Refactor, now using R6 class instead of S4

citizenair/DESCRIPTION

@@ -7,7 +7,6 @@ Authors@R: c(
     person('Jan', 'Wijffels', role = c('aut', 'cre', 'cph'), email = 'jwijffels@bnosac.be'), 
     person('BNOSAC', role = 'cph'))
 Description: Utilities for the Citizen Air application. 
-License: CC-BY-SA-4.0
+License: CC BY-SA 4.0
 RoxygenNote: 6.0.1
-Imports: readxl, cellranger, data.table, fasttime, rmarkdown, tools, utils, sensorweb4R, httr, methods
-Suggests: sp
+Imports: readxl, cellranger, data.table, fasttime, rmarkdown, tools, utils, sensorweb4R, httr, methods, sp, lubridate, R6

citizenair/NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.frame,citizenair_userdata)
-export(as_sp)
+export(CitizenAir)
 export(read_citizenair)
 export(read_stations)
 export(run_app)
-exportClasses(CitizenAir)
+import(R6)
 import(methods)
 importFrom(cellranger,cell_cols)
 importFrom(cellranger,cell_limits)
@@ -18,13 +18,24 @@ importFrom(data.table,setnames)
 importFrom(fasttime,fastPOSIXct)
 importFrom(httr,GET)
 importFrom(httr,content)
+importFrom(lubridate,as.interval)
 importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)
 importFrom(rmarkdown,run)
+importFrom(sensorweb4R,Station)
 importFrom(sensorweb4R,as.Endpoint)
+importFrom(sensorweb4R,as.Timeseries)
+importFrom(sensorweb4R,fetch)
+importFrom(sensorweb4R,firstValue)
+importFrom(sensorweb4R,getData)
 importFrom(sensorweb4R,id)
 importFrom(sensorweb4R,label)
+importFrom(sensorweb4R,lastValue)
 importFrom(sensorweb4R,resourceURL)
+importFrom(sensorweb4R,time)
+importFrom(sensorweb4R,timeseries)
+importFrom(sp,CRS)
+importFrom(sp,SpatialPointsDataFrame)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,capture.output)
 importFrom(utils,head)

citizenair/R/appdata.R

@@ -8,45 +8,103 @@ setClass(Class="citizenair_userdata",
                                        content = "list", 
                                        phenomena = "character"))
 
-#' @title Object of class CitizenAir
-#' @description Object of class CitizenAir
-#' @slot stations Object of class \code{citizenair_stations} as returned by \code{\link{read_stations}}
-#' @slot citizen_data Object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}
-#' @name CitizenAir-class
-#' @rdname CitizenAir-class
-#' @param endpoint An object of class Endpoint as returned by \code{as.Endpoint} 
-#' @export 
+citizenair_userdata_empty <- function(){
+  result <- list()
+  result$filename <- NA_character_
+  result$file <- NA_character_
+  result$time <- Sys.time()
+  result$content <- list()
+  result$phenomena <- character()
+  class(result) <- "citizenair_userdata"
+  result
+}
+
+#' @title CitizenAir app data
+#' @description CitizenAir app data
+#' @docType class
+#' @field endpoint object of class \code{Endpoint} as returned by \code{as.Endpoint}
+#' @field stations object of class \code{citizenair_stations} as returned by \code{\link{read_stations}}
+#' @field data object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}
+#' @format The CitizenAir object is an R6Class
+#' @section Methods:
+#' \describe{
+#'   \item{\code{fetch_timeseries(id = "123", time_span)}}{Get timeseries for Station with \code{id} and a certain time_span The argument \code{timespan.} Passed on to \code{sensorweb4R::getData}}
+#'   \item{\code{getStations()}}{Get a SpatialPointsDataFrame of all stations}
+#' }
+#' @export
 #' @examples
 #' library(sensorweb4R)
 #' e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
-#' ca <- new("CitizenAir", endpoint=e)
+#' ca <- CitizenAir$new(e)
 #' ca
-setClass(Class = "CitizenAir",
-         representation = representation(stations = "citizenair_stations", 
-                                       citizen_data = "citizenair_userdata"))
-setMethod(f = "initialize", 
-          signature = "CitizenAir",
-          definition = function(.Object, endpoint) {            
-            .Object@stations <- read_stations(endpoint)
-            .Object@citizen_data <- citizenair_userdata_empty()
-            .Object
-          })
-
-
-#' @title TODO
-#' @description TODO
-#' @param object the object
-#' @export
-as_sp <- function(object){
-  if(inherits(object, "citizenair_stations")){
-    x <- as.data.frame(object$stations)
-    x <- sp::SpatialPointsDataFrame(coords = x[, c("lon", "lat")], 
-                                    data = x, proj4string = CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"))  
-  }else{
-    stop("not implemented")
-  }
-  x
-}
-
-
-
+#' ca$getPhenomena()
+#' 
+#' library(sp)
+#' x <- ca$getStations()
+#' plot(x)
+#' 
+#' library(lubridate)
+#' x <- ca$fetch_timeseries(id = "1030")
+#' period <- as.interval(as.POSIXct(Sys.Date() - 14), Sys.time())
+#' x <- ca$fetch_timeseries(id = "1030", time_span = period)
+CitizenAir <- R6::R6Class("CitizenAir",
+                      public = list(
+                        endpoint = NULL,
+                        stations = NULL, 
+                        data = NULL,
+                        initialize = function(endpoint) {
+                          self$endpoint <- endpoint
+                          self$stations <- read_stations(endpoint)
+                          self$data <- citizenair_userdata_empty()
+                        },
+                        fetch_timeseries = function(id, time_span=NULL) {  
+                          stopifnot(length(id) == 1)
+                          ## Find and create a stations object
+                          x <- self$stations$stations
+                          x <- as.data.frame(x)
+                          x <- x[x$id %in% id, ]
+                          x <- sp::SpatialPointsDataFrame(coords = x[, c("lon", "lat")], 
+                                                          data = x, 
+                                                          proj4string = CRS("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"))  
+                          st <- sensorweb4R::Station(id = x$id, label = x$label, geometry = x, endpoint = self$endpoint)
+                          ## Get all metadata of time series of that station
+                          ts <- sensorweb4R::timeseries(self$endpoint, station = st)
+                          ts <- sensorweb4R::as.Timeseries(ts)
+                          ts <- sensorweb4R::fetch(ts)
+                          ## Fetch the data of the specified period
+                          result <- list()
+                          for(i in seq_along(ts)){
+                            x <- ts[i]
+                            if(is.null(time_span)){
+                              to <- sensorweb4R::time(sensorweb4R::lastValue(x))
+                              from <- as.POSIXct(seq.Date(from = as.Date(to), by = "-1 year", length.out = 2)[2], tz = "UTC")
+                              timespan <- lubridate::as.interval(from, to)  
+                            }else{
+                              timespan <- time_span
+                            }
+                            df <- sensorweb4R::getData(x, timespan = timespan)
+                            df <- as.data.frame(df)
+                            df$date <- as.Date(df$time)
+                            df$phenomena_id <- sensorweb4R::id(sensorweb4R::Phenomenon(x))
+                            df$phenomena <- self$phenomena_label(df$phenomena_id)
+                            df$phenomena_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
+                        },
+                        getPhenomena = function(){
+                          self$stations$phenomena$id
+                        }
+                      ),
+                      private = list()
+)

citizenair/R/data.R

+#' @title Sample object of class CitizenAir
+#' @description Sample object of class CitizenAir
+#' @docType data
+#' @name ca 
+#' @examples
+#' data("ca", package = "citizenair")
+#' ca
+NULL

citizenair/R/pkg.R

@@ -5,9 +5,12 @@
 #' @importFrom data.table rbindlist melt.data.table setnames as.data.table data.table
 #' @importFrom fasttime fastPOSIXct
 #' @importFrom rmarkdown run
-#' @importFrom sensorweb4R resourceURL id label as.Endpoint
+#' @importFrom sensorweb4R resourceURL id label as.Endpoint fetch timeseries as.Timeseries getData time lastValue firstValue Station
+#' @importFrom lubridate as.interval
 #' @importFrom httr GET content
+#' @importFrom sp CRS SpatialPointsDataFrame
 #' @import methods
+#' @import R6
 NULL
 
 

citizenair/R/read-citizendata.R

@@ -57,19 +57,8 @@ read_citizenair <- function(file = system.file(package = "citizenair", "data-raw
   result
 }
 
-citizenair_userdata_empty <- function(){
-  result <- list()
-  result$filename <- NA_character_
-  result$file <- NA_character_
-  result$time <- Sys.time()
-  result$content <- list()
-  result$phenomena <- character()
-  class(result) <- "citizenair_userdata"
-  result
-}
-
-#' @title Convert excel data to a data.frame
-#' @description Convert excel data to a data.frame
+#' @title Convert citizen Excel data imported with \code{read_citizenair} to a data.frame
+#' @description Convert citizen Excel data imported with \code{read_citizenair} to a data.frame
 #' @param x an object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}
 #' @param type either 'meta' to get the meta information as a data.frame or 'measurements' to get the measurements data.frame
 #' @param row.names not used
@@ -79,7 +68,7 @@ citizenair_userdata_empty <- function(){
 #' @return a data.frame is returned
 #' \enumerate{
 #' \item{in case type is meta: contains fields sheet_id, sheet, device, lat, lon, phenomena}
-#' \item{in case type is data: contains fields sheet_id, timepoint, date, phenomena, value}
+#' \item{in case type is data: contains fields sheet_id, time, date, phenomena, value}
 #' }
 #' @examples 
 #' filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
@@ -109,10 +98,10 @@ as.data.frame.citizenair_userdata <- function(x, row.names, optional, ..., type
       }
       x <- as.data.table(x)
       x <- data.table::melt.data.table(data = x, id.vars = "datum", measure.vars = measurements, na.rm = TRUE, value.name = "value", variable.name = "phenomena")
-      x <- data.table::setnames(x, old = "datum", new = "timepoint")
-      x$date <- as.Date(x$timepoint)
+      x <- data.table::setnames(x, old = "datum", new = "time")
+      x$date <- as.Date(x$time)
       x$sheet_id <- meta$sheet_id
-      x <- data.table::setcolorder(x, c("sheet_id", "timepoint", "date", "phenomena", "value"))
+      x <- data.table::setcolorder(x, c("sheet_id", "time", "date", "phenomena", "value"))
       x
     })
     x <- rbindlist(x)

citizenair/inst/apps/citizenair/citizenair.Rmd

@@ -23,13 +23,13 @@ library(rgeos)
 library(citizenair)
 library(DT)
 library(sp)
-data("BE_ADMIN_REGION")
+data("BE_ADMIN_REGION", package = "BelgiumMaps.StatBel")
 
 dashinput <- list()
 dashinput$endpoint <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
-dashinput$ca <- new("CitizenAir", endpoint = dashinput$endpoint)
+dashinput$ca <- CitizenAir$new(endpoint = dashinput$endpoint)
 dashinput$region <- subset(BE_ADMIN_REGION, TX_RGN_DESCR_NL %in% "Vlaams Gewest")
-dashinput$stations_sp <- as_sp(dashinput$ca@stations)
+dashinput$stations_sp <- dashinput$ca$getStations()
 dashinput$stations_sp <- dashinput$stations_sp[sapply(1:nrow(dashinput$stations_sp), 
                                                       FUN=function(idx) gIntersects(dashinput$region, dashinput$stations_sp[idx, ])), ]
 ```

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

@@ -38,7 +38,7 @@ citizenair_userdata <- reactive({
     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(), timepoint = as.POSIXct(character()), date = as.Date(character()), 
+    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
@@ -184,8 +184,7 @@ renderTable({
   userdata <- citizenair_userdata()
   x <- as.data.table(userdata$data$phenomena)
   if(nrow(x) > 0){
-    x <- x[, meetfrequentie := as.numeric(difftime(timepoint, shift(timepoint, type = "lag", n = 1L), units = "mins")), 
-           by = list(sheet_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)]
     x <- subset(x, !is.na(meetfrequentie))

citizenair/man/CitizenAir-class.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/appdata.R
-\docType{class}
-\name{CitizenAir-class}
-\alias{CitizenAir-class}
-\title{Object of class CitizenAir}
-\arguments{
-\item{endpoint}{An object of class Endpoint as returned by \code{as.Endpoint}}
-}
-\description{
-Object of class CitizenAir
-}
-\section{Slots}{
-
-\describe{
-\item{\code{stations}}{Object of class \code{citizenair_stations} as returned by \code{\link{read_stations}}}
-
-\item{\code{citizen_data}}{Object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}}
-}}
-
-\examples{
-library(sensorweb4R)
-e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
-ca <- new("CitizenAir", endpoint=e)
-ca
-}

citizenair/man/CitizenAir.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/appdata.R
+\docType{class}
+\name{CitizenAir}
+\alias{CitizenAir}
+\title{CitizenAir app data}
+\format{The CitizenAir object is an R6Class}
+\usage{
+CitizenAir
+}
+\description{
+CitizenAir app data
+}
+\section{Fields}{
+
+\describe{
+\item{\code{endpoint}}{object of class \code{Endpoint} as returned by \code{as.Endpoint}}
+
+\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}}}
+}}
+
+\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}
+}
+}
+
+\examples{
+library(sensorweb4R)
+e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
+ca <- CitizenAir$new(e)
+ca
+ca$getPhenomena()
+
+library(sp)
+x <- ca$getStations()
+plot(x)
+
+library(lubridate)
+x <- ca$fetch_timeseries(id = "1030")
+period <- as.interval(as.POSIXct(Sys.Date() - 14), Sys.time())
+x <- ca$fetch_timeseries(id = "1030", time_span = period)
+}
+\keyword{datasets}

citizenair/man/as.data.frame.citizenair_userdata.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/read-citizendata.R
 \name{as.data.frame.citizenair_userdata}
 \alias{as.data.frame.citizenair_userdata}
-\title{Convert excel data to a data.frame}
+\title{Convert citizen Excel data imported with \code{read_citizenair} to a data.frame}
 \usage{
 \method{as.data.frame}{citizenair_userdata}(x, row.names, optional, ...,
   type = c("meta", "measurements"))
@@ -22,11 +22,11 @@
 a data.frame is returned
 \enumerate{
 \item{in case type is meta: contains fields sheet_id, sheet, device, lat, lon, phenomena}
-\item{in case type is data: contains fields sheet_id, timepoint, date, phenomena, value}
+\item{in case type is data: contains fields sheet_id, time, date, phenomena, value}
 }
 }
 \description{
-Convert excel data to a data.frame
+Convert citizen Excel data imported with \code{read_citizenair} to a data.frame
 }
 \examples{
 filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")

citizenair/man/as_sp.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/appdata.R
-\name{as_sp}
-\alias{as_sp}
-\title{TODO}
-\usage{
-as_sp(object)
-}
-\arguments{
-\item{object}{the object}
-}
-\description{
-TODO
-}

citizenair/man/ca.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{ca}
+\alias{ca}
+\title{Sample object of class CitizenAir}
+\description{
+Sample object of class CitizenAir
+}
+\examples{
+data("ca", package = "citizenair")
+ca
+}