Combine citizen + official timeseries

citizenair/R/appdata.R

@@ -26,6 +26,7 @@ citizenair_userdata_empty <- function(){
 #' @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.
+#' @field timeseries timeseries
 #' @format The CitizenAir object is an R6Class
 #' @section Methods:
 #' \describe{
@@ -75,6 +76,7 @@ CitizenAir <- R6::R6Class("CitizenAir",
                         endpoint = NULL,
                         stations = NULL, 
                         data = NULL,
+                        timeseries = NULL,
                         closest_station = NA_character_,
                         initialize = function(endpoint, stations_area) {
                           self$endpoint <- endpoint
@@ -87,6 +89,7 @@ CitizenAir <- R6::R6Class("CitizenAir",
                             self$stations$stations <- self$stations$stations[self$stations$stations$id %in% stations_in_region$id, ]
                           }
                           self$data <- citizenair_userdata_empty()
+                          self$timeseries <- private$default_timeseries
                           self$closest_station <- NA_character_
                         },
                         setCitizenData = function(file, name=basename(file)){
@@ -97,7 +100,19 @@ CitizenAir <- R6::R6Class("CitizenAir",
                         setComparisonStation = function(id = NA_character_){
                           self$closest_station <- as.character(id)
                         },
-                        fetch_timeseries = function(id = self$getComparisonStation(), time_span=NULL) {  
+                        setCombinedTimeseries = function(data){
+                          if(missing(data)){
+                            self$timeseries <- private$default_timeseries 
+                          }else if(is.null(data)){
+                            self$timeseries <- private$default_timeseries 
+                          }else{
+                            self$timeseries <- data  
+                          }
+                        },
+                        fetch_timeseries = function(id = self$getComparisonStation(), time_span=NULL) {
+                          if(length(id) == 0){
+                            return(private$default_timeseries)
+                          }
                           stopifnot(length(id) == 1)
                           stopifnot(!is.na(id))
                           ## Find and create a stations object
@@ -128,8 +143,10 @@ CitizenAir <- R6::R6Class("CitizenAir",
                             df$date <- as.Date(df$time)
                             df$phenomena_id <- sensorweb4R::id(sensorweb4R::phenomenon(x))
                             df$phenomena <- self$getPhenomenaLabel(df$phenomena_id)
-                            df$phenomena_label <- sensorweb4R::label(x)
-                            result[[i]] <- df[, c("phenomena_id", "phenomena", "phenomena_label", "time", "value")]
+                            df$timeseries_id <- sensorweb4R::id(x)
+                            df$timeseries_label <- sensorweb4R::label(x)
+                            df$type <- rep("official", nrow(df))
+                            result[[i]] <- df[, c("type", "timeseries_id", "timeseries_label", "phenomena_id", "phenomena", "time", "date", "value")]
                           }
                           result <- rbindlist(result)
                           result
@@ -165,6 +182,9 @@ CitizenAir <- R6::R6Class("CitizenAir",
                           }
                           station
                         },
+                        getCombinedTimeseries = function(){
+                          self$timeseries
+                        },
                         getCitizenData = function(type = c("meta", "timeseries", "phenomena", "fileinfo")){
                           type <- match.arg(type)
                           if(type == "meta"){
@@ -178,11 +198,16 @@ CitizenAir <- R6::R6Class("CitizenAir",
                             
                           }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)
+                              x <- private$default_timeseries
                             }else{
                               x <- as.data.frame(self$data, type = "measurements")
                             }
+                            x$type <- rep("citizen", nrow(x))
+                            x$phenomena_id <- rep(NA_character_, nrow(x))
+                            x$timeseries_id <- as.character(x$sheet_id)
+                            sheetinfo <- self$getCitizenData("meta")
+                            x$timeseries_label <- txt_recode(x$sheet_id, from = sheetinfo$sheet_id, to = sheetinfo$sheet)
+                            x <- x[, c("type", "timeseries_id", "timeseries_label", "phenomena_id", "phenomena", "time", "date", "value")]
                           }else if(type == "phenomena"){
                             if(is.na(self$data$filename)){
                               x <- character()
@@ -204,6 +229,11 @@ CitizenAir <- R6::R6Class("CitizenAir",
                         nearest_station = function(stations, x){
                           d <- sp::spDistsN1(stations, x, longlat = TRUE)
                           stations[which.min(d), ]
-                        }
+                        },
+                        default_timeseries = data.frame(type = character(), 
+                                                        timeseries_id = character(), timeseries_label = character(), 
+                                                        phenomena_id = character(), phenomena = character(), 
+                                                        time = as.POSIXct(character()), date = as.Date(character(), tz = "UTC"), 
+                                                        value = numeric(), stringsAsFactors = FALSE)
                       )
 )

citizenair/inst/apps/citizenair/citizenair.Rmd

@@ -34,6 +34,8 @@ data("ca", package = "citizenair")
 #save(ca, file = "citizenair/data/ca.RData")
 
 APPDATA <- ca
+#APPDATA$setCitizenData(file = system.file(package = "citizenair", "data-raw", "citizenair-example.xls"))
+#APPDATA$setComparisonStation(id = "1155")
 APPDATA <- CitizenAir$new(endpoint = as.Endpoint("http://geo.irceline.be/sos/api/v1"), 
                           stations_area = subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL %in% "Vlaams Gewest"))
 ```
@@ -66,7 +68,11 @@ citizenair_userdata <- reactive({
       result$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, 
+      x <- APPDATA$getCitizenData("timeseries")
+      APPDATA$setCombinedTimeseries(x)
+      x$sheet <- x$timeseries_label
+      x <- x[, c("sheet", "phenomena", "time", "value")]
+      output$uiOutput_rawdata <- renderDT(datatable(x, rownames = FALSE, 
                                                     caption = 'Overzicht van alle meetgegevens per sheet/tijdstip/type meting', 
                                                     filter = 'top', options = list(pageLength = 5, autoWidth = TRUE, searching = FALSE)))  
       showModal(popups$cleaned_data)

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

@@ -144,6 +144,7 @@ renderTable({
   userdata <- citizenair_userdata()
   x <- as.data.table(userdata$appdata$getCitizenData("timeseries"))
   if(nrow(x) > 0){
+    x$sheet_id <- as.integer(x$timeseries_id)
     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)]

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

 ## Sidebar {.sidebar}
 
+```{r}
+plot_timeseries <- function(x){
+  if(nrow(x) > 0){
+    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)
+    g <- dyRangeSelector(g, height = 20)
+    g <- dyLegend(g, show = "always")
+    g  
+  }else{
+    g <- NULL
+  }
+  g
+}
+# isolate({
+#     input$uiInput_aggregationlevel
+#     input$uiInput_sheet
+#     input$uiInput_period 
+#     input$uiOutput_select_station_marker_click
+#   })
+```
+
+#### Vergelijk met ...
+
+```{r}
+actionBttn(inputId = "uiInput_selectstation", label = "Vergelijk met ander officieel station", style = "gradient")
+```
+
 #### Vergelijkingsbasis
 
 ```{r}
 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"), 
+radioButtons(inputId = "uiInput_aggregationlevel", label = "Vergelijk", 
+             choices = c("Per minuut" = "minute", "Per uur" = "hour", "Per dag" = "day", "Per maand" = "month", "Op basis van 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}
-actionBttn(inputId = "uiInput_selectstation", label = "Vergelijk met ander officieel station", style = "gradient")
+## MAIN REACTIVE WHICH COMBINES CITIZEN DATA + OFFICIAL DATA
+observeEvent(input$uiInput_refresh, {
+  result <- list()
+  result$userdata <- citizenair_userdata()
+  citizen <- result$userdata$appdata$getCitizenData("timeseries")
+  result$station <- result$userdata$appdata$getComparisonStation()
+  if(length(result$station) > 0){
+    showNotification("Haalt data af vanaf de IRCEL webservice")
+  }
+  official <- try(result$userdata$appdata$fetch_timeseries(result$station))
+  if(inherits(official, "try-error")){
+      showNotification(sprintf("Er loopt iets fout met het ophalen van de data vanaf de IRCEL webservice: %s", error_message(official)), 
+                       type = "error", duration = 15)
+      official <- result$userdata$appdata$fetch_timeseries(NULL)
+  }else{
+    if(nrow(official) > 0){
+      showNotification("Data werd afgehaald vanaf de IRCEL webservice en werd gecombineerd met uw meetgegevens", type = "message")    
+    }
+  }
+  result$data <- list()
+  result$data$citizen <- citizen
+  result$data$official <- official
+  result$data <- rbindlist(result$data, use.names = TRUE)
+  APPDATA$setCombinedTimeseries(result$data)
+  output$uiOutput_timeseries <- renderDygraph(plot_timeseries(result$data))
+})
 ```
 
 
@@ -23,8 +76,6 @@ actionBttn(inputId = "uiInput_selectstation", label = "Vergelijk met ander offic
 
 ### Verken je metingen
 
-
-
 ```{r}
 fillCol(
   tags$div("Hieronder tonen we een overzicht van jouw metingen en de dichtstbijzijnde VMM-meetplaats in
@@ -32,44 +83,13 @@ fillCol(
            uur, per dag enz. Als je een goed zicht hebt op je data, ga dan naar de volgende stap."),
   dygraphOutput("uiOutput_timeseries"),
   flex = c(NA, 1)
-  )
+)
 output$uiOutput_timeseries <- renderDygraph({
+  ## Default call when user only uploaded his own data
   userdata <- citizenair_userdata()
-  x <- userdata$appdata$getCitizenData("timeseries")
-  if(nrow(x) > 0){
-   x <- setDT(x)
-   x$phenomena_label <- paste("Sheet ", x$sheet_id, ": ", x$phenomena, sep = "")
-   ts <- dcast.data.table(data = x, formula = time ~ phenomena_label, fun.aggregate = mean, value.var = "value")
-   ts <- setDF(ts)
-   g <- xts(ts[, -1], order.by=ts[,1])
-   g <- dygraph(g, main = "Tijdreeks van uw metingen")
-   g <- dyRangeSelector(g, height = 20)
-   g <- dyLegend(g, show = "always")
-   ui <- g 
-  }else{
-    ui <- NULL
-  }
-  ui
+  x <- userdata$appdata$getCombinedTimeseries()
+  plot_timeseries(x)
 })
-observeEvent(input$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  
-  }
-})
-})
-
 ```
 
 
@@ -174,6 +194,7 @@ output$summaryValid <- renderTable({reactive[["summaryValid"]]})
 
 ```{r}
 renderValueBox({
+  ## Triggers each time a user clicks on the leaflet app or when a user uploads new data
   input$uiOutput_select_station_marker_click
   userdata <- citizenair_userdata()
   userdata$nearest_station <- userdata$appdata$getComparisonStation()

citizenair/man/CitizenAir.Rd

@@ -21,6 +21,8 @@ CitizenAir app data
 \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.}
+
+\item{\code{timeseries}}{timeseries}
 }}
 
 \section{Methods}{