Start on constructing appdate + use S4

citizenair/DESCRIPTION

@@ -9,5 +9,5 @@ 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
+Imports: readxl, cellranger, data.table, fasttime, rmarkdown, tools, utils, sensorweb4R, httr, methods
 Suggests: sp

citizenair/NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
-S3method(as.data.frame,citizenair)
+S3method(as.data.frame,citizenair_userdata)
 export(read_citizenair)
+export(read_stations)
 export(run_app)
+exportClasses(CitizenAir)
+import(methods)
 importFrom(cellranger,cell_cols)
 importFrom(cellranger,cell_limits)
 importFrom(cellranger,cell_rows)
 importFrom(data.table,as.data.table)
+importFrom(data.table,data.table)
 importFrom(data.table,melt.data.table)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setnames)
 importFrom(fasttime,fastPOSIXct)
+importFrom(httr,GET)
+importFrom(httr,content)
 importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)
 importFrom(rmarkdown,run)
+importFrom(sensorweb4R,as.Endpoint)
+importFrom(sensorweb4R,id)
+importFrom(sensorweb4R,label)
+importFrom(sensorweb4R,resourceURL)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,capture.output)
 importFrom(utils,head)

citizenair/R/appdata.R

+setClass(Class="citizenair_stations",
+         representation=representation(phenomena = "data.frame", 
+                                       stations = "data.frame"))
+setClass(Class="citizenair_userdata",
+         representation=representation(filename = "character", 
+                                       file = "character", 
+                                       time = "POSIXct", 
+                                       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 
+#' @examples
+#' library(sensorweb4R)
+#' e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
+#' ca <- new("CitizenAir", endpoint=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
+          })
+
+
+
+

citizenair/R/pkg.R

@@ -2,9 +2,12 @@
 #' @importFrom cellranger cell_rows cell_cols cell_limits
 #' @importFrom utils head tail capture.output
 #' @importFrom tools file_path_sans_ext
-#' @importFrom data.table rbindlist melt.data.table setnames as.data.table
+#' @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 httr GET content
+#' @import methods
 NULL
 
 

citizenair/R/read-citizendata.R

@@ -6,7 +6,7 @@
 #' @param name the name of the file, defaults to the basename of the file
 #' @export
 #' @return 
-#' an object of class \code{citizenair} which is a list with elements
+#' an object of class \code{citizenair_userdata} which is a list with elements
 #' \enumerate{
 #' \item{filename: the name of the file}
 #' \item{file: the full path to the excel file}
@@ -30,7 +30,7 @@
 #' \item{several columns, one for each phenomena indicated in the \code{meta} element}
 #' }
 #' @examples 
-#' filename <- system.file(package = "citizenair", "data-raw", "test_dummy.xls")
+#' filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
 #' x <- read_citizenair(filename)
 #' meta <- as.data.frame(x, type = "meta")
 #' measurements <- as.data.frame(x, type = "measurements")
@@ -53,13 +53,24 @@ read_citizenair <- function(file = system.file(package = "citizenair", "data-raw
     result$content[[sheet]]$data <- read_sheet_measurements(file, sheet, sheet_details)
   }
   result$phenomena <- unique(sort(unlist(lapply(result$content, FUN=function(x) names(x$meta$phenomena)))))
-  class(result) <- "citizenair"
+  class(result) <- "citizenair_userdata"
+  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
-#' @param x an object of class \code{citizenair} as returned by \code{\link{read_citizenair}}
+#' @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
 #' @param optional not used
@@ -71,11 +82,11 @@ read_citizenair <- function(file = system.file(package = "citizenair", "data-raw
 #' \item{in case type is data: contains fields sheet_id, timepoint, date, phenomena, value}
 #' }
 #' @examples 
-#' filename <- system.file(package = "citizenair", "data-raw", "test_dummy.xls")
+#' filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
 #' x <- read_citizenair(filename)
 #' meta <- as.data.frame(x, type = "meta")
 #' measurements <- as.data.frame(x, type = "measurements")
-as.data.frame.citizenair <- function(x, row.names, optional, ..., type = c("meta", "measurements")){
+as.data.frame.citizenair_userdata <- function(x, row.names, optional, ..., type = c("meta", "measurements")){
   type <- match.arg(type)
   if(type == "meta"){
     x <- lapply(x$content, FUN=function(x){
@@ -153,7 +164,7 @@ read_sheet_info <- function(file, sheet){
                  measurements_columns = measurements_columns, 
                  measurements_fields = measurements_fields, 
                  data_n = length(datums))
-  class(result) <- "citizenair_excel_locations"
+  class(result) <- "citizenair_userdata_excel_locations"
   result
 }
 

citizenair/R/read-stations.R

+
+#' @title Get CitizenAir Stations
+#' @description Get CitizenAir Stations
+#' @param x an object of class \code{Endpoint} as returned by \code{as.Endpoint}
+#' @export
+#' @return 
+#' an object of class \code{citizenair_stations} which is a list with elements \code{phenomena} and \code{stations}\cr
+#' Element phenomena is a data.table with all phenomena containing fields
+#' \enumerate{
+#' \item{id: identifier of the phenomena}
+#' \item{label: label of the phenomena}
+#' }
+#' Element stations is a data.table with all stations containing fields
+#' \enumerate{
+#' \item{id: identifier of the station}
+#' \item{label: label of the station}
+#' \item{lon: longitude of the station}
+#' \item{lat: latitude of the station}
+#' \item{phenomena: a list of phenomena identifiers for each station}
+#' \item{timeseries: a list of timeseries identifiers for each station}
+#' }
+#' @examples 
+#' library(sensorweb4R)
+#' e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
+#' x <- read_stations(e)
+read_stations <- function(x = sensorweb4R::as.Endpoint("http://geo.irceline.be/sos/api/v1")){
+  stopifnot(inherits(x, "Endpoint"))
+  e <- x
+  url <- sensorweb4R::resourceURL(e)
+  
+  phe <- data.table(id = sensorweb4R::id(sensorweb4R::phenomena(e)),
+                    label = sensorweb4R::label(sensorweb4R::phenomena(e)), 
+                    stringsAsFactors = FALSE)
+  phe <- phe[order(phe$label, decreasing = FALSE), ]
+
+  sta <- httr::GET(url = sprintf("%s/%s", url, "stations"), query = list(expanded="true"))
+  sta <- httr::content(sta)
+  sta <- lapply(sta, FUN=function(x){
+    out <- list(id = x$properties$id, 
+               label = x$properties$label, 
+               lon = x$geometry$coordinates[[1]], 
+               lat = x$geometry$coordinates[[2]], 
+               phenomena = sort(unique(sapply(x$properties$timeseries, FUN=function(x) x$phenomenon$id))),
+               timeseries = sort(unique(names(x$properties$timeseries))))
+    out
+  })
+  stat <- rbindlist(lapply(sta, FUN=function(x) x[c("id", "label", "lon", "lat")]))
+  stat$phenomena <- lapply(sta, FUN=function(x) x$phenomena)
+  stat$timeseries <- lapply(sta, FUN=function(x) x$timeseries)
+  result <- list()
+  result$phenomena <- phe
+  result$stations <- stat
+  class(result) <- "citizenair_stations"
+  result
+}
\ No newline at end of file

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

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/read-citizendata.R
-\name{as.data.frame.citizenair}
-\alias{as.data.frame.citizenair}
+\name{as.data.frame.citizenair_userdata}
+\alias{as.data.frame.citizenair_userdata}
 \title{Convert excel data to a data.frame}
 \usage{
-\method{as.data.frame}{citizenair}(x, row.names, optional, ...,
+\method{as.data.frame}{citizenair_userdata}(x, row.names, optional, ...,
   type = c("meta", "measurements"))
 }
 \arguments{
-\item{x}{an object of class \code{citizenair} as returned by \code{\link{read_citizenair}}}
+\item{x}{an object of class \code{citizenair_userdata} as returned by \code{\link{read_citizenair}}}
 
 \item{row.names}{not used}
 
@@ -29,7 +29,7 @@ a data.frame is returned
 Convert excel data to a data.frame
 }
 \examples{
-filename <- system.file(package = "citizenair", "data-raw", "test_dummy.xls")
+filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
 x <- read_citizenair(filename)
 meta <- as.data.frame(x, type = "meta")
 measurements <- as.data.frame(x, type = "measurements")

citizenair/man/read_citizenair.Rd

@@ -13,7 +13,7 @@ read_citizenair(file = system.file(package = "citizenair", "data-raw",
 \item{name}{the name of the file, defaults to the basename of the file}
 }
 \value{
-an object of class \code{citizenair} which is a list with elements
+an object of class \code{citizenair_userdata} which is a list with elements
 \enumerate{
 \item{filename: the name of the file}
 \item{file: the full path to the excel file}
@@ -41,7 +41,7 @@ Content element data is a data.frame with the measurements containing
 Read in a CitizenAir excel file
 }
 \examples{
-filename <- system.file(package = "citizenair", "data-raw", "test_dummy.xls")
+filename <- system.file(package = "citizenair", "data-raw", "citizenair-example.xls")
 x <- read_citizenair(filename)
 meta <- as.data.frame(x, type = "meta")
 measurements <- as.data.frame(x, type = "measurements")

citizenair/man/read_stations.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read-stations.R
+\name{read_stations}
+\alias{read_stations}
+\title{Get CitizenAir Stations}
+\usage{
+
+  read_stations(x = sensorweb4R::as.Endpoint("http://geo.irceline.be/sos/api/v1"))
+}
+\arguments{
+\item{x}{an object of class \code{Endpoint} as returned by \code{as.Endpoint}}
+}
+\value{
+an object of class \code{citizenair_stations} which is a list with elements \code{phenomena} and \code{stations}\cr
+Element phenomena is a data.table with all phenomena containing fields
+\enumerate{
+\item{id: identifier of the phenomena}
+\item{label: label of the phenomena}
+}
+Element stations is a data.table with all stations containing fields
+\enumerate{
+\item{id: identifier of the station}
+\item{label: label of the station}
+\item{lon: longitude of the station}
+\item{lat: latitude of the station}
+\item{phenomena: a list of phenomena identifiers for each station}
+\item{timeseries: a list of timeseries identifiers for each station}
+}
+}
+\description{
+Get CitizenAir Stations
+}
+\examples{
+library(sensorweb4R)
+e <- as.Endpoint("http://geo.irceline.be/sos/api/v1")
+x <- read_stations(e)
+}