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SO2_P21_1907.R
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SO2_P21_1907.R
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###########################################################################################################################
## Project: NEXTDATA ##
## Parameter: SO2 ##
## Script first purpose: create a formatted Level-1 and Level-2 dataset (in EBAS format) from Level-0 data ##
## Script second purpose: none ##
## Run time: the script may run daily (e.g. by using a crontab) or may be used when needed ##
##_______________________________________________________________________________________________________________________##
## Authors: Luca Naitza, Davide Putero ##
## Organization: National Research Council of Italy, Institute for Atmospheric Science and Climate (CNR-ISAC) ##
## Address: Via Gobetti 101, 40129, Bologna, Italy ##
## Project Contact: Paolo Cristofanelli ##
## Email: P.Cristofanelli@isac.cnr.it ##
## Phone number: (+39) 051 639 9597 ##
##_______________________________________________________________________________________________________________________##
## Script filename: SO2_P21_1810.R ##
## Version Date: July 2019
## Jul. 31st, 2019: "days_ref" substituted with "dependent_col", i.e., the number of dependent data columns (in the header)
###########################################################################################################################
# > > > > > > > > > > > > > > I N S T R U C T I O N S < < < < < < < < < < < < < < < < < < < < < < < < #
#
# This script consists of several parts and sub-parts.
#
# Part 0 is the setting section, in which the User should replace the marked values (e.g. directory paths)
# Part 0.1 defines environmental variables, such as raw data and destination directories. The user should modify these values.
# Part 0.2 specifies some characteristics of raw data tables, such as file extension, fields separators, etc. The user should
# modify these values according to his/her tables format. If the procedure requires more than one parameter
# setting, Part 0.2 is divided in sub-sub-parts (e.g. 0.2.1 , 0.2.2,...)
# Part 0.3 specifies the characteristics of User Station/Laboratory/Instrument/parameter. Most of these variables are used
# as metadata in the EBAS file format header. The User should provide proper information.
#
# Part 1 is another setting section; it should not be modified by the User unless strictly needed.
# Part 1.1 sets and loads the most commonly used R libraries. The User should not modify this sub-part.
# Part 1.2 specifies the time variables used in the processing. The User should not modify this sub-part. If the User needs
# to apply the script to data older than the current year, he/she may modify the lines explicitly marked for this purpose.
#
# Part 2 is the data processing section, it should not be modified by the User.
# Part 2.x contain the code to produce the EBAS format file and to process data. The User should not modify this sub-part(s).
#
#
# > > > > > > > > > > > > > > > > > > > > > > > > > > > < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < #
###########################################################################################################################
## # PART 0.1 #
## ______________________________________________________________________________________________________________________##
## Setting environmental variables
## ______________________________________________________________________________________________________________________##
## USE: set the following paths of origin raw data and of destination processing data, replacing values with yours
# WARNING: Proper setting up of the following paths and values is crucial. Please, replace the strings correctly
#
setwd("~/")
# -------- RAW DATA PATH ----------------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
CALIB_DIR = '../naitza/NEXTDATA/PROD/CIMONE/GAS/SO2/RAW_DATA_UTC/CALIB'
RAW_DIR = '../naitza/NEXTDATA/PROD/CIMONE/GAS/SO2/RAW_DATA_UTC'
#
# -------- DATA DESTINATION PATH --------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
L0_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/LEVEL_0'
L1_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/LEVEL_1'
L2_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/LEVEL_2'
L0_ANCIL_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/LEVEL_0/ANCILLARY'
#
# -------- GRAPH DESTINATION PATH -------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
REP_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT'
REP_GRAPH_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT/DAILY_GRAPH'
PLOT_DIR_M = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT/MONTHLY_GRAPH'
PLOT_DIR_S = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT/SEASONAL_GRAPH'
PLOT_DIR_Y = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT/ANNUAL_GRAPH'
PLOT_DIR_Y_PDF = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT/ANNUAL_GRAPH/PDF'
PLOT_DIR_T = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/GAS/SO2/REPORT/TIMEVARIATION_GRAPH'
#
# -------- SCRIPTS PATH ----------------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
SCRIPT_DIR = '../naitza/NEXTDATA/R_SCRIPT'
## Loading functions for numflags
## The "NXD_numflag_functions_180301.R" scripts assigns the numflag value to the Data set, according to EBAS Flag List
## (https://ebas-submit.nilu.no/Submit-Data/List-of-Data-flags)
## The "NXD_EBAS_numflag_FullList_180103.txt" text file contains the EBAS Flag List, reporting codes, category and description
## Please, do NOT apply any change to the following function settings, unless you need to specify a different table of flags
#
source(paste(SCRIPT_DIR,"NXD_numflag_functions_180301.R", sep="/"))
tab_nf <- read.table(file = paste(SCRIPT_DIR,"NXD_EBAS_numflag_FullList_180103.txt",sep="/"),
sep = ";", header = TRUE, quote = NULL)
## # END PART 0.1 #
###########################################################################################################################
###########################################################################################################################
## # PART 0.3 #
## ______________________________________________________________________________________________________________________##
## Setting time and name variables
## Setting EBAS metadata information
## ______________________________________________________________________________________________________________________##
# Station/Laboratory/Instrument/parameter variables
#
# -------- EBAS HEADER FILE (METADATA) -----------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
s_code <- "IT0009R" # replace the value with your Station code
s_WDCA_ID <- "GAWANO_CMN" # replace the value with your WDCA ID code
s_GAW_Name <- "Monte Cimone" # replace the value with your Station GAW name
s_GAW_ID <- "CMN" # replace the value with your Station GAW ID
s_lat <- "44.16667" # replace the value with your Station latitude
s_lon <- "10.68333" # replace the value with your Station longitude
s_alt <- "2165m" # replace the value with your Station altitude (meters)
s_l_use <- "Remote park" # replace the value with your Station land use
s_setting <- "Mountain" # replace the value with your Station setting
s_GAW_t <- "G" # replace the value with your Station GAW type
s_WMO_reg <- "6" # replace the value with your Station WMO region
lab_code <- "IT06L" # replace the value with your laboratory code
inst_type <- "UV_fluorescence" # replace the value with your instrument type
inst_manu <- "Thermo" # replace the value with your instrument manufacter
inst_modl <- "43iTLE" # replace the value with your instrument model
inst_name <- "43i" # replace the value with your your instrument name
inst_s_n <- " " # replace the value with your instrument serial number
meth_ref <- "IT06L_43i_uvfl" # replace the value with method reference
dependent_col <- "3" # replace the value with the total number of columns of the file in addition to start_time (i.e., total-1)
component <- "sulphur dioxide" # replace the value with proper component
matrix <- "air" # replace the value with proper matrix
meas_unit <- "ppb" # replace the value with proper measurement unit
meas_lat <- "44.16667" # replace the value with the your Measure latitude
meas_lon <- "10.68333" # replace the value with the your Measure longitude
meas_alt <- "2165m" # replace the value with the your Measure altitude (meters)
Period_code <- "1y" # replace the value with the proper Period code
Resolution_code <- "1mn" # replace the value with the proper Resolution code
Sample_duration <- "1mn" # replace the value with the proper Sample duration
Orig_time_res <- "1mn" # replace the value with the proper Original time resolution
std_meth <- "SOP=GAW_209(2013)" # replace the value with Standard method
inlet_type <- "Hat or hood" # replace the value with Inlet type
inlet_desc <- "The air intake is composed by an external (outside building) steel pipe (internally covered by Teflon) and the internal (inside building) Pyrex pipe" # replace the value with Inlet description
inlet_mat <- "Teflon" # replace the value with Inlet material
inlet_out_d <- "6.35 mm" # replace the value with Inlet outer diameter
inlet_in_d <- "" # replace the value with Inlet inner diameter
inlet_lenght <- "1.5 m" # replace the value with Inlet tube length
flow_rate <- "0.40 l/min" # replace the value with Flow rate
zero_check <- "automatic" # replace the value with Zero/span check type
zero_inter <- "1d" # replace the value with Zero/span check interval
hum_temp_c <- "none" # replace the value with Humidity/temperature control
hum_temp_c_desc <- "" # replace the value with Humidity/temperature control description
vol_std_t <- "293.15 K" # replace the value with Volume std. temperature
vol_std_p <- "1013.25 hPa" # replace the value with Volume std. pressure
detec_lim <- "0.11 ppb" # replace the value with Detection limit
absorp_cs <- "" # replace the value with Absorption cross section
qa_mes_id <- "not available" # replace the value with QA measure ID
#qa_date <- "not available" # replace the value with QA date
qa_doc <- "not available" # replace the value with QA document URL
qa_bias <- "0.2 ppb" # replace the value with QA bias
# The following variabiles concern the originator and the submitter names, surnames, emails and addresses
# NOTE: Please, change these variables with proper names, surnames, emails and addresses
#
# -------- ORIGINATORS (set min 1 originator, max 5) ---------------------------------------------------------------# REPLACE THE FOLLOWING VALUES
Origin_1_n <- "Paolo"
Origin_1_s <- "Cristofanelli"
Origin_1_e <- "p.cristofanelli@isac.cnr.it"
Origin_1_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_2_n <- "Luca"
Origin_2_s <- "Naitza"
Origin_2_e <- "l.naitza@isac.cnr.it"
Origin_2_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_3_n <- "Davide"
Origin_3_s <- "Putero"
Origin_3_e <- "d.putero@isac.cnr.it"
Origin_3_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_4_n <- "Francescopiero"
Origin_4_s <- "Calzolari"
Origin_4_e <- "f.calzolari@isac.cnr.it"
Origin_4_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_5_n <- ""
Origin_5_s <- ""
Origin_5_e <- ""
Origin_5_i <- ""
# -------- SUBMITTER (set the submitter) --------------------------------------------------------------------------# REPLACE THE FOLLOWING VALUES
Submit_1_n <- "Paolo"
Submit_1_s <- "Cristofanelli"
Submit_1_e <- "p.cristofanelli@isac.cnr.it"
Submit_1_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
mycomment <- ""
#
# Setting the lines of the header
#
if (nchar(Origin_2_n) == 0 && nchar(Origin_3_n) == 0 && nchar(Origin_4_n) == 0 && nchar(Origin_5_n) == 0) { L1_n_lines <- 80 + 0 ; L2_n_lines <- 81 + 0 ; }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) == 0 && nchar(Origin_4_n) == 0 && nchar(Origin_5_n) == 0) { L1_n_lines <- 80 + 1 ; L2_n_lines <- 81 + 1 ; }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) > 0 && nchar(Origin_4_n) == 0 && nchar(Origin_5_n) == 0) { L1_n_lines <- 80 + 2 ; L2_n_lines <- 81 + 2 ; }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) > 0 && nchar(Origin_4_n) > 0 && nchar(Origin_5_n) == 0) { L1_n_lines <- 80 + 3 ; L2_n_lines <- 81 + 3 ; }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) > 0 && nchar(Origin_4_n) > 0 && nchar(Origin_5_n) > 0) { L1_n_lines <- 80 + 4 ; L2_n_lines <- 81 + 4 ; }
#
# -------------------------------------------------------------------------------------------
## # END PART 0.3 #
###########################################################################################################################
###########################################################################################################################
## # PART 1.0 #
## ______________________________________________________________________________________________________________________##
## Loading libraries
## ______________________________________________________________________________________________________________________##
## NOTE: some of the following libraries may not be actually used by this script
# Please, do NOT apply any change, unless it is necessary to load specific libraries
#
library(data.table)
library(openair)
library(lattice)
library(RColorBrewer)
library(latticeExtra)
library(proto)
library(gsubfn)
library(RSQLite)
library(padr)
library(caTools)
library(zoo)
library(plyr)
library(forecast)
library("sqldf")
library(TTR)
library(ggplot2)
library(reshape2)
library(stringr)
library(png)
#
## # END PART 1.0 #
###########################################################################################################################
###########################################################################################################################
## # PART 1.1 #
## ______________________________________________________________________________________________________________________##
## Setting time and name variables
## Cleaning destination directory
## ______________________________________________________________________________________________________________________##
#
#
# -------------------------------------------------------------------------------------------
# Time variables
# NOTE: the following variables should not be modified, except those with explicit comments
#
questo_anno <-format(Sys.Date(), "%Y")
#
# -------- PREVIOUS YEAR(S) DATA PROCESSING ---------------------------------------# IF NEEDED, UN-COMMENT THE FOLLOWING LINE
#questo_anno <-as.numeric(questo_anno) -1 # the value "-1" means "last year". Change to "-2" or "-3" etc. for previous
#
questo_mese <-format(Sys.Date(), "%m")
questo_mese_nome <-format(Sys.Date(), "%B")
questo_giorno <-format(Sys.Date(), "%d")
if (questo_mese == "01" & questo_giorno == "01") { questo_anno == questo_anno-1 }
questo_capodanno <-paste(questo_anno,"01","01",sep="-")
questo_annomesegiorno <-paste(questo_anno,questo_mese,questo_giorno,sep="")
questa_ora <-format(Sys.time(), "%H")
questo_minuto <-format(Sys.time(), "%M")
questo_inizioanno <-paste(questo_anno,"0101000000",sep = "")
questi_dati <-paste(s_code,questo_inizioanno,sep = ".")
questa_start_time <-as.Date(paste(paste(questo_anno,"01","01",sep = "-"), " 00:00:00",sep = ""))
myweekday <-as.POSIXlt(Sys.Date())$wday
questo_startdate <-paste(questo_anno,"0101",sep="")
new_date <-gsub("-","",
gsub(" ","",
gsub(":","",
as.character(strptime(Sys.time(),
format = "%Y - %m - %d %H : %M")))))
new_date_name <-paste(".",new_date,sep="")
rev_datime <-gsub("-","",
gsub(" ","",
gsub(":","",
as.character(strptime(new_date,
format = "%Y%m%d%H%M%S")-3600))))
DATA_OSS <-paste(questo_anno,"01 01")
DATA_REV <-gsub("-"," ",Sys.Date())
DATA_INSERT <-paste(DATA_OSS,DATA_REV,sep=" ")
#
# -------------------------------------------------------------------------------------------
# Reading EBAS Level-0 data
# NOTE: Please, do NOT change these variables
#
DEST_lsdata <- list.files(path = L0_DIR, pattern = paste(s_code,questo_inizioanno,sep = "."), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA <-as.character(DEST_lsdata[1])
#
#
# -------------------------------------------------------------------------------------------
# File name variables
# NOTE: the following variables should not be modified
#
old_date <-substr(LISTA, 23, 37)
EBAS_L1_FILENAME <-gsub("lev0","lev1",gsub(old_date,new_date_name,LISTA))
EBAS_L1_FULLFILENAME <-paste(L1_DIR,EBAS_L1_FILENAME,sep = "/")
EBAS_L2_FILENAME <-gsub("lev0","lev2",gsub("1mn","1h",gsub(old_date,new_date_name,LISTA)))
EBAS_L2_FULLFILENAME <-paste(L2_DIR,EBAS_L2_FILENAME,sep = "/")
# -------------------------------------------------------------------------------------------
# Check point: printing variables
#
questo_anno
questo_mese
questo_mese_nome
questo_giorno
questo_capodanno
questo_annomesegiorno
questa_ora
questo_minuto
questo_inizioanno
questa_start_time
myweekday
questo_startdate
new_date
new_date_name
rev_datime
old_date
EBAS_L1_FILENAME
EBAS_L1_FULLFILENAME
EBAS_L2_FILENAME
EBAS_L2_FULLFILENAME
#
## # END PART 1.1 #
###########################################################################################################################
###########################################################################################################################
## # PART 2.0 #
## ______________________________________________________________________________________________________________________##
## Creation of Level-1 data file
## Cleaning Destination directory
## Formatting Level-1 header
## ______________________________________________________________________________________________________________________##
#
# -------------------------------------------------------------------------------------------
# Deleting temporary files in the destination directory (if present)
#
FILE_TMP <-list.files(path = L1_DIR, pattern = glob2rx("temp_*"), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA_FILE_TMP <-as.character(FILE_TMP)
LISTA_FILE_TMP
for(f in LISTA_FILE_TMP) { file.remove(paste(L1_DIR,f,sep = "/")) }
#
# -------------------------------------------------------------------------------------------
# Cleaning Destination directory
# NOTE: the following process deletes old EBAS Level-0 files within the destination directory
#
MYOLD_FILE <-paste(s_code,".",questo_anno,sep = "")
FILE_L1 <-list.files(path = L1_DIR, pattern = glob2rx(paste(MYOLD_FILE,"*",sep = "")), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA_FILE_OLD<-as.character(FILE_L1)
for(f in LISTA_FILE_OLD) { file.remove(paste(L1_DIR,f,sep = "/")) }
FILE_L2 <-list.files(path = L2_DIR, pattern = glob2rx(paste(MYOLD_FILE,"*",sep = "")), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA_FILE_OLD<-as.character(FILE_L2)
for(f in LISTA_FILE_OLD) { file.remove(paste(L2_DIR,f,sep = "/")) }
#
# -------------------------------------------------------------------------------------------
# Creating the new EBAS LEVEL-1 data file
# NOTE: the following process deletes old EBAS Level-1 files within the destination directory
#
write.table(" ", file=EBAS_L1_FULLFILENAME,row.names=F,col.names = F, append = F,sep=" ")
#
# -------------------------------------------------------------------------------------------
# Formatting EBAS LEVEL-0 header and adding information to the data file
# NOTE: information contained in the following lines should be modified with proper station and instrumentation information
#
cat(
paste(L1_n_lines,"1001",sep=" "),
gsub("; $","",gsub("; ;","",paste(paste(Origin_1_n,Origin_1_s,sep=", "),
ifelse(nchar(Origin_2_n)>0,
(paste(Origin_2_n,Origin_2_s,sep=", ")), ""),
ifelse(nchar(Origin_3_n)>0,
(paste(Origin_3_n,Origin_3_s,sep=", ")), ""),
ifelse(nchar(Origin_4_n)>0,
(paste(Origin_4_n,Origin_4_s,sep=", ")), ""),
ifelse(nchar(Origin_5_n)>0,
(paste(Origin_5_n,Origin_5_s,sep=", ")), ""),
sep="; "))),
paste(lab_code, Origin_1_i,sep=", "),
paste(Submit_1_n, Submit_1_s, sep=", "),
"GAW-WDCA, ACTRIS
1 1",
DATA_INSERT,
"0
Days from the file reference point (start_time)",
dependent_col,
"1 1 1
9999.99999999 9999.99 9.999999999
end_time, days from the file reference point
sulphur_dioxide, ppb
numflag sulphur_dioxide, no unit
0",
(L1_n_lines - 17),
"Data definition: EBAS_1.1
Data level: 1
Version: 1
Version description: initial revision
Set type code: TI",
paste("Station code: ",s_code,sep=""),
paste("Platform code: ",gsub("R","S",s_code)),
"Timezone: UTC",
paste("Startdate: ",questo_inizioanno[1],sep=""),
paste("Revision date: ",as.numeric(new_date)-7200,sep=""),
paste("Component: ",component,sep=""),
paste("Matrix: ",matrix,sep=""),
paste("Unit: ",meas_unit,sep=""),
paste("Period code: ",Period_code,sep=""),
paste("Resolution code: ",Resolution_code,sep=""),
paste("Sample duration: ",Sample_duration,sep=""),
paste("Orig. time res.: ",Orig_time_res,sep=""),
paste("Laboratory code: ",lab_code,sep=""),
paste("Instrument type: ",inst_type,sep=""),
paste("Instrument manufacturer: ",inst_manu,sep=""),
paste("Instrument model: ",inst_modl,sep=""),
paste("Instrument name: ",inst_name,sep=""),
paste("Instrument serial number: ",inst_s_n,sep=""),
paste("Method ref: ",meth_ref,sep=""),
paste("File name: ",EBAS_L1_FILENAME,sep=""),
paste("File creation: ",rev_datime[1],sep=""),
paste("Station WDCA-ID: ",s_WDCA_ID,sep=""),
paste("Station GAW-Name: ",s_GAW_Name,sep=""),
paste("Station GAW-ID: ",s_GAW_ID,sep=""),
paste("Station latitude: ",s_lat,sep=""),
paste("Station longitude: ",s_lon,sep=""),
paste("Station altitude: ",s_alt,sep=""),
paste("Station land use: ",s_l_use,sep=""),
paste("Station setting: ",s_setting,sep=""),
paste("Station GAW type: ",s_GAW_t,sep=""),
paste("Station WMO region: ",s_WMO_reg,sep=""),
paste("Measurement latitude: ",meas_lat,sep=""),
paste("Measurement longitude: ",meas_lon,sep=""),
paste("Measurement altitude: ",meas_alt,sep=""),
paste("Inlet type: ",inlet_type,sep=""),
paste("Inlet description: ",inlet_desc,sep=""),
paste("Inlet tube material: ",inlet_mat,sep=""),
paste("Inlet tube outer diameter: ",inlet_out_d,sep=""),
paste("Inlet tube inner diameter: ",inlet_in_d,sep=""),
paste("Inlet tube length: ",inlet_lenght,sep=""),
paste("Humidity/temperature control: ",hum_temp_c,sep=""),
paste("Humidity/temperature control description: ",hum_temp_c_desc,sep=""),
paste("Volume std. temperature: ",vol_std_t,sep=""),
paste("Volume std. pressure: ",vol_std_p,sep=""),
paste("Detection limit: ",detec_lim,sep=""),
paste("Absorption cross section: ",absorp_cs,sep=""),
paste("Zero/span check type: ",zero_check,sep=""),
paste("Zero/span check interval: ",zero_inter,sep=""),
paste("Standard method: ",std_meth,sep=""),
paste("QA measure ID ",qa_mes_id,sep=""),
paste("QA date: ",paste(questo_anno,questo_mese,questo_giorno,sep=""),sep=""),
paste("QA1 bias: ",qa_bias,sep=""),
paste("QA document URL: ",qa_doc,sep=""),
paste("Originator: ",paste(Origin_1_n,Origin_1_s,Origin_1_e,Origin_1_i,sep=", "),sep=""),
paste("Originator: ",paste(Origin_2_n,Origin_2_s,Origin_2_e,Origin_2_i,sep=", "),sep=""),
paste("Originator: ",paste(Origin_3_n,Origin_3_s,Origin_3_e,Origin_3_i,sep=", "),sep=""),
if(nchar(Origin_4_n)>0) {paste("Originator: ",paste(Origin_4_n,Origin_4_s,Origin_4_e,Origin_4_i,sep=", "),sep="")},
if(nchar(Origin_5_n)>0) {paste("Originator: ",paste(Origin_5_n,Origin_5_s,Origin_5_e,Origin_5_i,sep=", "),sep="")},
paste("Submitter: ",paste(Submit_1_n,Submit_1_s,Submit_1_e,Submit_1_i,sep=", "),sep=""),
paste("Comment: ",mycomment,sep=""),
"Acknowledgement: Request acknowledgment details from data originator",
paste("start_time","end_time","so2","numflag_so2",sep=" "),
file=EBAS_L1_FULLFILENAME, append=F, sep = "\n")
#
## # END PART 2.0 #
###########################################################################################################################
###########################################################################################################################
## # PART 2.1 #
## ______________________________________________________________________________________________________________________##
## Importing Level-0 data
## Processing, manipulation, transformation of Level-0 data
## Level-1 data flagging
## Writing data in Level-1 data file (EBAS format)
## ______________________________________________________________________________________________________________________##
#
# -------------------------------------------------------------------------------------------
#Reading header lines of Level-0 Data sheet
#
L0_n_lines <- as.integer(unlist(strsplit(readLines(paste(L0_DIR,LISTA,sep = "/"), n=1), " "))[1])
#
# Creating temporary table from Level-0
#
temp_data <- read.table(paste(L0_DIR,LISTA,sep = "/"),skip = L0_n_lines-1, header = T,fill = T)
temp_data$numflag <- temp_data$numflag_so2
#
# -------------------------------------------------------------------------------------------
# Converting JD values to date
#
temp_data$jd <-as.integer(temp_data$start_time)
temp_data$day <-as.Date(temp_data$start_time, origin=questa_start_time)
temp_data$time.dec <-temp_data$start_time-temp_data$jd
temp_data$time <-temp_data$time.dec*1440+0.01
temp_data$hour <-as.integer(temp_data$time/60)
temp_data$min <-as.integer(temp_data$time-temp_data$hour*60)
temp_data$date <-paste(temp_data$day," ",temp_data$hour,":",temp_data$min,":00",sep="")
temp_data$date <-as.POSIXct(strptime(temp_data$date, format = "%Y-%m-%d %H:%M:%S"))
#
# -------------------------------------------------------------------------------------------
# Padding data from January 1st to today
#
temp_data <- pad(temp_data,
start_val = as.POSIXct(paste(questa_start_time," 00:00:00")),
end_val = tail(temp_data$date,1),
interval = "min", by = "date")
#
# -------------------------------------------------------------------------------------------
#
# Updating start_time and end_time, after padding
#
jd <-strptime(temp_data$date, "%Y-%m-%d %H:%M")$yday
h <-strptime(temp_data$date, "%Y-%m-%d %H:%M")$hour
m <-strptime(temp_data$date, "%Y-%m-%d %H:%M")$min
time <-h*60+m
time.dec <-time/1440
time1.dec <-time.dec+0.00069444
temp_data$start_time <-jd+time.dec
temp_data$end_time <-jd+time1.dec
#
# -------------------------------------------------------------------------------------------
# Retrieving valid or not numflags and setting the invalid values to NA
#
temp_data$calc <- temp_data$so2
temp_data$nf_validity <- sapply(temp_data$numflag, nf_val_check, tab_nf$numflag, tab_nf$category)
temp_data$calc[temp_data$nf_validity != "V"] <- NA
#
# -------------------------------------------------------------------------------------------
# Calculating running mean and sd
#
time_frame <- 60*24*7
temp_data$calc_mean <- runmean(temp_data$calc, time_frame, align = "center", endrule = "mean")
temp_data$calc_sd <- runsd (temp_data$calc, time_frame, align = "center", endrule = "sd")
temp_data$nf_bad <- 0
for (i in 1:length(temp_data$date))
{ if (!is.na(temp_data$calc[i]) &
(abs((temp_data$calc[i]-temp_data$calc_mean[i])) > 7*temp_data$calc_sd[i]))
{ temp_data$nf_bad[i] <- 1 }
}
#
# -------------------------------------------------------------------------------------------
# Correction of negative values with smoothing values
#
temp_data$so2_smooth <- runmean(temp_data$calc, time_frame, align = "left" , endrule = "mean")
for (i in 1:nrow(temp_data))
{
if (!is.na(temp_data$so2_smooth[i]) &
(temp_data$so2_smooth[i] < 0))
{ temp_data$so2[i] <- temp_data$so2[i] - temp_data$so2_smooth[i] }
}
#
# -------------------------------------------------------------------------------------------
# Setting numflag codes to invalid and special cases
#
temp_data$so2 [is.na(temp_data$so2) ] <- 9999.99
#
temp_data$numflag [temp_data$so2 == 9999.99] <- 0.999
temp_data$numflag [is.na(temp_data$numflag)] <- 0.999
temp_data$numflag_so2 <- temp_data$numflag
#
# -------------------------------------------------------------------------------------------
# Writing the final Data set
# Formatting the output matrix as required by EBAS format Level-1
#
myEBAS <- temp_data[,c("start_time","end_time","so2","numflag_so2")]
#
sprintf_formats <- c(rep("%.6f", 2), "%.2f", "%.9f")
myEBAS[] <- mapply(sprintf, sprintf_formats, myEBAS)
#
# Appending Data set to EBAS Level-1 Header
#
write.table(myEBAS, file=EBAS_L1_FULLFILENAME,row.names=F,col.names = F, append = T, quote = F,sep=" ")
#
# -------------------------------------------------------------------------------------------
# Deleting temporary files in the destination directory (if present)
#
FILE_TMP <-list.files(path = L1_DIR, pattern = glob2rx("temp_*"), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA_FILE_TMP <-as.character(FILE_TMP)
LISTA_FILE_TMP
for(f in LISTA_FILE_TMP) { file.remove(paste(L1_DIR,f,sep = "/")) }
# -------------------------------------------------------------------------------------------
## # END PART 2.1 #
###########################################################################################################################
###########################################################################################################################
## # PART 2.2 #
## ______________________________________________________________________________________________________________________##
## Creation of Level-2 data file
## Cleaning Destination directory
## Formatting Level-2 header
## ______________________________________________________________________________________________________________________##
#
# -------------------------------------------------------------------------------------------
# Deleting temporary files in the destination directory (if present)
#
FILE_TMP <-list.files(path = L2_DIR, pattern = glob2rx("temp_*"), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA_FILE_TMP <-as.character(FILE_TMP)
LISTA_FILE_TMP
for(f in LISTA_FILE_TMP) { file.remove(paste(L2_DIR,f,sep = "/")) }
# -------------------------------------------------------------------------------------------
#
write.table("",file=EBAS_L2_FULLFILENAME,row.names=F,col.names = F, append = F, quote = F)
#
# -------------------------------------------------------------------------------------------
# Formatting EBAS LEVEL-2 header and adding information to the data file
#
cat(
paste(L2_n_lines,"1001",sep=" "),
gsub("; $","",gsub("; ;","",paste(paste(Origin_1_n,Origin_1_s,sep=", "),
ifelse(nchar(Origin_2_n)>0,
(paste(Origin_2_n,Origin_2_s,sep=", ")), ""),
ifelse(nchar(Origin_3_n)>0,
(paste(Origin_3_n,Origin_3_s,sep=", ")), ""),
ifelse(nchar(Origin_4_n)>0,
(paste(Origin_4_n,Origin_4_s,sep=", ")), ""),
ifelse(nchar(Origin_5_n)>0,
(paste(Origin_5_n,Origin_5_s,sep=", ")), ""),
sep="; "))),
paste(lab_code, Origin_1_i,sep=", "),
paste(Submit_1_n, Submit_1_s, sep=", "),
"GAW-WDCA, ACTRIS
1 1",
DATA_INSERT,
"0.041667
Days from the file reference point (start_time)
5
1 1 1 1 1
999.999999 999.99 9.999999999 999.99 9.999999999
end_time of measurement, days from the file reference point
SO2, nmol/mol, Statistics=arithmetic mean
numflag SO2, no unit, Statistics=arithmetic mean
SO2, nmol/mol, Statistics=stddev
numflag
0",
(L2_n_lines - 19),
"Data definition: EBAS_1.1
Data level: 2
Version: 1
Version description: initial revision, automatically inspected
Set type code: TU",
paste("Station code: ",s_code,sep=""),
paste("Platform code: ",gsub("R","S",s_code)),
"Timezone: UTC",
paste("Startdate: ",questo_inizioanno[1],sep=""),
paste("Revision date: ",as.numeric(new_date)-7200,sep=""),
paste("Component: ","sulphur dioxide",sep=""),
paste("Matrix: ",matrix,sep=""),
paste("Unit: ",meas_unit,sep=""),
paste("Period code: ","1y",sep=""),
paste("Resolution code: ","1h",sep=""),
paste("Sample duration: ","1h",sep=""),
paste("Orig. time res.: ",Orig_time_res,sep=""),
paste("Laboratory code: ",lab_code,sep=""),
paste("Instrument type: ",inst_type,sep=""),
paste("Instrument manufacturer: ",inst_manu,sep=""),
paste("Instrument model: ",inst_modl,sep=""),
paste("Instrument name: ",paste(inst_manu,inst_modl,s_GAW_ID,sep = "_"),sep=""),
paste("Instrument serial number: ",inst_s_n,sep=""),
paste("Method ref: ","IT06L_43i_uvfl",sep=""),
paste("File name: ",EBAS_L2_FILENAME,sep=""),
paste("File creation: ",rev_datime[1],sep=""),
paste("Station WDCA-ID: ",s_WDCA_ID,sep=""),
paste("Station GAW-Name: ",s_GAW_Name,sep=""),
paste("Station GAW-ID: ",s_GAW_ID,sep=""),
paste("Station latitude: ",s_lat,sep=""),
paste("Station longitude: ",s_lon,sep=""),
paste("Station altitude: ",s_alt,sep=""),
paste("Station land use: ",s_l_use,sep=""),
paste("Station setting: ",s_setting,sep=""),
paste("Station GAW type: ",s_GAW_t,sep=""),
paste("Station WMO region: ",s_WMO_reg,sep=""),
paste("Measurement latitude: ",meas_lat,sep=""),
paste("Measurement longitude: ",meas_lon,sep=""),
paste("Measurement altitude: ",meas_alt,sep=""),
paste("Inlet type: ",inlet_type,sep=""),
paste("Inlet description: ",inlet_desc,sep=""),
paste("Inlet tube material: ",inlet_mat,sep=""),
paste("Inlet tube outer diameter: ",inlet_out_d,sep=""),
paste("Inlet tube inner diameter: ",inlet_in_d,sep=""),
paste("Inlet tube length: ",inlet_lenght,sep=""),
paste("Humidity/temperature control: ",hum_temp_c,sep=""),
paste("Humidity/temperature control description: ",hum_temp_c_desc,sep=""),
paste("Volume std. temperature: ",vol_std_t,sep=""),
paste("Volume std. pressure: ",vol_std_p,sep=""),
paste("Detection limit: ",detec_lim,sep=""),
paste("Absorption cross section: ",absorp_cs,sep=""),
paste("Zero/span check type: ",zero_check,sep=""),
paste("Zero/span check interval: ",zero_inter,sep=""),
paste("Standard method: ",std_meth,sep=""),
paste("QA measure ID ",qa_mes_id,sep=""),
paste("QA date: ",paste(questo_anno,questo_mese,questo_giorno,sep=""),sep=""),
paste("QA document URL: ",qa_doc,sep=""),
paste("Originator: ",paste(Origin_1_n,Origin_1_s,Origin_1_e,Origin_1_i,sep=", "),sep=""),
paste("Originator: ",paste(Origin_2_n,Origin_2_s,Origin_2_e,Origin_2_i,sep=", "),sep=""),
paste("Originator: ",paste(Origin_3_n,Origin_3_s,Origin_3_e,Origin_3_i,sep=", "),sep=""),
if(nchar(Origin_4_n)>0) {paste("Originator: ",paste(Origin_4_n,Origin_4_s,Origin_4_e,Origin_4_i,sep=", "),sep="")},
if(nchar(Origin_5_n)>0) {paste("Originator: ",paste(Origin_5_n,Origin_5_s,Origin_5_e,Origin_5_i,sep=", "),sep="")},
paste("Submitter: ",paste(Submit_1_n,Submit_1_s,Submit_1_e,Submit_1_i,sep=", "),sep=""),
paste("Comment: ",mycomment,sep=""),
"Acknowledgement: Request acknowledgment details from data originator",
paste("start_time","end_time","so2","flag_so2","so2std","flag_so2std",sep=" "),
file=EBAS_L2_FULLFILENAME, append=F, sep = "\n")
#
# -------------------------------------------------------------------------------------------
## # END PART 2.2 #
###########################################################################################################################
###########################################################################################################################
## # PART 2.3 #
## ______________________________________________________________________________________________________________________##
## Processing, manipulation, transformation of Level-1 data
## Level-2 data flagging
## Writing data in Level-2 data file (EBAS format)
## ______________________________________________________________________________________________________________________##
#
# -------------------------------------------------------------------------------------------
# Checking valid and invalid data
# Preparing Level-2 data
#
temp_data$nf_validity <- sapply(temp_data$numflag, nf_val_check, tab_nf$numflag, tab_nf$category)
temp_data_sub <- subset(temp_data, temp_data$nf_validity == "V",
select=c("so2","numflag","date"))
temp_data_sub$numflag <- as.numeric(temp_data_sub$numflag)
#
# Setting NA to invalid data
# -------------------------------------------------------------------------------------------
#
temp_data_sub$so2 [temp_data_sub$so2 == 9999.99] <- NA
#
# Calculating 1h data averages
# -------------------------------------------------------------------------------------------
#
# Calculating last observed day (not necessarily the last acquisition day)
#
final_time <-as.POSIXct(ISOdatetime(questo_anno,questo_mese,questo_giorno,23,59,0), tz = "UTC") - 60*60*24
#
# -------------------------------------------------------------------------------------------
# Calculating 1h data averages
#
lev2_SO2_avg <- timeAverage(temp_data_sub,
avg.time = "hour", statistic = "mean",
start.date = questo_capodanno,
end.date = as.character(final_time))
lev2_SO2_sd <- timeAverage(temp_data_sub,
avg.time = "hour",
statistic = "sd",
start.date=questo_capodanno,
end.date = as.character(final_time))
lev2_SO2_perc16 <- timeAverage(temp_data_sub,
avg.time = "hour",
statistic = "percentile", percentile = 15.87,
start.date=questo_capodanno,
end.date = as.character(final_time))
lev2_SO2_perc84 <- timeAverage(temp_data_sub,
avg.time = "hour",
statistic = "percentile", percentile = 84.13,
start.date=questo_capodanno,
end.date = as.character(final_time))
lev2_SO2_n <- timeAverage(temp_data_sub,
avg.time = "hour",
statistic = "frequency",
start.date = paste(questo_anno,"01-01",sep = "-"),
end.date = as.character(final_time))
#
# -------------------------------------------------------------------------------------------
# Calculating JD from date
#
jd <- strptime(lev2_SO2_avg$date, "%Y-%m-%d %H:%M")$yday
h <- strptime(lev2_SO2_avg$date, "%Y-%m-%d %H:%M")$hour
time <- h*60
time.dec <- time/1440
lev2_SO2_avg$start_time <- jd+time.dec
lev2_SO2_avg$end_time <- lev2_SO2_avg$start_time+1/24
#
# Formatting the EBAS format Level-2 matrix
#
EBAS_lev2_SO2 <- data.frame(cbind (lev2_SO2_avg$start_time,
lev2_SO2_avg$end_time,
lev2_SO2_avg$so2,
lev2_SO2_sd$so2,
lev2_SO2_perc16$so2,
lev2_SO2_perc84$so2,
lev2_SO2_n$so2))
colnames(EBAS_lev2_SO2) <- c("start_time","end_time","so2","so2std","so2_16","so2_84","freq")
#
# -------------------------------------------------------------------------------------------
# Setting NAs data and flagging data
#
bad_numflags <- c("000",as.character(tab_nf$numflag[tab_nf$category != "V"]))
EBAS_lev2_SO2$numflag <- sapply(EBAS_lev2_SO2$start_time,
nf_lev2,
numflags_mm=myEBAS$numflag,
startime_mm=myEBAS$start_time,
nv_numflags=bad_numflags)
EBAS_lev2_SO2$numflag [!is.na(EBAS_lev2_SO2$freq)
& EBAS_lev2_SO2$freq >= 30 &
EBAS_lev2_SO2$freq < 45] <- sapply(EBAS_lev2_SO2$numflag[!is.na(EBAS_lev2_SO2$freq) &
EBAS_lev2_SO2$freq >= 30 &
EBAS_lev2_SO2$freq < 45] ,
nf_aggreg, nf_new = 0.392)
EBAS_lev2_SO2$numflag [!is.na(EBAS_lev2_SO2$freq) &
EBAS_lev2_SO2$freq < 30] <- sapply(EBAS_lev2_SO2$numflag[!is.na(EBAS_lev2_SO2$freq) &
EBAS_lev2_SO2$freq < 30] ,
nf_aggreg, nf_new = 0.390)
EBAS_lev2_SO2$so2 [is.na(EBAS_lev2_SO2$so2) ]<- 9999.9
EBAS_lev2_SO2$so2std [is.na(EBAS_lev2_SO2$so2std)]<- 9999.9
EBAS_lev2_SO2$numflag [EBAS_lev2_SO2$so2 == 9999.9]<- 0.999
EBAS_lev2_SO2$numflag_sd <- EBAS_lev2_SO2$numflag
#
# Appending Data set to EBAS Level-0 Header
#
EBAS_lev2_SO2 <-EBAS_lev2_SO2[,c("start_time","end_time","so2","numflag","so2std", "numflag_sd")]
#
# -------------------------------------------------------------------------------------------
# Writing the final Level-2 Data set
# Formatting the output matrix as required by EBAS format Level-2
# Appending Data set to EBAS Level-2 Header
#
sprintf_formats_l2 <- c(rep("%.6f", 2), "%.2f", "%.9f", "%.2f", "%.9f")
#
EBAS_lev2_SO2[] <- mapply(sprintf, sprintf_formats_l2, EBAS_lev2_SO2)
#
write.table(EBAS_lev2_SO2, file=EBAS_L2_FULLFILENAME,row.names=F,col.names = F, append = T, quote = F,sep=" ")
#
# -------------------------------------------------------------------------------------------
## # END PART 2.3 #
###########################################################################################################################
# #
## End of SO2_P21_1810.R #
# #
###################################################################################### Authors: L u C A, Davide ###########