of all stations}
+#'   \item{TODO}{TODO}
 #' }
 #' @export
 #' @examples
@@ -37,12 +39,19 @@ citizenair_userdata_empty <- function(){
 #' e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
 #' ca <- CitizenAir$new(e)
 #' ca
+#' library(BelgiumMaps.StatBel)
+#' data("BE_ADMIN_REGION", package = "BelgiumMaps.StatBel")
+#' vlaanderen <- subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL %in% "Vlaams Gewest")
+#' ca <- CitizenAir$new(e, stations_area = vlaanderen)
+#' ca
 #' ca$getPhenomena()
+#' ca$getPhenomenaLabel("20")
 #' 
 #' ## get stations
 #' library(sp)
 #' x <- ca$getStations()
 #' plot(x)
+#' plot(ca$getStationsArea())
 #' 
 #' ## get official measurements
 #' library(lubridate)
@@ -52,18 +61,45 @@ citizenair_userdata_empty <- function(){
 #' ## set citizen measurements
 #' filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
 #' ca$setCitizenData(filename)
+#' x <- ca$getCitizenData("meta")
+#' x <- ca$getCitizenData("timeseries")
+#' x <- ca$getCitizenData("phenomena")
+#' x <- ca$getCitizenData("fileinfo")
+#' ca$getClosestStation()
+#' id <- ca$getClosestStation()
+#' ca$setComparisonStation(id)
+#' x <- ca$fetch_timeseries(id)
+#' x <- ca$fetch_timeseries()
 CitizenAir <- R6::R6Class("CitizenAir",
                       public = list(
                         endpoint = NULL,
                         stations = NULL, 
                         data = NULL,
-                        initialize = function(endpoint) {
+                        closest_station = NA_character_,
+                        initialize = function(endpoint, stations_area) {
                           self$endpoint <- endpoint
                           self$stations <- read_stations(endpoint)
+                          if(!missing(stations_area)){
+                            private$stations_area <- stations_area
+                            stations_in_region <- self$getStations()
+                            stations_in_region <- stations_in_region[sapply(1:nrow(stations_in_region), 
+                                                                            FUN=function(idx) rgeos::gIntersects(stations_area, stations_in_region[idx, ])), ]
+                            self$stations$stations <- self$stations$stations[self$stations$stations$id %in% stations_in_region$id, ]
+                          }
                           self$data <- citizenair_userdata_empty()
+                          self$closest_station <- NA_character_
+                        },
+                        setCitizenData = function(file, name=basename(file)){
+                          x <- read_citizenair(file)
+                          self$setComparisonStation()
+                          self$data <- x
                         },
-                        fetch_timeseries = function(id, time_span=NULL) {  
+                        setComparisonStation = function(id = NA_character_){
+                          self$closest_station <- as.character(id)
+                        },
+                        fetch_timeseries = function(id = self$getComparisonStation(), time_span=NULL) {  
                           stopifnot(length(id) == 1)
+                          stopifnot(!is.na(id))
                           ## Find and create a stations object
                           x <- self$stations$stations
                           x <- as.data.frame(x)
@@ -91,28 +127,83 @@ CitizenAir <- R6::R6Class("CitizenAir",
                             df <- as.data.frame(df)
                             df$date <- as.Date(df$time)
                             df$phenomena_id <- sensorweb4R::id(sensorweb4R::phenomenon(x))
-                            df$phenomena <- self$phenomena_label(df$phenomena_id)
+                            df$phenomena <- self$getPhenomenaLabel(df$phenomena_id)
                             df$phenomena_label <- sensorweb4R::label(x)
                             result[[i]] <- df[, c("phenomena_id", "phenomena", "phenomena_label", "time", "value")]
                           }
                           result <- rbindlist(result)
                           result
                         },
-                        phenomena_label = function(id){
-                          txt_recode(id, from = self$stations$phenomena$id, to = self$stations$phenomena$label)
-                        },
                         getStations = function(){
                           x <- as.data.frame(self$stations$stations)
                           x <- sp::SpatialPointsDataFrame(coords = x[, c("lon", "lat")], 
                                                           data = x, proj4string = CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"))
                           x
                         },
+                        getStationsArea = function(){
+                          private$stations_area
+                        },
                         getPhenomena = function(){
                           self$stations$phenomena$id
                         },
-                        setCitizenData = function(file, name=basename(file)){
-                          self$data <- read_citizenair(file)
+                        getPhenomenaLabel = function(id){
+                          stopifnot(all(id %in% self$stations$phenomena$id))
+                          txt_recode(id, from = self$stations$phenomena$id, to = self$stations$phenomena$label)
+                        },
+                        getComparisonStation = function(){
+                          self$closest_station
+                        },
+                        getClosestStation = function(){
+                          ## Get locations of own measurements
+                          point <- self$getCitizenData(type = "meta")
+                          point <- point[!is.na(point$lon) & !is.na(point$lat), ]
+                          station <- NA_character_
+                          if(nrow(point) > 0){
+                            point <- head(point, 1)
+                            station <- private$nearest_station(stations = self$getStations(), as.matrix(point[, c("lon", "lat")]))  
+                            station <- station$id
+                          }
+                          station
+                        },
+                        getCitizenData = function(type = c("meta", "timeseries", "phenomena", "fileinfo")){
+                          type <- match.arg(type)
+                          if(type == "meta"){
+                            if(is.na(self$data$filename)){
+                              x <- data.frame(sheet_id = integer(), sheet = character(), device = character(), 
+                                              lat = numeric(), lon = numeric(), 
+                                              phenomena = character(), stringsAsFactors = FALSE)
+                            }else{
+                              x <- as.data.frame(self$data, type = "meta")  
+                            }
+                            
+                          }else if(type == "timeseries"){
+                            if(is.na(self$data$filename)){
+                              x <- data.frame(sheet_id = integer(), time = as.POSIXct(character()), date = as.Date(character()), 
+                                              phenomena = character(), value = numeric(), stringsAsFactors = FALSE)
+                            }else{
+                              x <- as.data.frame(self$data, type = "measurements")
+                            }
+                          }else if(type == "phenomena"){
+                            if(is.na(self$data$filename)){
+                              x <- character()
+                            }else{
+                              x <- self$data$phenomena
+                            }
+                          }else if(type == "fileinfo"){
+                            if(is.na(self$data$filename)){
+                              x <- data.frame(name = character(), file = character(), stringsAsFactors = FALSE)
+                            }else{
+                              x <- data.frame(name = self$data$filename, file = self$data$file, stringsAsFactors = FALSE)
+                            }
+                          }
+                          x
                         }
                       ),
-                      private = list()
+                      private = list(
+                        stations_area = NULL,
+                        nearest_station = function(stations, x){
+                          d <- sp::spDistsN1(stations, x, longlat = TRUE)
+                          stations[which.min(d), ]
+                        }
+                      )
 )

citizenair/R/pkg.R

@@ -9,6 +9,7 @@
 #' @importFrom lubridate as.interval
 #' @importFrom httr GET content
 #' @importFrom sp CRS SpatialPointsDataFrame
+#' @importFrom rgeos gIntersects
 #' @import methods
 #' @import R6
 NULL

citizenair/R/read-citizendata.R

@@ -85,7 +85,7 @@ as.data.frame.citizenair_userdata <- function(x, row.names, optional, ..., type
       x
     })
     x <- rbindlist(x)
-  }else{
+  }else if(type == "measurements"){
     x <- lapply(x$content, FUN=function(x){
       meta <- x$meta
       x <- x$data

citizenair/R/utils.R

+
+
+#' @title Get the error message of a try-error object
+#' @description Get the error message of a try-error object
+#' @param x an object
+#' @param ... not used
+#' @export
+#' @return a character string with the error message or an empty character string
+#' @examples 
+#' x <- try(log("a"))
+#' error_message(x)
+#' x <- try(log(10))
+#' error_message(x)
+error_message <- function(x, ...){
+  UseMethod("error_message")
+}
+
+#' @export
+#' @describeIn error_message Default functionality
+error_message.default <- function(x, ...){
+  if(inherits(x, "try-error")){
+    as.character(attributes(x)$condition)
+  }else{
+    character()  
+  }
+  
+}
+
+
 txt_recode <- function (x, from = c(), to = c()) {
   stopifnot(length(from) == length(to))
   nongiven <- unique(x[!is.na(x)])

citizenair/inst/apps/citizenair/citizenair.Rmd

@@ -30,14 +30,12 @@ library(openair)
 data("BE_ADMIN_REGION", package = "BelgiumMaps.StatBel")
 data("ca", package = "citizenair")
 
-dashinput <- list()
-dashinput$endpoint <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
-dashinput$appdata <- ca
-#dashinput$appdata <- CitizenAir$new(endpoint = dashinput$endpoint)
-dashinput$region <- subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL %in% "Vlaams Gewest")
-dashinput$stations_sp <- dashinput$appdata$getStations()
-dashinput$stations_sp <- dashinput$stations_sp[sapply(1:nrow(dashinput$stations_sp), 
-                                                      FUN=function(idx) gIntersects(dashinput$region, dashinput$stations_sp[idx, ])), ]
+#ca <- CitizenAir$new(endpoint = as.Endpoint("http://geo.irceline.be/sos/api/v1"), stations_area = subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL %in% "Vlaams Gewest"))
+#save(ca, file = "citizenair/data/ca.RData")
+
+APPDATA <- ca
+APPDATA <- CitizenAir$new(endpoint = as.Endpoint("http://geo.irceline.be/sos/api/v1"), 
+                          stations_area = subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL %in% "Vlaams Gewest"))
 ```
 
 
@@ -52,57 +50,35 @@ popups$cleaned_data <- modalDialog(
   DT::dataTableOutput("uiOutput_rawdata", width = "100%", height = "auto"),
   size = "l", footer = modalButton("Sluit"), easyClose = TRUE)
 
+## MAIN REACTIVE WHICH LOADS THE EXCEL FILE
 citizenair_userdata <- reactive({
   input$uiInput_xl
-  isolate({
-    default <- data.frame(name = character(), size = integer(), type = character(), datapath = character(), stringsAsFactors = FALSE)
-    result <- list()
-    result$stations <- dashinput$stations_sp
-    result$name <- input$uiInput_xl$name
-    result$file <- input$uiInput_xl$datapath
-    result$data <- list()
-    result$data$phenomena <- character()
-    result$data$meta <- data.frame(sheet_id = integer(), sheet = character(), device = character(), 
-                                   lat = numeric(), lon = numeric(), 
-                                   phenomena = character(), stringsAsFactors = FALSE)
-    result$data$phenomena <- data.frame(sheet_id = integer(), time = as.POSIXct(character()), date = as.Date(character()), 
-                                        phenomena = character(), value = numeric(), stringsAsFactors = FALSE)
-    if(is.null(input$uiInput_xl)){
-      result$file <- default
+  result <- list()
+  result$appdata <- APPDATA
+  result$nearest_station <- result$appdata$getClosestStation()
+  if(!is.null(input$uiInput_xl)){
+    showNotification("We lezen uw Excel bestand in wacht even...", duration = 5)
+    x <- try(result$appdata$setCitizenData(file = input$uiInput_xl$datapath, name = input$uiInput_xl$name))
+    if(inherits(x, "try-error")){
+      showNotification(sprintf("Er loopt iets fout, is uw data bestand wel een correct bestand? %s", error_message(x)), 
+                       type = "error", duration = 15)
     }else{
-      showNotification("We lezen uw Excel bestand in wacht even...")
-      x <- try(dashinput$appdata$setCitizenData(result$file))
-      if(inherits(x, "try-error")){
-        showNotification(sprintf("Er loopt iets fout, is uw data bestand wel een correct bestand? %s", as.character(attributes(x)$condition)))
-      }else{
-        x <- dashinput$appdata$data
-        result$data$polluenten <- x$phenomena
-        result$data$meta <- as.data.frame(x, type = "meta")
-        result$data$phenomena <- as.data.frame(x, type = "measurements")
-        
-        nearest_station <- function(stations, x){
-          d <- sp::spDistsN1(stations, x, longlat = TRUE)
-          stations[which.min(d), ]
-        }
-        point <- as.matrix(data.frame(lon = 51.20, lat = 4.54))
-        point <- subset(result$data$meta, !is.na(lon))
-        if(nrow(point) > 0){
-          result$nearest_station <- nearest_station(stations = dashinput$stations_sp, as.matrix(point[1, c("lon", "lat")]))  
-          result$nearest_station <- result$nearest_station$id
-        }else{
-          result$nearest_station <- character()
-        }
-        output$uiOutput_rawmeta <- renderTable(result$data$meta)
-        output$uiOutput_rawdata <- renderDT(datatable(result$data$phenomena, rownames = FALSE, 
-                                                      caption = 'Overzicht van alle meetgegevens per sheet/tijdstip/type meting', 
-                                                      filter = 'top', options = list(pageLength = 5, autoWidth = TRUE)))  
-        showModal(popups$cleaned_data)
-      }
-      
+      result$nearest_station <- result$appdata$getClosestStation()
+      APPDATA$setComparisonStation(result$nearest_station)
+      output$uiOutput_rawmeta <- renderTable(APPDATA$getCitizenData("meta"))
+      output$uiOutput_rawdata <- renderDT(datatable(APPDATA$getCitizenData("timeseries"), rownames = FALSE, 
+                                                    caption = 'Overzicht van alle meetgegevens per sheet/tijdstip/type meting', 
+                                                    filter = 'top', options = list(pageLength = 5, autoWidth = TRUE, searching = FALSE)))  
+      showModal(popups$cleaned_data)
     }
-  })
+  }
   result
 })
+reactive({
+  ## On click on the station selection leaflet user interface, change the comparison station
+  input$uiOutput_select_station_marker_click
+  APPDATA$setComparisonStation(input$uiOutput_select_station_marker_click$id)
+})
 ```
 
 ```{r}

citizenair/inst/apps/citizenair/page01-introduction.Rmd

@@ -38,9 +38,10 @@ fileInput("uiInput_xl", label = "Selecteer het bestand met uw metingen: ", accep
 leafletOutput("uiOutput_stations")
 output$uiOutput_stations <- renderLeaflet({
   userdata <- citizenair_userdata()
-  meta <- userdata$data$meta
-  stations <- userdata$stations
-  map <- leaflet(data = dashinput$region)
+  meta     <- userdata$appdata$getCitizenData("meta")
+  stations <- APPDATA$getStations()
+  region   <- APPDATA$getStationsArea()
+  map <- leaflet(data = region)
   map <- addTiles(map)
   map <- addPolygons(map, weight = 3, fillOpacity = 0)
   map <- addCircleMarkers(map = map, data = stations, radius = 5, opacity = 0.3, fillOpacity = 1, weight = 3, 
@@ -48,7 +49,7 @@ output$uiOutput_stations <- renderLeaflet({
                                          FUN=function(id, label, phenomena){
                                            sprintf("<b>Station %s: %s</b> <br>Meetwaardes:<br> %s", id, label, paste(sprintf(" - %s ", phenomena), collapse = "<br>"))
                                            })))
-  if(length(userdata$nearest_station) > 0){
+  if(!is.na(userdata$nearest_station)){
     stations <- subset(stations, id %in% userdata$nearest_station)
     stations <- head(stations, 1)
     map <- addPopups(map, data = stations, popup = sprintf("Dichtste meetstation<br>%s: %s", stations$id, stations$label))
@@ -74,7 +75,7 @@ output$uiOutput_stations <- renderLeaflet({
 ```{r}
 renderValueBox({
   userdata <- citizenair_userdata()
-  n <- nrow(userdata$data$meta)
+  n <- nrow(userdata$appdata$getCitizenData("meta"))
   if(n > 0){
     valueBox(n, caption = "Uw meetpunten", icon = "fa-thumbs-up", color = "green")
   }else{
@@ -88,10 +89,14 @@ renderValueBox({
 ```{r}
 renderValueBox({
   userdata <- citizenair_userdata()
-  stations <- userdata$stations
+  stations <- userdata$appdata$getStations()
   stations <- subset(stations, id %in% userdata$nearest_station)
   if(nrow(stations) > 0){
-    vb <- valueBox(stations$label, caption = "Dichtste officieel meetstation")  
+    txt <- stations$label
+    txt <- strsplit(txt, "-")[[1]]
+    txt <- trimws(txt)
+    txt <- HTML(paste(txt, collapse = "<br>"))
+    vb <- valueBox(txt, caption = "Dichtste officieel meetstation")  
   }else{
     vb <- NULL
   }
@@ -111,7 +116,7 @@ eventReactive(input$uiInput_showdata, {
 ```{r}
 renderText({
   userdata <- citizenair_userdata()
-  userdata$data$polluenten
+  userdata$appdata$getCitizenData("phenomena")
 })
 ```
 
@@ -120,7 +125,7 @@ renderText({
 ```{r}
 renderTable({
   userdata <- citizenair_userdata()
-  x <- as.data.table(userdata$data$phenomena)
+  x <- as.data.table(userdata$appdata$getCitizenData("timeseries"))
   if(nrow(x) > 0){
     x <- x[, list(start = as.character(min(date, na.rm=TRUE)),
                   stop = as.character(max(date, na.rm=TRUE)))]
@@ -137,14 +142,14 @@ renderTable({
 ```{r}
 renderTable({
   userdata <- citizenair_userdata()
-  x <- as.data.table(userdata$data$phenomena)
+  x <- as.data.table(userdata$appdata$getCitizenData("timeseries"))
   if(nrow(x) > 0){
     x <- x[, meetfrequentie := as.numeric(difftime(time, shift(time, type = "lag", n = 1L), units = "mins")), by = list(sheet_id)]
     x <- x[, list(n = .N), by = list(sheet_id, meetfrequentie)]
     x <- x[, pct := round(100 * n / sum(n), 1), by = list(sheet_id)]
     x <- subset(x, !is.na(meetfrequentie))
     x <- x[order(n, decreasing=TRUE), ]
-    x <- merge(x, userdata$data$meta, by = "sheet_id")
+    x <- merge(x, userdata$appdata$getCitizenData("meta"), by = "sheet_id")
     x <- as.data.frame(x)  
     x <- x[!duplicated(x$sheet_id), c("sheet_id", "device", "meetfrequentie")]
     x$meetfrequentie <- sprintf("elke %s minuten", round(x$meetfrequentie, 2))
@@ -154,9 +159,3 @@ renderTable({
   x
 })
 ```
-
-
-
-
-
-

citizenair/inst/apps/citizenair/page02-exploratory.Rmd

 ## Sidebar {.sidebar}
 
-#### Selectiecriteria
+#### Vergelijkingsbasis
 
 ```{r}
-actionBttn(inputId = "uiInput_selectstation", label = "Vergelijk met ander officieel station", style = "gradient")
+inputPanel(
+radioButtons(inputId = "uiInput_periode", label = "Vergelijk op basis van", 
+             choices = c("Per minuut" = "minute", "Per uur" = "hour", "Per dag" = "day", "Per maand" = "month", "Ruwe data" = "rawdata"), 
+             selected = "rawdata"),
+dateRangeInput(inputId = "uiInput_period", label = "Verander de periode", start = Sys.Date()-365, end = Sys.Date()),
+actionButton(inputId = "uiInput_refresh", label = "Herbereken")
+)
 ```
 
+#### Vergelijk met ...
+
 ```{r}
-radioButtons(inputId = "uiInput_periode", label = "Vergelijk op basis van", 
-             choices = c("Per minuut" = "minute", "Per uur" = "hour", "Per dag" = "day", "Per maand" = "month"), 
-             selected = "day")
-dateRangeInput(inputId = "uiInput_period", label = "Verander de periode", start = Sys.Date()-365, end = Sys.Date())
-actionButton(inputId = "uiInput_refresh", label = "Herbereken")
+actionBttn(inputId = "uiInput_selectstation", label = "Vergelijk met ander officieel station", style = "gradient")
 ```
 
+
 ## Verken je metingen {.tabset}
 
 ### Verken je metingen
@@ -22,23 +27,48 @@ actionButton(inputId = "uiInput_refresh", label = "Herbereken")
 
 ```{r}
 fillCol(
-  tags$div("Hieronder tonen we een overzicht van jouw meting en de dichtstbijzijnde VMM-meetplaats in
-functie van de tijd. Verken je meting hieronder en kijk eens wat er gebeurt als je uitmiddelt per
-uur, per dag enz. Als je een goed zicht hebt op je data, ga dan naar de volgende stap."),
+  tags$div("Hieronder tonen we een overzicht van jouw metingen en de dichtstbijzijnde VMM-meetplaats in
+           functie van de tijd. Verken je meting hieronder en kijk eens wat er gebeurt als je uitmiddelt per
+           uur, per dag enz. Als je een goed zicht hebt op je data, ga dan naar de volgende stap."),
   dygraphOutput("uiOutput_timeseries"),
   flex = c(NA, 1)
-)
+  )
 output$uiOutput_timeseries <- renderDygraph({
-    x <- dashinput$appdata$fetch_timeseries("1030")
-x <- setDT(x)
-ts <- dcast.data.table(data = x, formula = time ~ phenomena_label, fun.aggregate = mean, value.var = "value")
-ts <- setDF(ts)
-g <- xts(ts[, -1], order.by=ts[,1])
-g <- dygraph(g, main = "Tijdreeks van 1030 - Under construction")
-g <- dyRangeSelector(g, height = 20)
-g
-  })
-
+  userdata <- citizenair_userdata()
+  x <- userdata$appdata$getCitizenData("timeseries")
+  if(nrow(x) > 0){
+   x <- setDT(x)
+   x$phenomena_label <- paste("Sheet ", x$sheet_id, ": ", x$phenomena, sep = "")
+   ts <- dcast.data.table(data = x, formula = time ~ phenomena_label, fun.aggregate = mean, value.var = "value")
+   ts <- setDF(ts)
+   g <- xts(ts[, -1], order.by=ts[,1])
+   g <- dygraph(g, main = "Tijdreeks van uw metingen")
+   g <- dyRangeSelector(g, height = 20)
+   g <- dyLegend(g, show = "always")
+   ui <- g 
+  }else{
+    ui <- NULL
+  }
+  ui
+})
+observeEvent(input$uiInput_refresh, {
+  output$uiOutput_timeseries <- renderDygraph({
+  ## should depend on selected station
+  id <- APPDATA$getComparisonStation()
+  showNotification(sprintf("Getting data of station %s at the IRCEL web service", id))
+  if(!is.na(id)){
+    x <- APPDATA$fetch_timeseries(id)
+    x <- setDT(x)
+    ts <- dcast.data.table(data = x, formula = time ~ phenomena, fun.aggregate = mean, value.var = "value")
+    ts <- setDF(ts)
+    g <- xts(ts[, -1], order.by=ts[,1])
+    g <- dygraph(g, main = sprintf("Tijdreeks van officieel meetstation %s", id))
+    g <- dyRangeSelector(g, height = 20)
+    g <- dyLegend(g, show = "always")
+    g  
+  }
+})
+})
 
 ```
 
@@ -49,8 +79,7 @@ g
 ```{r}
 leafletOutput("uiOutput_select_station", width = "100%", height = 400)
 output$uiOutput_select_station <- renderLeaflet({
-  ca <- dashinput$appdata
-  stations <- ca$getStations()
+  stations <- APPDATA$getStations()
   map <- leaflet(data = stations)
   map <- addTiles(map)
   map <- addCircleMarkers(map = map, data = stations, radius = 5, opacity = 0.3, fillOpacity = 1, weight = 3, 
@@ -137,17 +166,25 @@ output$summaryRaw <- renderTable({reactive[["summaryRaw"]]})
 output$summaryValid <- renderTable({reactive[["summaryValid"]]})
 ```
 
+
 ## Inputs {data-width=150}
 
-### 
+
+###
 
 ```{r}
 renderValueBox({
+  input$uiOutput_select_station_marker_click
   userdata <- citizenair_userdata()
-  stations <- userdata$stations
+  userdata$nearest_station <- userdata$appdata$getComparisonStation()
+  stations <- userdata$appdata$getStations()
   stations <- subset(stations, id %in% userdata$nearest_station)
   if(nrow(stations) > 0){
-    ui <- valueBox(stations$label, caption = "Vergelijk met officieel meetstation")  
+    txt <- stations$label
+    txt <- strsplit(txt, "-")[[1]]
+    txt <- trimws(txt)
+    txt <- HTML(paste(txt, collapse = "<br>"))
+    ui <- valueBox(txt, caption = "Vergelijk met officieel meetstation")  
   }else{
     ui <- NULL
   }
@@ -155,11 +192,13 @@ renderValueBox({
 })
 ```
 
+
 ### 
 
 ```{r}
 renderValueBox({
-  filename <- citizenair_userdata()$name
+  userdata <- citizenair_userdata()
+  filename <- userdata$appdata$getCitizenData("fileinfo")$name
   if(length(filename) > 0){
     ui <- valueBox("Uw excel file", caption = citizenair_userdata()$name)    
   }else{
@@ -174,10 +213,9 @@ renderValueBox({
 ```{r}
 renderUI({
   userdata <- citizenair_userdata()
-  x <- userdata$data$meta
+  x <- userdata$appdata$getCitizenData("meta")
   if(is.data.frame(x) && nrow(x) > 0){
-    choices <- as.list(x$sheet_id)
-    names(choices) <- x$sheet
+    choices <- structure(as.list(x$sheet_id), .Names = x$sheet)
     ui <- selectInput(inputId = "uiInput_sheet", label = "Selecteer sheet", choices = choices, selected = choices, multiple = TRUE)
   }else{
     ui <- NULL
@@ -185,11 +223,3 @@ renderUI({
   ui
 })
 ```
-
-###
-
-```{r}
-renderPrint({
-  input$uiOutput_select_station_marker_mouseover
-})
-```
\ No newline at end of file

citizenair/man/CitizenAir.Rd

@@ -19,6 +19,8 @@ CitizenAir app data
 \item{\code{stations}}{object of class \code{citizenair_stations} as returned by \code{\link{read_stations}}}
 
 \item{\code{data}}{object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}}
+
+\item{\code{closest_station}}{a character string with the id of the closest station.}
 }}
 
 \section{Methods}{
@@ -26,6 +28,7 @@ CitizenAir app data
 \describe{
   \item{\code{fetch_timeseries(id = "123", time_span)}}{Get timeseries for Station with \code{id} and a certain time_span The argument \code{timespan.} Passed on to \code{sensorweb4R::getData}}
   \item{\code{getStations()}}{Get a SpatialPointsDataFrame of all stations}
+  \item{TODO}{TODO}
 }
 }
 
@@ -34,12 +37,19 @@ library(sensorweb4R)
 e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
 ca <- CitizenAir$new(e)
 ca
+library(BelgiumMaps.StatBel)
+data("BE_ADMIN_REGION", package = "BelgiumMaps.StatBel")
+vlaanderen <- subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL \%in\% "Vlaams Gewest")
+ca <- CitizenAir$new(e, stations_area = vlaanderen)
+ca
 ca$getPhenomena()
+ca$getPhenomenaLabel("20")
 
 ## get stations
 library(sp)
 x <- ca$getStations()
 plot(x)
+plot(ca$getStationsArea())
 
 ## get official measurements
 library(lubridate)
@@ -49,5 +59,14 @@ x <- ca$fetch_timeseries(id = "1030", time_span = period)
 ## set citizen measurements
 filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
 ca$setCitizenData(filename)
+x <- ca$getCitizenData("meta")
+x <- ca$getCitizenData("timeseries")
+x <- ca$getCitizenData("phenomena")
+x <- ca$getCitizenData("fileinfo")
+ca$getClosestStation()
+id <- ca$getClosestStation()
+ca$setComparisonStation(id)
+x <- ca$fetch_timeseries(id)
+x <- ca$fetch_timeseries()
 }
 \keyword{datasets}

citizenair/man/error_message.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{error_message}
+\alias{error_message}
+\alias{error_message.default}
+\title{Get the error message of a try-error object}
+\usage{
+error_message(x, ...)
+
+\method{error_message}{default}(x, ...)
+}
+\arguments{
+\item{x}{an object}
+
+\item{...}{not used}
+}
+\value{
+a character string with the error message or an empty character string
+}
+\description{
+Get the error message of a try-error object
+}
+\section{Methods (by class)}{
+\itemize{
+\item \code{default}: Default functionality
+}}
+
+\examples{
+x <- try(log("a"))
+error_message(x)
+x <- try(log(10))
+error_message(x)
+}