Nothing
R/ChileAirQuality.R
In AtmChile: Download Air Quality and Meteorological Information of Chile
Defines functions
ChileAirQuality
Documented in
ChileAirQuality
#' @title ChileAirQuality
#' @description function that compiles air quality data from the National Air Quality System (S.I.N.C.A.)
#' @param Comunas data vector containing the names or codes of the monitoring
#' stations. Available stations: "P. O'Higgins","Cerrillos 1","Cerrillos","Cerro Navia",
#' "El Bosque","Independecia","La Florida","Las Condes","Pudahuel","Puente Alto","Quilicura",
#' "Quilicura 1","Alto Hospicio","Arica","Las Encinas Temuco","Nielol Temuco",
#' "Museo Ferroviario Temuco","Padre Las Casas I","Padre Las Casas II","La Union",
#' "CESFAM Lago Ranco","Mafil","Fundo La Ribera","Vivero Los Castanos","Valdivia I",
#' "Valdivia II","Osorno","Entre Lagos","Alerce","Mirasol","Trapen Norte","Trapen Sur",
#' "Puerto Varas","Coyhaique I","Coyhaique II","Punta Arenas".
#' To see the full list of stations use ChileAirQuality()
#' @param Parametros data vector containing the names of the air quality parameters.
#' Available parameters: "PM10", "PM25", "CO","SO2", "NOX", "NO2", "NO", "O3",
#' "temp" (temperature), "RH" (relative humidity), "ws" ( wind speed),
#' "wd" (wind direction).
#' @param fechadeInicio text string containing the start date of the data request
#' @param fechadeTermino text string containing the end date of the data request
#' @param Curar logical value that activates data curation for particulate matter,
#' nitrogen oxides, relative humidity and wind direction.
#' @param st logical value that includes validation reports from S.I.N.C.A. "NV": No validated, "PV": Pre-validated, "V": Validated.
#' @param Site logical value that allows entering the code of the monitoring
#' station in the variable "Comunas"
#' @return A data frame with air quality data.
#' @source <https://sinca.mma.gob.cl/>
#' @export
#' @import utils
#' @examples
#'
#' try({
#' stations <- ChileAirQuality()
#' }, silent =TRUE)
#'
#' try({
#' data <- ChileAirQuality(Comunas = "El Bosque",
#' Parametros = c("PM10", "PM25"), fechadeInicio = "01/01/2020",
#' fechadeTermino = "02/01/2020")
#' }, silent =TRUE)
#'
#' try({
#' head(ChileAirQuality(Comunas = c("EB", "SA"),
#' Parametros = "PM10", fechadeInicio = "01/01/2020",
#' fechadeTermino = "01/03/2020", Site = TRUE))
#' }, silent = TRUE)
#'
ChileAirQuality <- function(Comunas = "INFO", Parametros, fechadeInicio, fechadeTermino, Site = FALSE, Curar = TRUE, st = FALSE){
#Find csv file location with list of monitoring stations
sysEstaciones <- system.file("extdata", "SINCA.CSV", package = "AtmChile")
#Data frame with monitoring stations
estationMatrix <- read.csv(sysEstaciones, sep = ",", dec =".", encoding = "UTF-8")
if(any(tolower(Comunas) == "info")){
#Return data frame of stations
return((estationMatrix))
}else{
if(any(tolower(Parametros) =="all")){Parametros <- c("PM10", "PM25", "CO","SO2",
"NOX", "NO2", "NO", "O3", "temp",
"RH" , "ws", "wd")}
if (any(tolower(Comunas) == "all")) {
Comunas <- estationMatrix[[1]] # Extrae la primera columna como vector
Site <- TRUE
}
# input "INFO" to request information from monitoring stations
#Start date format
Fecha_inicio <- as.POSIXct(strptime(paste(fechadeInicio,"1:00"), format = "%d/%m/%Y %H:%M"))
#End date format
Fecha_termino<- as.POSIXct(strptime(paste(fechadeTermino,"23:00"), format = "%d/%m/%Y %H:%M"))
#date range code for url
id_fecha <- gsub(" ","",paste("from=", as.character(format(Fecha_inicio, "%y%m%d")),
"&to=", as.character(format(Fecha_termino, "%y%m%d"))))
#time interval in hours
horas <- (as.numeric(Fecha_termino)/3600-as.numeric(Fecha_inicio)/3600)
#url part 1: Protocol, subdomain, domain and directory
urlSinca <- "https://sinca.mma.gob.cl/cgi-bin/APUB-MMA/apub.tsindico2.cgi?outtype=xcl¯o=./"
#url part 2: query generals parameters
urlSinca2 <- "&path=/usr/airviro/data/CONAMA/&lang=esp&rsrc=¯opath="
# Cleaning variable date
date = NULL
#Date column
date <- seq(Fecha_inicio, Fecha_termino, by = "hour")
#Date column format
date <- format(date, format = "%d/%m/%Y %H:%M")
#Patch that avoids an ERROR
data <- data.frame(date)
#Empty data frame
data_total <- data.frame()
##Selector
#loop input variable "Comunas"
for (i in 1:length(Comunas)) {
try({
## Assign inputs in "Comunas"to variable
inEstation <- Comunas[i]
for(j in 1:nrow(estationMatrix)){
mSite <- estationMatrix[j, 1] #Assign site to variable
mCod <- estationMatrix[j, 2] #Assign code to variable
mLon <- estationMatrix[j, 3] #Assign latitude to variable
mLat <- estationMatrix[j, 4] #Assign longitude to variable
mEstation <- estationMatrix[j, 5] #Assign station to variable
#Verify "Site" control parameter
if(Site){
#Compare "Comunas" with the Sites column
aux <- mSite
}else{
#Compare "Comunas" with the Full Names column
aux <- mEstation
}
##If the comparison is fulfilled, do:
if(inEstation == aux){
try({
#Generate site column
site <- rep(mSite, horas + 1)
#Generate longitude and latitude column
longitude <- rep(mLat, horas + 1)
latitude <- rep(mLon, horas + 1)
# Join the columns dates, longitude and latitude
data <- data.frame(date, site, longitude, latitude)
{
#Loop input variable "Parametros"
for(p in 1:length(Parametros))
{
#Assign "Parametros" to variable
inParametro <- Parametros[p]
# If input parameter is PM10, do:
if(tolower(inParametro) == "pm10")
{
#sub query for the parameter PM10
codParametro <- "/Cal/PM10//PM10.horario.horario.ic&"
#Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
PM10_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
PM10 <- apply(PM10_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.PM10 <- apply(PM10_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(PM10) == 0 && st) s.PM10 <- rep("", horas + 1)
data <- data.frame(data, s.PM10)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(PM10) == 0){PM10 <- rep("", horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, PM10)
# Print success message
print(paste(inParametro, inEstation))
}
,silent = T)
}
# If input parameter is PM25, do:
else if(tolower(inParametro) == "pm25")
{
#sub query for the parameter
codParametro <- "/Cal/PM25//PM25.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca,
mCod, codParametro, id_fecha,
urlSinca2))
try(
{
#Download csv file
PM25_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
PM25 <- apply(PM25_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.PM25 <- apply(PM25_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(PM25) == 0 && st) s.PM25 <- rep("", horas + 1)
data <- data.frame(data, s.PM25)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(PM25) == 0){PM25 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,PM25)
# Print success message
print(paste(inParametro, inEstation))
}
, silent = TRUE)
}
# If input parameter is Ozone, do:
else if(tolower(inParametro) == "o3")
{
#sub query for the parameter
codParametro <- "/Cal/0008//0008.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro,
id_fecha, urlSinca2))
try(
{
#Download csv file
O3_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
O3 <- apply(O3_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.O3 <- apply(O3_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(O3) == 0 && st) s.O3 <- rep("", horas + 1)
data <- data.frame(data, s.O3)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(O3) == 0){O3 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, O3)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is carbon monoxide, do:
else if( tolower(inParametro) == "co")
{
# sub query for the parameter
codParametro <- "/Cal/0004//0004.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro,
id_fecha, urlSinca2))
try(
{
#Download csv file
CO_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
CO <- apply(CO_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.CO <- apply(CO_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(CO) == 0 && st) s.CO <- rep("", horas + 1)
data <- data.frame(data, s.CO)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(CO) == 0){CO <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, CO)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is nitrogen monoxide, do:
else if(tolower(inParametro) == "no")
{
# sub query for the parameter
codParametro <- "/Cal/0002//0002.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro,
id_fecha, urlSinca2))
try(
{
#Download csv file
NO_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
NO <- apply(NO_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.NO <- apply(NO_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(NO) == 0 && st) s.NO <- rep("", horas + 1)
data <- data.frame(data, s.NO)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(NO) == 0){NO <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, NO)
# Print success message
print(paste(inParametro,inEstation))
}
,silent = T)
}
# If input parameter is nitrogen dioxide, do:
else if(tolower(inParametro) == "no2")
{
# sub query for the parameter
codParametro <- "/Cal/0003//0003.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
NO2_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
NO2 <- apply(NO2_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.NO2 <- apply(NO2_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(NO2) == 0 && st) s.NO2 <- rep("", horas + 1)
data <- data.frame(data, s.NO2)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(NO2) == 0){NO2 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, NO2)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is nitrogen oxide, do:
else if(tolower(inParametro) == "nox")
{
# sub query for the parameter
codParametro <- "/Cal/0NOX//0NOX.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
NOX_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
NOX <- apply(NOX_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.NOX <- apply(NOX_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(NOX) == 0 && st) s.NOX <- rep("", horas + 1)
data <- data.frame(data, s.NOX)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(NOX) == 0){NOX <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, NOX)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is sulfur dioxide, do:
else if(tolower(inParametro) == "so2")
{
# sub query for the parameter
codParametro <- "/Cal/0001//0001.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
SO2_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
SO2 <- apply(SO2_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.SO2 <- apply(SO2_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(SO2) == 0 && st) s.SO2 <- rep("", horas + 1)
data <- data.frame(data, s.SO2)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(SO2) == 0){SO2 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, SO2)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is temperature, do:
else if(tolower(inParametro) == "temp")
{
# sub query for the parameter
codParametro <- "/Met/TEMP//horario_000.ic&"
codParametro_alt <- "/Met/TEMP//horario_002.ic&"
# Concatenate URL
url <- gsub(" ", "", paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download CSV file
temp_bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(temp_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
temp_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
temp_col1 <- temp_bruto$X
temp <- gsub("NA","",gsub(" ", "",temp_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(temp) == 0){temp <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, temp)
# Print success message
print(paste(inParametro, inEstation))
}
, silent = TRUE)
}
#If input parameter is RH, do:
else if(tolower(inParametro) %in% c("hr", "rh"))
{
# sub query for the parameter
codParametro <- "/Met/RHUM//horario_000.ic&"
codParametro_alt <-"/Met/RHUM//horario_002.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca,
mCod, codParametro, id_fecha,
urlSinca2))
try(
{
#Download CSV file
HR_bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(HR_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
HR_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
HR_col1 <- HR_bruto$X
HR <- gsub("NA","",gsub(" ", "",HR_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(HR) == 0){HR <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,HR)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
#If input parameter is wind direction, do:
else if(tolower(inParametro) == "wd")
{
# sub query for the parameter
codParametro <- "/Met/WDIR//horario_000_spec.ic&"
codParametro_alt <- "/Met/WDIR//horario_010_spec.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download CSV file
wd_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(wd_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
wd_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
wd_col1 <- wd_bruto$X
wd <- gsub("NA","",gsub(" ", "",wd_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(wd) == 0 ){wd <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,wd)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
#If input parameter is wind speed, do:
else if(tolower(inParametro) == "ws")
{
# sub query for the parameter
codParametro <- "/Met/WSPD//horario_000.ic&"
codParametro_alt <- "/Met/WSPD//horario_010.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download CSV file
ws_bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(ws_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
ws_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
ws_col1 <- ws_bruto$X
ws <- gsub("NA","",gsub(" ", "",ws_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(ws) == 0){ws <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,ws)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
#If the input parameter is not one of the list, do:
else
{
# Print failure message
print(paste("Parametro",inParametro,"no soportado en la libreria")) #Generar mensaje de fracaso
}
}
try(
{
# Join the df of each station to the global dataframe
data_total <- rbind(data_total, data)
}
, silent = T)
}
}
, silent = T)
}
}
}, silent = T)
}
#Control mechanism: If "Curar" is true, do:
if(Curar){
#Variable that stores the number of rows in the dataframe
len = nrow(data_total)
## First data curation tool: nitrogen oxides
## As long as the nitrogen oxides are not empty columns, do:
if((length(data_total$NO) != 0) &
(length(data_total$NO2) != 0) &
(length(data_total$NOX) != 0)){
try({
for (i in 1:len)
{
try(
{
#If the sum of NO and NO2 is greater than NOX Eliminate the data of NO, NO2 and NOX considering an error of 0.1%
if((as.numeric(data_total$NO[i]) + as.numeric(data_total$NO2[i])) > as.numeric(data_total$NOX[i]) * 1.001){
data_total$NO[i] = ""
data_total$NO2[i] = ""
data_total$NOX[i] = ""
}
}
, silent = T)
}
}, silent = T)
}
#Second data curation tool: particulate matter
if((length(data_total$PM25) != 0) &
(length(data_total$PM10) != 0)){
try({
for (i in 1:len)
{
try(
{
# If PM25 is greater than PM10, delete PM10 and PM25, considering an error of 0.1%
if(as.numeric(data_total$PM25[i]) > as.numeric(data_total$PM10[i])*1.001){
data_total$PM10[i] = ""
data_total$PM25[i] = ""
}
}
,silent = T)
}
}, silent = T)
}
try({
#Third control mechanism: wind direction
for (i in 1:len)
{
try({
#If the wind direction is less than 0 or greater than 360, delete the data
if(as.numeric(data_total$wd[i]) > 360||as.numeric(data_total$wd[i]) < 0){
data_total$wd[i] = ""
}
}, silent = T)
}
}, silent = T)
try({
i =NULL
#Fourth control mechanism: Relative humidity
for (i in 1:len)
{
try(
{
##If the relative humidity is greater than 100% delete the data
if(as.numeric(data_total$HR[i]) > 100||as.numeric(data_total$HR[i]) <0){
data_total$HR[i] = ""
}
}, silent = T)
}
}, silent = T)
}
#transform columns into numeric variables
if(!st){
for(i in 3:ncol(data_total)){
data_total[[i]] <- as.numeric(data_total[[i]])
}
}else{
for(i in 3:ncol(data_total)){
val <- TRUE
j <- 1
while(val){
if(data_total[j, i] == ""| is.na(data_total[j, i])){
j <- j + 1
if(j > nrow(data_total)){
val <- FALSE
}
}
if(data_total[j, i] != "NV" & data_total[j, i] != "PV" & data_total[j, i] != "V"){
data_total[[i]] <- as.numeric(data_total[[i]])
val <- FALSE
}else{
val <- FALSE
}
}
}
}
#print final success message
print("Datos Capturados!")
#return df global
return(data_total)
}
}
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Defines functions ChileAirQuality
Documented in ChileAirQuality
#' @title ChileAirQuality
#' @description function that compiles air quality data from the National Air Quality System (S.I.N.C.A.)
#' @param Comunas data vector containing the names or codes of the monitoring
#' stations. Available stations: "P. O'Higgins","Cerrillos 1","Cerrillos","Cerro Navia",
#' "El Bosque","Independecia","La Florida","Las Condes","Pudahuel","Puente Alto","Quilicura",
#' "Quilicura 1","Alto Hospicio","Arica","Las Encinas Temuco","Nielol Temuco",
#' "Museo Ferroviario Temuco","Padre Las Casas I","Padre Las Casas II","La Union",
#' "CESFAM Lago Ranco","Mafil","Fundo La Ribera","Vivero Los Castanos","Valdivia I",
#' "Valdivia II","Osorno","Entre Lagos","Alerce","Mirasol","Trapen Norte","Trapen Sur",
#' "Puerto Varas","Coyhaique I","Coyhaique II","Punta Arenas".
#' To see the full list of stations use ChileAirQuality()
#' @param Parametros data vector containing the names of the air quality parameters.
#' Available parameters: "PM10", "PM25", "CO","SO2", "NOX", "NO2", "NO", "O3",
#' "temp" (temperature), "RH" (relative humidity), "ws" ( wind speed),
#' "wd" (wind direction).
#' @param fechadeInicio text string containing the start date of the data request
#' @param fechadeTermino text string containing the end date of the data request
#' @param Curar logical value that activates data curation for particulate matter,
#' nitrogen oxides, relative humidity and wind direction.
#' @param st logical value that includes validation reports from S.I.N.C.A. "NV": No validated, "PV": Pre-validated, "V": Validated.
#' @param Site logical value that allows entering the code of the monitoring
#' station in the variable "Comunas"
#' @return A data frame with air quality data.
#' @source <https://sinca.mma.gob.cl/>
#' @export
#' @import utils
#' @examples
#'
#' try({
#' stations <- ChileAirQuality()
#' }, silent =TRUE)
#'
#' try({
#' data <- ChileAirQuality(Comunas = "El Bosque",
#' Parametros = c("PM10", "PM25"), fechadeInicio = "01/01/2020",
#' fechadeTermino = "02/01/2020")
#' }, silent =TRUE)
#'
#' try({
#' head(ChileAirQuality(Comunas = c("EB", "SA"),
#' Parametros = "PM10", fechadeInicio = "01/01/2020",
#' fechadeTermino = "01/03/2020", Site = TRUE))
#' }, silent = TRUE)
#'
ChileAirQuality <- function(Comunas = "INFO", Parametros, fechadeInicio, fechadeTermino, Site = FALSE, Curar = TRUE, st = FALSE){
#Find csv file location with list of monitoring stations
sysEstaciones <- system.file("extdata", "SINCA.CSV", package = "AtmChile")
#Data frame with monitoring stations
estationMatrix <- read.csv(sysEstaciones, sep = ",", dec =".", encoding = "UTF-8")
if(any(tolower(Comunas) == "info")){
#Return data frame of stations
return((estationMatrix))
}else{
if(any(tolower(Parametros) =="all")){Parametros <- c("PM10", "PM25", "CO","SO2",
"NOX", "NO2", "NO", "O3", "temp",
"RH" , "ws", "wd")}
if (any(tolower(Comunas) == "all")) {
Comunas <- estationMatrix[[1]] # Extrae la primera columna como vector
Site <- TRUE
}
# input "INFO" to request information from monitoring stations
#Start date format
Fecha_inicio <- as.POSIXct(strptime(paste(fechadeInicio,"1:00"), format = "%d/%m/%Y %H:%M"))
#End date format
Fecha_termino<- as.POSIXct(strptime(paste(fechadeTermino,"23:00"), format = "%d/%m/%Y %H:%M"))
#date range code for url
id_fecha <- gsub(" ","",paste("from=", as.character(format(Fecha_inicio, "%y%m%d")),
"&to=", as.character(format(Fecha_termino, "%y%m%d"))))
#time interval in hours
horas <- (as.numeric(Fecha_termino)/3600-as.numeric(Fecha_inicio)/3600)
#url part 1: Protocol, subdomain, domain and directory
urlSinca <- "https://sinca.mma.gob.cl/cgi-bin/APUB-MMA/apub.tsindico2.cgi?outtype=xcl¯o=./"
#url part 2: query generals parameters
urlSinca2 <- "&path=/usr/airviro/data/CONAMA/&lang=esp&rsrc=¯opath="
# Cleaning variable date
date = NULL
#Date column
date <- seq(Fecha_inicio, Fecha_termino, by = "hour")
#Date column format
date <- format(date, format = "%d/%m/%Y %H:%M")
#Patch that avoids an ERROR
data <- data.frame(date)
#Empty data frame
data_total <- data.frame()
##Selector
#loop input variable "Comunas"
for (i in 1:length(Comunas)) {
try({
## Assign inputs in "Comunas"to variable
inEstation <- Comunas[i]
for(j in 1:nrow(estationMatrix)){
mSite <- estationMatrix[j, 1] #Assign site to variable
mCod <- estationMatrix[j, 2] #Assign code to variable
mLon <- estationMatrix[j, 3] #Assign latitude to variable
mLat <- estationMatrix[j, 4] #Assign longitude to variable
mEstation <- estationMatrix[j, 5] #Assign station to variable
#Verify "Site" control parameter
if(Site){
#Compare "Comunas" with the Sites column
aux <- mSite
}else{
#Compare "Comunas" with the Full Names column
aux <- mEstation
}
##If the comparison is fulfilled, do:
if(inEstation == aux){
try({
#Generate site column
site <- rep(mSite, horas + 1)
#Generate longitude and latitude column
longitude <- rep(mLat, horas + 1)
latitude <- rep(mLon, horas + 1)
# Join the columns dates, longitude and latitude
data <- data.frame(date, site, longitude, latitude)
{
#Loop input variable "Parametros"
for(p in 1:length(Parametros))
{
#Assign "Parametros" to variable
inParametro <- Parametros[p]
# If input parameter is PM10, do:
if(tolower(inParametro) == "pm10")
{
#sub query for the parameter PM10
codParametro <- "/Cal/PM10//PM10.horario.horario.ic&"
#Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
PM10_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
PM10 <- apply(PM10_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.PM10 <- apply(PM10_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(PM10) == 0 && st) s.PM10 <- rep("", horas + 1)
data <- data.frame(data, s.PM10)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(PM10) == 0){PM10 <- rep("", horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, PM10)
# Print success message
print(paste(inParametro, inEstation))
}
,silent = T)
}
# If input parameter is PM25, do:
else if(tolower(inParametro) == "pm25")
{
#sub query for the parameter
codParametro <- "/Cal/PM25//PM25.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca,
mCod, codParametro, id_fecha,
urlSinca2))
try(
{
#Download csv file
PM25_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
PM25 <- apply(PM25_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.PM25 <- apply(PM25_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(PM25) == 0 && st) s.PM25 <- rep("", horas + 1)
data <- data.frame(data, s.PM25)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(PM25) == 0){PM25 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,PM25)
# Print success message
print(paste(inParametro, inEstation))
}
, silent = TRUE)
}
# If input parameter is Ozone, do:
else if(tolower(inParametro) == "o3")
{
#sub query for the parameter
codParametro <- "/Cal/0008//0008.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro,
id_fecha, urlSinca2))
try(
{
#Download csv file
O3_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
O3 <- apply(O3_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.O3 <- apply(O3_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(O3) == 0 && st) s.O3 <- rep("", horas + 1)
data <- data.frame(data, s.O3)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(O3) == 0){O3 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, O3)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is carbon monoxide, do:
else if( tolower(inParametro) == "co")
{
# sub query for the parameter
codParametro <- "/Cal/0004//0004.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro,
id_fecha, urlSinca2))
try(
{
#Download csv file
CO_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
CO <- apply(CO_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.CO <- apply(CO_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(CO) == 0 && st) s.CO <- rep("", horas + 1)
data <- data.frame(data, s.CO)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(CO) == 0){CO <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, CO)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is nitrogen monoxide, do:
else if(tolower(inParametro) == "no")
{
# sub query for the parameter
codParametro <- "/Cal/0002//0002.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro,
id_fecha, urlSinca2))
try(
{
#Download csv file
NO_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
NO <- apply(NO_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.NO <- apply(NO_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(NO) == 0 && st) s.NO <- rep("", horas + 1)
data <- data.frame(data, s.NO)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(NO) == 0){NO <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, NO)
# Print success message
print(paste(inParametro,inEstation))
}
,silent = T)
}
# If input parameter is nitrogen dioxide, do:
else if(tolower(inParametro) == "no2")
{
# sub query for the parameter
codParametro <- "/Cal/0003//0003.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
NO2_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
NO2 <- apply(NO2_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.NO2 <- apply(NO2_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(NO2) == 0 && st) s.NO2 <- rep("", horas + 1)
data <- data.frame(data, s.NO2)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(NO2) == 0){NO2 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, NO2)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is nitrogen oxide, do:
else if(tolower(inParametro) == "nox")
{
# sub query for the parameter
codParametro <- "/Cal/0NOX//0NOX.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
NOX_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
NOX <- apply(NOX_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.NOX <- apply(NOX_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(NOX) == 0 && st) s.NOX <- rep("", horas + 1)
data <- data.frame(data, s.NOX)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(NOX) == 0){NOX <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, NOX)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is sulfur dioxide, do:
else if(tolower(inParametro) == "so2")
{
# sub query for the parameter
codParametro <- "/Cal/0001//0001.horario.horario.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download csv file
SO2_Bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
# Join columns of files
SO2 <- apply(SO2_Bruto[, c("Registros.validados", "Registros.preliminares", "Registros.no.validados")], 1,
function(row) gsub("NA", "", paste0(row, collapse = "")))
if (st) {
s.SO2 <- apply(SO2_Bruto[, c("Registros.validados",
"Registros.preliminares",
"Registros.no.validados")], 1,
function(row) {
if (!is.na(row[1])) "V"
else if (!is.na(row[2])) "PV"
else if (!is.na(row[3])) "NV"
else ""
})
# Asegurar que las longitudes coincidan
if (length(SO2) == 0 && st) s.SO2 <- rep("", horas + 1)
data <- data.frame(data, s.SO2)
}
# Control mechanism: if the file is not found, it generates an empty column
if(length(SO2) == 0){SO2 <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, SO2)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
# If input parameter is temperature, do:
else if(tolower(inParametro) == "temp")
{
# sub query for the parameter
codParametro <- "/Met/TEMP//horario_000.ic&"
codParametro_alt <- "/Met/TEMP//horario_002.ic&"
# Concatenate URL
url <- gsub(" ", "", paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download CSV file
temp_bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(temp_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
temp_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
temp_col1 <- temp_bruto$X
temp <- gsub("NA","",gsub(" ", "",temp_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(temp) == 0){temp <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data, temp)
# Print success message
print(paste(inParametro, inEstation))
}
, silent = TRUE)
}
#If input parameter is RH, do:
else if(tolower(inParametro) %in% c("hr", "rh"))
{
# sub query for the parameter
codParametro <- "/Met/RHUM//horario_000.ic&"
codParametro_alt <-"/Met/RHUM//horario_002.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca,
mCod, codParametro, id_fecha,
urlSinca2))
try(
{
#Download CSV file
HR_bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(HR_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
HR_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
HR_col1 <- HR_bruto$X
HR <- gsub("NA","",gsub(" ", "",HR_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(HR) == 0){HR <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,HR)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
#If input parameter is wind direction, do:
else if(tolower(inParametro) == "wd")
{
# sub query for the parameter
codParametro <- "/Met/WDIR//horario_000_spec.ic&"
codParametro_alt <- "/Met/WDIR//horario_010_spec.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download CSV file
wd_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(wd_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
wd_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
wd_col1 <- wd_bruto$X
wd <- gsub("NA","",gsub(" ", "",wd_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(wd) == 0 ){wd <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,wd)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
#If input parameter is wind speed, do:
else if(tolower(inParametro) == "ws")
{
# sub query for the parameter
codParametro <- "/Met/WSPD//horario_000.ic&"
codParametro_alt <- "/Met/WSPD//horario_010.ic&"
# Concatenate URL
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro, id_fecha, urlSinca2))
try(
{
#Download CSV file
ws_bruto <- read.csv(url,dec =",", sep= ";",na.strings= "")
if(length(ws_bruto)<2){
url <- gsub(" ", "",paste(urlSinca, mCod, codParametro_alt, id_fecha, urlSinca2))
ws_bruto <-read.csv(url,dec =",", sep= ";",na.strings= "")
}
# Join columns of files
ws_col1 <- ws_bruto$X
ws <- gsub("NA","",gsub(" ", "",ws_col1))
# Control mechanism: if the file is not found, it generates an empty column
if(length(ws) == 0){ws <- rep("",horas + 1)}
# Incorporate the column into the station data frame
data <- data.frame(data,ws)
# Print success message
print(paste(inParametro,inEstation))
}
, silent = TRUE)
}
#If the input parameter is not one of the list, do:
else
{
# Print failure message
print(paste("Parametro",inParametro,"no soportado en la libreria")) #Generar mensaje de fracaso
}
}
try(
{
# Join the df of each station to the global dataframe
data_total <- rbind(data_total, data)
}
, silent = T)
}
}
, silent = T)
}
}
}, silent = T)
}
#Control mechanism: If "Curar" is true, do:
if(Curar){
#Variable that stores the number of rows in the dataframe
len = nrow(data_total)
## First data curation tool: nitrogen oxides
## As long as the nitrogen oxides are not empty columns, do:
if((length(data_total$NO) != 0) &
(length(data_total$NO2) != 0) &
(length(data_total$NOX) != 0)){
try({
for (i in 1:len)
{
try(
{
#If the sum of NO and NO2 is greater than NOX Eliminate the data of NO, NO2 and NOX considering an error of 0.1%
if((as.numeric(data_total$NO[i]) + as.numeric(data_total$NO2[i])) > as.numeric(data_total$NOX[i]) * 1.001){
data_total$NO[i] = ""
data_total$NO2[i] = ""
data_total$NOX[i] = ""
}
}
, silent = T)
}
}, silent = T)
}
#Second data curation tool: particulate matter
if((length(data_total$PM25) != 0) &
(length(data_total$PM10) != 0)){
try({
for (i in 1:len)
{
try(
{
# If PM25 is greater than PM10, delete PM10 and PM25, considering an error of 0.1%
if(as.numeric(data_total$PM25[i]) > as.numeric(data_total$PM10[i])*1.001){
data_total$PM10[i] = ""
data_total$PM25[i] = ""
}
}
,silent = T)
}
}, silent = T)
}
try({
#Third control mechanism: wind direction
for (i in 1:len)
{
try({
#If the wind direction is less than 0 or greater than 360, delete the data
if(as.numeric(data_total$wd[i]) > 360||as.numeric(data_total$wd[i]) < 0){
data_total$wd[i] = ""
}
}, silent = T)
}
}, silent = T)
try({
i =NULL
#Fourth control mechanism: Relative humidity
for (i in 1:len)
{
try(
{
##If the relative humidity is greater than 100% delete the data
if(as.numeric(data_total$HR[i]) > 100||as.numeric(data_total$HR[i]) <0){
data_total$HR[i] = ""
}
}, silent = T)
}
}, silent = T)
}
#transform columns into numeric variables
if(!st){
for(i in 3:ncol(data_total)){
data_total[[i]] <- as.numeric(data_total[[i]])
}
}else{
for(i in 3:ncol(data_total)){
val <- TRUE
j <- 1
while(val){
if(data_total[j, i] == ""| is.na(data_total[j, i])){
j <- j + 1
if(j > nrow(data_total)){
val <- FALSE
}
}
if(data_total[j, i] != "NV" & data_total[j, i] != "PV" & data_total[j, i] != "V"){
data_total[[i]] <- as.numeric(data_total[[i]])
val <- FALSE
}else{
val <- FALSE
}
}
}
}
#print final success message
print("Datos Capturados!")
#return df global
return(data_total)
}
}
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