Add more tabs with dev plots

README.md

@@ -22,7 +22,7 @@ run_app('citizenair.Rmd')
 install.packages(c('flexdashboard', 'shiny', 'shinyWidgets', 'rmarkdown', 'DT'))
 install.packages(c('data.table', 'httr', 'readxl', 'magrittr', 'cellranger', 'fasttime'))
 install.packages(c('leaflet', 'sp', 'rgeos'))
-install.packages(c('dygraphs', 'xts'))
+install.packages(c('dygraphs', 'xts', 'openair', 'ggplot2'))
 devtools::install_github('bnosac/BelgiumMaps.Statbel')
 devtools::install_github('52North/sensorweb4R')
 devtools::install_git('https://www.datatailor.be/vmm/citizenair', subdir = 'citizenair')

citizenair-shinyproxy/Dockerfile

@@ -6,7 +6,7 @@ RUN R -e "install.packages(c('devtools'), repos='https://cloud.r-project.org/')"
 RUN R -e "install.packages(c('flexdashboard', 'shiny', 'shinyWidgets', 'rmarkdown', 'DT'), repos='https://cloud.r-project.org/')"
 RUN R -e "install.packages(c('data.table', 'httr', 'readxl', 'magrittr', 'cellranger', 'fasttime'), repos='https://cloud.r-project.org/')"
 RUN R -e "install.packages(c('leaflet', 'sp', 'rgeos'), repos='https://cloud.r-project.org/')"
-RUN R -e "install.packages(c('dygraphs', 'xts'), repos='https://cloud.r-project.org/')"
+RUN R -e "install.packages(c('dygraphs', 'xts', 'openair', 'ggplot2'), repos='https://cloud.r-project.org/')"
 RUN R -e "devtools::install_github('bnosac/BelgiumMaps.Statbel')"
 RUN R -e "devtools::install_github('52North/sensorweb4R')"
 RUN git -c http.sslVerify=false clone https://www.datatailor.be/vmm/citizenair

citizenair/inst/apps/citizenair/citizenair.Rmd

 ---
-title: "Citizen Air: meet - evalueer - vergelijk"
+title: "Citizen Air - meet - evalueer - vergelijk"
 runtime: shiny 
 output: 
   flexdashboard::flex_dashboard:
@@ -25,13 +25,15 @@ library(DT)
 library(sp)
 library(xts)
 library(dygraphs)
+library(ggplot2)
+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$endpoint)
+#dashinput$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), 
@@ -103,6 +105,32 @@ citizenair_userdata <- reactive({
 })
 ```
 
+```{r}
+## DEV APP SETTINGS
+reactive <-  reactiveValues()
+plots <- reactiveValues()
+mydata <- data.frame(date = as.POSIXct(seq.Date(Sys.Date(), Sys.Date()-999, by = "-1 day"), tz = "UTC"), 
+                     REF = rnorm(1000), 
+                     SENSOR = rnorm(1000))
+linear_model <- lm(mydata$SENSOR ~ mydata$REF)
+PI <- data.frame(predict(linear_model, interval="predict", level = 0.95))
+colnames(PI) <- c("OLSQ", "lower PI", "upper PI")
+CI <- data.frame(predict(linear_model, interval="confidence", level = 0.95))
+colnames(CI) <- c("OLSQ", "lower CI", "upper CI")
+mydata <- cbind(mydata, "OLSQ" = CI$OLSQ,"lower_CI" = CI$`lower CI`, "upper_CI"=CI$`upper CI`, "lower_PI" = PI$`lower PI`, "upper_PI" = PI$`upper PI`)
+mydata$e <- mydata$OLSQ - mydata$SENSOR
+mydata <- mydata[order(mydata[,1]), ]
+summary <- data.frame(do.call(cbind, lapply(mydata, summary)))[-7,]
+summary$date <- as.character(as.POSIXct(summary$date, origin="1970-01-01"))
+summary <- rbind(summary,"# Valid"=colSums(!is.na(mydata)))
+summary <- rbind(summary,"# NA's"=colSums(is.na(mydata)))
+variables <- c("min", "25th Perc", "median", "mean","75th Perc", "max","# Valid", "# NA's")
+summary <- cbind("variable"=variables,summary)
+reactive[["linear_model"]] <- linear_model
+reactive[["regData"]]<- mydata
+reactive[["summaryRaw"]] <- summary
+```
+
 # Data {data-icon="fa-cloud-upload"}
 
 ```{r child="page01-introduction.Rmd", eval=TRUE}

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

@@ -21,7 +21,7 @@ tags$ul(
           downloadLink("citizenair-example.xls", "citizenair-example.xls")),
   tags$li("Download een lege excel file waarin je je data kan copy-pasten: ", 
           downloadLink("citizenair-blank.xls", "citizenair-blank.xls")),
-  tags$li("Ga naar de handleiding: ", 
+  tags$li("Ga naar de handleiding op ", 
           tags$a(href="https://hoemeetiklucht.eu", "hoemeetiklucht.eu"))
 )
 ```

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

@@ -55,9 +55,79 @@ output$uiOutput_select_station <- renderLeaflet({
 ```
 
 
-### Is mijn meettoestel correct
+### Meet mijn meettoestel zoals een officieel toestel
 
 
+```{r}
+fillCol(
+  tags$div(
+      tags$h4("De Vlaamse Milieu Maatschappij heeft meetresultaten die aan de strengste kwaliteitseisen voldoen. Hieronder tonen
+we een eenvoudige statistische vergelijking tussen onze meetgegevens en die van jouw. Verander ook de VMM-meetplaats eens, een andere meetplaats komt misschien beter me de jouwe overeen!"),
+      tags$h5("Onderstaande grafiek toont alle meetwaardes van uw toestel uitgezet tov alle meetwaardes van een toestel van de Vlaamse Milieu Maatschappij")),
+  fillRow(dropdownButton(
+    tags$h3("Selectie dagen van de week"),
+    radioButtons(inputId = "uiInput_dayofweek", label = "Vergelijk op basis van", 
+             choices = c("Alle dagen van de week" = "all", "Enkel weekdagen" = "weekdays", "Enkel weekend" = "weekend"), 
+             selected = "all"),
+    
+    tags$h3("Input voor de grafiek"),
+    sliderInput(inputId = "uiInput_slider", label = "TODO", value = 25, min = 5, max = 100, step = 1L, round = TRUE),
+    circle = TRUE, status = "info", icon = icon("gear"), width = "300px", size = "sm",
+    tooltip = tooltipOptions(title = "Verdere opties")),
+    plotOutput("uiOutput_comparison", height = "100%"),
+    flex = c(NA, 2)
+  ),
+  flex = c(NA, 2)
+)
+
+# Scatterplot of linear regression + CI & PI 
+output$uiOutput_comparison <- renderPlot({
+  req(c(reactive$regData,reactive$linear_model))
+  mydata <- reactive$regData
+  linear_model <- reactive$linear_model
+  plot_PI_CI <- ggplot(data = mydata, aes(x = REF, y = SENSOR)) + 
+    geom_ribbon(aes(ymin = lower_CI, ymax=upper_CI, fill = "CI"),alpha = 0.6) +
+    geom_ribbon(aes(ymin = lower_PI, ymax=upper_PI, fill = "PI"), alpha = 0.4) +
+    geom_point() +
+    geom_line(aes(y = OLSQ,col = "OLSQ")) +
+    geom_line(aes(y = REF,col = "y=x")) +
+    labs(title = paste("Scatterplot with regression estimates: intercept =",
+                       format(summary(linear_model)$coefficients[1,1], digits = 3),
+                       ",slope =",format(summary(linear_model)$coefficients[2,1], digits = 3),
+                       ",R² =",format(summary(linear_model)$r.squared, digits = 3)),
+         x = "Reference value",
+         y = "Sensor") +
+    scale_fill_manual(name="",values=c("CI"="blue","PI"= "grey")) +
+    scale_colour_manual(name="", values = c("y=x"="red","OLSQ"="black"))
+  plots[["scatter"]] <- plot_PI_CI
+  plot_PI_CI
+})
+```
+
+### Gevorderd overzicht van de vergelijking
+
+```{r}
+fillCol(
+  tableOutput("data"),
+  tags$hr(),
+  tableOutput("summaryRaw"),
+  flex = c(1, NA, 1)
+)
+```
+
+```{r}
+# outputs of dataframe & summaries
+output$data <- renderTable({ 
+  req(reactive[["regData"]])
+  mydata <- reactive[["regData"]]
+  avg.time <- "day"
+  mydata <- timeAverage(mydata, avg.time=avg.time, data.thresh=85,statistic="mean")
+  mydata$date <- as.character(as.POSIXct(mydata$date, origin="1970-01-01"))
+  mydata})
+output$summaryRaw <- renderTable({reactive[["summaryRaw"]]})
+output$summaryValid <- renderTable({reactive[["summaryValid"]]})
+```
+
 ## Inputs {data-width=150}
 
 ###