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qc_filter.R
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qc_filter.R
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# qc_filter This function is part of the
# R toolbox for accessing Argo float data.
#
# USAGE:
# Data_good = qc_filter(Data, variables, qc_flags)
#
# DESCRIPTION:
# This function generates a new data structure composed of chosen variables
# based on provided QC flag values.
#
# INPUTS:
# Data : list that must contain the given variables
# (_ADJUSTED fields are used if available), as returned by
# function load_float_data
# variables: name(s) of the measured field(s)
# This can be given as string (e.g., 'BBP700') for a single
# variable or vector for multiple variables, e.g.
# c('DOXY','NITRATE')
#
# OPTIONAL INPUTS:
# qc_flags: numerical array of QC flag values (default: c(1,2))
#
# raw : "yes", "no", "no_strict". "yes" (default) raw data will be used
# if no adjusted data are available, "no" : adjusted data for the
# given parameter. "no_strict": skip the float if one of the variable
# is not adjusted
#
#
# OUTPUT:
# Data_good: - if "format" option is not be specified:
# list that contains all the variables from the input Data
# values that match the given QC flags are conserved;
# all other values are set to NA (the size of the arrays is
# unchanged)
# - if "format" option is set to "dataframe": list will be
# converted to a data frame
#
# AUTHORS:
# Marin Cornec (NOAA-PMEL), Yibin Huang (NOAA-PMEL),
# Quentin Jutard (OSU ECCE TERRA), Raphaelle Sauzede (IMEV) and
# Catherine Schmechtig (OSU ECCE TERRA).
#
# CITATION:
# M. Cornec, Y. Huang, Q. Jutard, R. Sauzede, and C. Schmechtig, 2022.
# OneArgo-R: An R toolbox for accessing and visualizing Argo data.
# Zenodo. https://doi.org/10.5281/zenodo.6604650
#
# LICENSE: oneargo_r_license.m
#
# DATE: JUNE 28, 2023
#
qc_filter<-function(Data,
variables="PRES",
qc_flags=NULL,
format=NULL,
raw="yes"
){
# assign default qc_flags if none provided as input
if(is.null(qc_flags)){
qc_flags = c(1,2)
}
if ( is.null (format) ){ # Set to export the data in the format of list if "format" are not specific
format="list"
}
# Add pres variable
if("PRES" %in% variables==F){
if("PRES_ADJUSTED" %in% variables==F){
variables<-c(variables,"PRES")
}
}
nvar = length(variables)
# establish qc list to reference
qc_by_var<-list()
for (v in c(1:nvar)){
qc_by_var[[variables[v]]] = qc_flags
}
variables = names(qc_by_var)
nvar = length(variables)
floats = names(Data)
nfloats = length(floats)
Data_good<-list()
for (f in (1:nfloats)){
# create basic lists to build off of
Data_good[[floats[f]]]$CYCLE_NUMBER<-Data[[floats[f]]]$CYCLE_NUMBER
Data_good[[floats[f]]]$TIME<-Data[[floats[f]]]$TIME
Data_good[[floats[f]]]$LATITUDE<-Data[[floats[f]]]$LATITUDE
Data_good[[floats[f]]]$LONGITUDE<-Data[[floats[f]]]$LONGITUDE
Data_good[[floats[f]]]$JULD<-Data[[floats[f]]]$JULD
for (v in (1:nvar)){
if ( variables[v] %in% names(Data[[f]])==F){
warning(paste("float", floats[f] ,"does not contain variable", variables[v]))
}
else{
if (paste0(variables[v],"_ADJUSTED") %in% names(Data[[f]])==T &&
all(is.na(Data[[floats[f]]][[paste0(variables[v], '_ADJUSTED')]]))==F){
Data_good[[floats[f]]][[variables[v]]]<-
Data[[floats[f]]][[paste0(variables[v], '_ADJUSTED')]]
if(is.null(dim(Data_good[[floats[f]]][[variables[v]]]))){
for (uno in c(1:length(Data[[floats[f]]][[paste0(variables[v],"_ADJUSTED")]]))){
if(Data[[floats[f]]][[paste0(variables[v], '_ADJUSTED_QC')]][uno] %in% qc_by_var[[variables[v]]]==F){
Data_good[[floats[f]]][[variables[v]]][uno]<-NA
}
}
}else{
for (uno in c(1:dim(Data[[floats[f]]][[paste0(variables[v],"_ADJUSTED")]])[1])){
for(duo in c(1:dim(Data[[floats[f]]][[paste0(variables[v],"_ADJUSTED")]])[2])){
if(Data[[floats[f]]][[paste0(variables[v], '_ADJUSTED_QC')]][uno,duo] %in% qc_by_var[[variables[v]]]==F){
Data_good[[floats[f]]][[variables[v]]][uno,duo]<-NA
}
}
}
}
}else if(raw=="no_strict"){
warning(paste("adjusted values for float",floats[f],"for",
variables[v],"are not available, this float will not be used"))
Data_good[[floats[f]]]<-NULL
break
}else if(raw=="no"){
warning(paste("adjusted values for float",floats[f],"for",
variables[v],"are not available, this float will not be used"))
next
}else{
warning(paste("adjusted values for", variables[v],"are not available"))
Data_good[[floats[f]]][[variables[v]]]<-
Data[[floats[f]]][[variables[v]]]
if(is.null(dim(Data_good[[floats[f]]][[variables[v]]]))){
for (uno in c(1:length(Data[[floats[f]]][[variables[v]]]))){
if(Data[[floats[f]]][[variables[v]]][uno] %in% qc_by_var[[variables[v]]]==F){
Data_good[[floats[f]]][[variables[v]]][uno]<-NA
}
}
} else {
for (uno in c(1:dim(Data[[floats[f]]][[variables[v]]])[1])){
for(duo in c(1:dim(Data[[floats[f]]][[variables[v]]])[2])){
if(Data[[floats[f]]][[paste0(variables[v], '_QC')]][uno,duo] %in% qc_by_var[[variables[v]]]==F){
Data_good[[floats[f]]][[variables[v]]][uno,duo]<-NA
}
}
}
}
}
}
}
}
if (format!="dataframe"){
return(Data_good)
}
if (format=="dataframe"){ # convert the data into the data frame format
float_data_list_dtfr= vector("list",
length(Data_good)
)# Create a list to store the multiple data frame for each float data
for (i in 1:length(Data_good) ){ # loop for each float data
float_data_single=Data_good[[i]] # Pull out each float
length_float_data=length( float_data_single$CYCLE_NUMBER)
number_variable_float_data=length(float_data_single)
# create a matrix to deposit the float data
float_data_single_dtfr= matrix (nrow= length_float_data,
ncol= number_variable_float_data)
float_data_single_dtfr=as.data.frame( float_data_single_dtfr)
colnames(float_data_single_dtfr) = names(float_data_single) # names the data frame
# loop to transform the each variable
for (ii in 1: number_variable_float_data ){
float_data_single_dtfr[,ii]=as.vector(float_data_single[[ii]])
} # end loop in number_variable_float_data
float_data_single_dtfr$WMOID= names(Data[i]) # add the WMOID in data frame
# assign data frame into the list array
float_data_list_dtfr[[i]]= float_data_single_dtfr
names( float_data_list_dtfr)[i] <- names(Data_good[i]) # name the each element in list
}# end loop in float_data
# merge multiple dataframes into a single one
tryCatch( {
float_data_list_dtfr=bind_rows(float_data_list_dtfr)
}, error = function(e){
print("data exceeds the memorylimit of dataframe so data isinput as a list containing multiple data frame for each float ")
}
)
return( float_data_list_dtfr)
} # end loop format=="dataframe"
}