R/importADMS.R
In davidcarslaw/ggopenair: Tools for the Analysis of Air Pollution Data
##' CERC Atmospheric Dispersion Modelling System (ADMS) data import function(s) for openair
##'
##' Function(s) to import various ADMS file types into openair. Currently
##' handles ".met", ".bgd", ".mop" and ".pst" file structures. Uses
##' \code{read.csv} (in \code{utils}) to read in data, format for R and openair
##' and apply some file structure testing.
##'
##' The \code{importADMS} function were developed to help import various ADMS
##' file types into openair. In most cases the parent import function should
##' work in default configuration, e.g. \code{mydata <- importADMS()}. The
##' function currently recognises four file formats: \code{.bgd}, \code{.met},
##' \code{.mop} and \code{.pst}. Where other file extensions have been set but
##' the file structure is known, the import call can be forced by, e.g,
##' \code{mydata <- importADMS(file.type="bgd")}. Other options can be adjusted
##' to provide fine control of the data structuring and renaming.
##'
##' @aliases importADMS importADMSBgd importADMSMet importADMSMop importADMSPst
##' @param file The ADMS file to be imported. Default, \code{file.choose()}
##' opens browser. Use of \code{read.csv} (in \code{utils}) also allows this
##' to be a readable text-mode connection or url (although these options are
##' currently not fully tested).
##' @param file.type Type of ADMS file to be imported. With default, "unknown",
##' the import uses the file extension to identify the file type and, where
##' recognised, uses this to identify the file structure and import method to
##' be applied. Where file extension is not recognised the choice may be
##' forced by setting \code{file.type} to one of the known \code{file.type}
##' options: "bgd", "met", "mop" or "pst".
##' @param drop.case Option to convert all data names to lower case. Default,
##' \code{TRUE}. Alternative, \code{FALSE}, returns data with name cases as
##' defined in file.
##' @param drop.input.dates Option to remove ADMS "hour", "day", and "year"
##' data columns after generating openair "date" timeseries. Default,
##' \code{TRUE}. Alternative, \code{FALSE}, returns both "date" and the
##' associated ADMS data columns as part of openair data frame.
##' @param keep.units Option to retain ADMS data units. Default, \code{TRUE},
##' retains units (if recoverable) as character vector in data frame comment
##' if defined in \code{file}. Alternative, \code{FALSE}, discards units.
##' (NOTE: currently, only \code{.bgd} and \code{.pst} files assign units.
##' So, this option is ignored when importing \code{.met} or \code{.mop}
##' files.)
##' @param simplify.names Option to simplify data names in accordance with
##' common \code{openair} practices. Default, \code{TRUE}. Alternative,
##' \code{FALSE}, returns data with names as interpreted by standard R.
##' (NOTE: Some ADMS file data names include symbols and structures that R
##' does not allow as part of a name, so some renaming is automatic
##' regardless of \code{simplify.names} setting. For example, brackets or
##' symbols are removed from names or repaced with ".", and names in the form
##' "1/x" may be returned as "X1.x" or "recip.x".)
##' @param test.file.structure Option to test file structure before trying to
##' import. Default, \code{TRUE}, tests for expected file structure and halts
##' import operation if this is not found. Alternative, \code{FALSE},
##' attempts import regardless of structure.
##' @param drop.delim Option to remove delim columns from the data frame. ADMS
##' .mop files include two columns, "INPUT_DATA:" and "PROCESSED_DATA:", to
##' separate model input and output types. Default, \code{TRUE}, removes
##' these. Alternative, \code{FALSE}, retains them as part of import. (Note:
##' Option ignored when importing \code{.bgd}, \code{.met} or \code{.pst}
##' files.)
##' @param add.prefixes Option to add prefixes to data names. ADMS .mop files
##' include a number of input and process data types with shared names.
##' Prefixes can be automatically added to these so individual data can be
##' readily identified in the R/openair environment. Default, \code{TRUE},
##' adds "process." as a prefix to processed data. Other options include:
##' \code{FALSE} which uses no prefixes and leave all name rationalisation to
##' R, and character vectors which are treated as the required prefixes. If
##' one vector is sent, this is treated as processed data prefix. If two (or
##' more) vectors are sent, the first and second are treated as the input and
##' processed data prefixes, respectively. For example, the argument
##' (\code{add.prefixes="out"}) would add the "out" prefix to processed data
##' names, while the argument (\code{add.prefixes=c("in","out")}) would add
##' "in" and "out" prefixes to input and output data names, respectively.
##' (Note: Option ignored when importing \code{.bgd}, \code{.met} or
##' \code{.pst} files.)
##' @param names Option applied by \code{simplifyNamesADMS} when
##' \code{simplify.names} is enabled. All names are simplified for the
##' default setting, \code{NULL}.
##' @param ... Additional arguments, passed to \code{read.csv} as part of
##' import operation.
##' @export
##' @return In standard use \code{importADMS()} returns a data frame for use in
##' openair. By comparison to the original file, the resulting data frame is
##' modified as follows:
##'
##' Time and date information will combined in a single column "date",
##' formatted as a conventional timeseries (\code{as.POSIX*}). If
##' \code{drop.input.dates} is enabled data series combined to generated the
##' new "date" data series will also be removed.
##'
##' If \code{simplify.names} is enabled common chemical names may be
##' simplified, and some other parameters may be reset to openair standards
##' (e.g. "ws", "wd" and "temp") according to operations defined in
##' \code{simplifyNamesADMS}. A summary of simplfication operations can be
##' obtained using, e.g., the call \code{importADMS(simplify.names)}.
##'
##' If \code{drop.case} is enabled all upper case characters in names will be
##' converted to lower case.
##'
##' If \code{keep.units} is enabled data units information may also be retained
##' as part of the data frame comment if available.
##'
##' With \code{.mop} files, input and processed data series names may also been
##' modified on the basis of \code{drop.delim} and \code{add.prefixes}
##' settings
##' @note Times are assumed to be in GMT. Zero wind directions reset to 360 as
##' part of \code{.mop} file import.
##' @author Karl Ropkins, David Carslaw and Matthew Williams (CERC).
##' @seealso Generic import function \code{\link{import}}, for possible
##' alternative import methods. Other dedicated import functions available
##' for other file types, including \code{\link{importKCL}},
##' \code{\link{importAURN}}, etc.
##' @keywords methods
##' @examples
##'
##'
##' ##########
##' #example 1
##' ##########
##' #To be confirmed
##'
##'
##' #all current simplify.names operations
##' importADMS(simplify.names)
##'
##' #to see what simplify.names does to adms data series name PHI
##' new.name <- importADMS(simplify.names, names="PHI")
##' new.name
##'
##'
importADMS <- function(file=file.choose(), file.type="unknown",
drop.case = TRUE, drop.input.dates = TRUE, keep.units = TRUE,
simplify.names = TRUE, test.file.structure = TRUE,
drop.delim = TRUE, add.prefixes = TRUE,
names = NULL,
...)
{
#importADMS
#v0.2 kr
#parent with four daughters (below)
#Bgd, Mop and Met import methods and simplifyNamesADMS
if(substitute(file)=="simplify.names") { return(simplifyNamesADMS(names)) }
if(file.type=="unknown"){
file.type <- tolower(substr(file, nchar(file)-3, nchar(file)))
if(substr(file.type,1,1)=="."){
file.type <- substr(file.type,2,4)
} else {
stop("File extension not recognised\n [If valid ADMS file, try setting file.type to one of: bgd, mop or met]",
call. = FALSE)
}
}
if(file.type=="bgd") {
return(importADMSBgd(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
if(file.type=="mop") {
return(importADMSMop(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
if(file.type=="met") {
return(importADMSMet(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
if(file.type=="pst") {
return(importADMSPst(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
stop("File extension not recognised\n [If valid ADMS file, try setting file.type to one of: bgd, mop, met or pst]",
call. = FALSE)
}
###############
##daughter
##importADMSBgd
importADMSBgd <- function(file=file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
bgd <- readLines(file, n = -1)
bgd <- sub('[[:space:]]+$', '', bgd) #strip out tail spaces
loc.start <- which(tolower(bgd) == "backgroundversion2")
if(test.file.structure){
if(length(loc.start)==0){
stop("File not recognised ADMS.bgd structure\n [please contact openair if valid]",
call. = FALSE)
}
}
if(length(loc.start) > 1){
warning("Multiple possible variable starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
loc.start <- loc.start[length(loc.start)]
}
no.var <- suppressWarnings(as.numeric(bgd[loc.start + 1]))[1]
if(test.file.structure & is.na(no.var)) {
stop("File not recognised ADMS.bgd structure\n [please contact openair if valid]",
call. = FALSE)
}
variables <- bgd[(loc.start + 2) : (loc.start + 1 + no.var)]
if(simplify.names) {variables <- simplifyNamesADMS(variables)}
#drop messy name handling
variables <- gsub("[.][.]", ".", variables)
variables <- gsub("^[.]", "", variables)
if(drop.case) { variables <- tolower(variables) }
units.start <- which(substr(bgd, 1, 6) == "UNITS:")
if(length(units.start)==0){
warning("Data units not extracted from ADMS.bgd\n [please contact file structure if problems encountered]",
call. = FALSE)
units <- "units: undefined"
}
if(length(units.start) > 1){
warning("Multiple possible unit starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
units.start <- units.start[length(units.start)]
}
units <- bgd[(units.start + 1) : (units.start + no.var)]
if(length(units)==0){
units <- "units: undefined"
} else {
units <- paste("units: ",paste(units, sep = "", collapse = ", "), sep="")
}
data.start <- which(substr(bgd, 1, 5) == "DATA:")
if(length(data.start)==0){
stop("Data start not not located ADMS.bgd\n [please contact file structure if problems encountered]",
call. = FALSE)
}
if(length(data.start) > 1){
warning("Multiple possible data starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
data.start <- data.start[length(data.start)]
}
ans <- read.csv(file, header = FALSE, skip = data.start
, na.strings = c("", "NA", "-999", "-999.0")
, ...)
ans[] <- lapply(ans, function(x) { replace(x, x == -999, NA) })
########################
#screening for missing data
#confirm formats, if they get any with bgd files, etc.
#might not be necessary
date<- paste(ans[,1], ans[,2], ans[,3], sep = "-")
date <- as.POSIXct(strptime(date, format = "%Y-%j-%H"), "GMT")
ans <- cbind(date = date, ans)
if(length(variables) != ncol(ans) - 4){
warning("Variable data mismatch, taking shortest\n [please contact if openair problems encountered]",
call. = FALSE)
variables <- variables[1: min(c(length(variables), ncol(ans) - 4), na.rm = TRUE)]
ans <- ans[, 1:(length(variables) + 4)]
}
names(ans) <- c("date", "bgd.year", "bgd.day", "bgd.hour", variables)
if(drop.input.dates==TRUE){
ans <- ans[, c(1, 5:ncol(ans))]
}
if(keep.units) {
comment(ans) <- c(comment(ans), units)
}
#error handling for bad days
ids <- which(is.na(ans$date))
if (length(ids) > 0) {
if(length(ids)==nrow(ans)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]"
, call. = FALSE)
}
ans <- ans[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids), "line", sep=" ")
if(length(ids) > 1) { reply <- paste(reply, "s", sep = "") }
warning(reply, call. = FALSE)
}
print(unlist(sapply(ans, class)))
ans
}
###############
##daughter
##importADMSMet
importADMSMet <- function (file = file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
met <- readLines(file, n = -1)
met <- sub('[[:space:]]+$', '', met) #strip out tail spaces
loc.start <- which(met == "VARIABLES:")
if(test.file.structure){
if(length(loc.start)==0){
stop("File not recognised ADMS.met structure\n [please contact openair if valid]",
call. = FALSE)
}
}
if(length(loc.start) > 1){
warning("Multiple possible variable starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
loc.start <- loc.start[length(loc.start)]
}
variables <- suppressWarnings(as.numeric(met[loc.start + 1]))[1]
if(test.file.structure & is.na(variables)) {
stop("File not recognised ADMS.met structure\n [please contact openair if valid]",
call. = FALSE)
}
variables <- met[(loc.start + 2) : (loc.start + 1 + variables)]
data.start <- which(met == "DATA:")
if(test.file.structure){
if(length(data.start)==0){
stop("File not recognised ADMS.met structure\n [please contact openair if valid]",
call. = FALSE)
}
}
if(length(data.start) > 1){
warning("Multiple possible data starts, taking last\n [please contact openair if problems encountered]",
call. = FALSE)
data.start <- data.start[length(data.start)]
}
met <- read.csv(file, skip = data.start, header = FALSE, na.strings = c("-999",
"-999.0"))
met[] <- lapply(met, function(x) {
replace(x, x == -999, NA)
})
## met <- met[, sapply(met, function(x) !all(is.na(x)))]
if(length(variables) != ncol(met)){
warning("Variable data mismatch, taking shortest\n [please contact if openair problems encountered]",
call. = FALSE)
variables <- variables[1: min(c(length(variables), ncol(met)), na.rm = TRUE)]
met <- met[, 1:length(variables)]
}
names(met) <- make.names(variables, unique = TRUE)
#multiple year day hour name options
fun.temp <- function(x, y, z){
if(all(!y %in% names(x))){
stop(paste(z,
" not extracted\n [please contact openair if valid file]",
sep = ""), call. = FALSE)
}
ans <- x[, y[y %in% names(x)]]
if(!is.null(ncol(ans))) { ans <- ans[, 1] }
ans
}
year <- fun.temp(met, c("YEAR"), "year")
day <- fun.temp(met, c("DAY", "TDAY"), "day")
hour <- fun.temp(met, c("HOUR", "THOUR"), "hour")
met <- cbind(date = paste(year, day, hour, sep = "-"), met)
met$date <- as.POSIXct(strptime(met$date, format = "%Y-%j-%H"),
"GMT")
if (drop.input.dates) {
met <- met[, !names(met) %in%
c("YEAR", "TDAY", "THOUR", "DAY", "HOUR", "MONTH", "DAY.OF.MONTH")]
}
if (simplify.names) {
names(met) <- simplifyNamesADMS(names(met))
}
#drop messy name handling
names(met) <- gsub("[.][.]", ".", names(met))
names(met) <- gsub("^[.]", "", names(met))
if (drop.case) {
names(met) <- tolower(names(met))
}
met[] <- lapply(met, function(x) {
replace(x, x == -999, NA)
})
ids <- which(is.na(met$date))
if (length(ids) > 0) {
if (length(ids) == nrow(met)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]",
call. = FALSE)
}
met <- met[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids),
"line", sep = " ")
if (length(ids) > 1) {
reply <- paste(reply, "s", sep = "")
}
warning(reply, call. = FALSE)
}
print(unlist(sapply(met, class)))
met
}
###############
##daughter
##importADMSMop
importADMSMop <- function(file=file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
#problem
#mismatch in file header line end with lr; data lines end with comma then lr
#########
#written a catch for this
#problem
#no obvious file structure for testing
########
#provisional tester based on delim names
#problem
#r handling of x(y) names and x: names is messy
############
#added tidy to correct for this
#might need to rationalise names
#problem
#file contains lots of same names, input and processed
##############
#added an add.prefixes option to handle this
#problem
#no keep.units options
##############
#no option to use
######################
#code
#read top line/data headers
check.names <- read.csv(file, header=FALSE, nrow=1, ...)
check.names <- make.names(as.vector(apply(check.names, 1, as.character)))
##tidy () handling; renaming x(y) as x.y. is messy
check.names <- ifelse(
substr(check.names,nchar(check.names),nchar(check.names))=="."
, substr(check.names,1,nchar(check.names)-1)
, check.names
)
##tidy 1/LMN
check.names <- gsub("X1.LMO", "RECIP.LMO", check.names)
x.1 <- which(check.names=="INPUT_DATA")
x.2 <- which(check.names=="PROCESSED_DATA")
if(test.file.structure){
#check for delim columns
if(length(x.1)==0 | length(x.2)==0){
stop("File not recognised ADMS.mop structure\n [please contact openair if valid]"
, call. = FALSE
)
}
}
#read in data
ans <- read.csv(file, header=FALSE, skip=1
, na.strings = c("", "NA", "-999", "-999.0")
, ...
)
ans[] <- lapply(ans, function(x) { replace(x, x == -999, NA) })
##check for extra empty column
if(length(ans[,ncol(ans)][!is.na(ans[,ncol(ans)])])==0) {
ans <- ans[,1:(ncol(ans)-1)]
}
if(ncol(ans)!=length(check.names)){
warning("Unexpected name/data mismatch, handled pragmatically\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
if(simplify.names) check.names <- simplifyNamesADMS(check.names)
##restructure names and data according to arguments and put together
if(is.logical(add.prefixes)==TRUE){
if(add.prefixes==TRUE){
check.names[(x.2[1]+1): length(check.names)] <- paste("PROCESS", check.names[(x.2[1]+1): length(check.names)], sep=".")
}
} else {
if(length(add.prefixes)==1){
check.names[(x.2[1]+1): length(check.names)] <- paste(add.prefixes[1], check.names[(x.2[1]+1): length(check.names)], sep=".")
} else {
if(length(add.prefixes)>1){
check.names[(x.1[1]+4): (x.2[1]-1)] <- paste(add.prefixes[1], check.names[(x.1[1]+4): (x.2[1]-1)], sep=".")
check.names[(x.2[1]+1): length(check.names)] <- paste(add.prefixes[2], check.names[(x.2[1]+1): length(check.names)], sep=".")
} else {
warning("Unexpected add.prefixes option, option treated as FALSE\n [check openair import settings]"
, call. = FALSE)
}
}
}
names(ans) <- make.names(check.names, unique=TRUE)
##reset wd 0 to 360
##get current PHI terminology
temp <- if(simplify.names) simplifyNamesADMS("PHI") else "PHI"
temp <- if(length(add.prefixes)>1) paste(add.prefixes[1], temp, sep=".") else temp
if(temp %in% names(ans)) {
ans[, temp][ans[, temp]==0] <- 360
warning("Zero wind directions encountered, resetting to 360"
, call. = FALSE)
}
#if(simplify.names){
# names(ans) <- simplifyNamesADMS(names(ans))
#}
#drop messy name handling
names(ans) <- gsub("[.][.]", ".", names(ans))
names(ans) <- gsub("^[.]", "", names(ans))
date <- paste(ans$TYEAR, ans$TDAY, ans$THOUR, sep = "-")
date <- as.POSIXct(strptime(date, format = "%Y-%j-%H"), "GMT")
if(drop.input.dates==TRUE){
ans <- ans[,!names(ans) %in% c("TYEAR", "TDAY", "THOUR")]
}
if(drop.delim==TRUE){
ans <- ans[,!names(ans) %in% c("PROCESSED_DATA", "INPUT_DATA")]
}
ans <- cbind(date=date,ans)
if(drop.case==TRUE) {
names(ans) <- tolower(names(ans))
}
#error handling for bad days
ids <- which(is.na(ans$date))
if (length(ids) > 0) {
if(length(ids)==nrow(ans)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
ans <- ans[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids), "line", sep=" ")
if(length(ids)>1) { reply <- paste(reply,"s",sep="") }
warning(reply, call. = FALSE)
}
print(unlist(sapply(ans, class)))
ans
}
###############
#daughter
#importADMSPst
#kr v0.2
#08 nov 2010
importADMSPst <- function(file=file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
#notes
#########
#used the header/data dimension mismatcher handler from importADMSMop
#maybe not be needed.
#########
#no obvious file structure for testing
#provisional tester checks Hour, Day, Year and Receptor.name in file names
#########
#units are recovered from names row
#########
#drops Time(s) if empty
#problems
#########
#my name simplifications on Conc terms may need work
#due to compiler can't catch mu.g/m3 units
#talk to Matt/David re mug, ug and mg
######################
#code
#read top line/data headers
check.names <- read.csv(file, header=FALSE, nrow=1, ...)
check.names <- as.vector(apply(check.names, 1, as.character))
check.names <- sub('[[:space:]]+$', '', check.names) #strip out tail spaces
check.names <- sub('^[[:space:]]{1,}', '', check.names) #strip leading space (safer?)
check.names <- make.names(check.names) #after removing front spaces or X.m. conflict
#test structure
if(test.file.structure){
temp <- c("Hour", "Day", "Year", "Receptor.name")
test <- temp[temp %in% check.names]
if(!identical(temp, test))
stop("File not recognised ADMS.pst structure\n [please contact openair if valid]"
, call. = FALSE)
}
#read in data
ans <- read.csv(file, header=FALSE, skip=1
, na.strings = c("", "NA", "-999", "-999.0")
, ...
)
ans[] <- lapply(ans, function(x) { replace(x, x == -999, NA) })
#match up data and names
if(ncol(ans)!=length(check.names)){
warning("Unexpected name/data mismatch, handled pragmatically\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
names(ans) <- make.names(check.names, unique=TRUE)
#setup date/time
date <- paste(ans$Year, ans$Day, ans$Hour, sep = "-")
date <- as.POSIXct(strptime(date, format = "%Y-%j-%H"), "GMT")
if(drop.input.dates==TRUE)
ans <- ans[,!names(ans) %in% c("Year", "Day", "Hour")]
#drop Time.s. if empty
if(all(is.na(ans$Time.s.)))
ans <- ans[,!names(ans) %in% c("Time.s.")]
#recover units from names
units <- rep(NA, ncol(ans))
units[grep("[.]s[.]", names(ans))] <- "s"
units[grep("^.[.]m", names(ans))] <- "m"
units[grep("[.]ug.m.", names(ans))] <- "ug/m3" #both 3 and superscript 3
units[grep("[.]ppb", names(ans))] <- "ppb"
units[grep("[.]ppm", names(ans))] <- "ppm"
if(length(na.omit(units))==0)
units <- "units: unknown" else
units <- paste("units: ",paste(units, sep = "", collapse = ", "), sep="")
if(simplify.names){
names(ans) <- simplifyNamesADMS(names(ans))
}
ans <- cbind(date=date,ans)
if(drop.case==TRUE) {
names(ans) <- tolower(names(ans))
}
comment(ans) <- c(comment(ans), units)
#error handling for bad days
ids <- which(is.na(ans$date))
if (length(ids) > 0) {
if(length(ids)==nrow(ans)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
ans <- ans[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids), "line", sep=" ")
if(length(ids)>1) { reply <- paste(reply,"s",sep="") }
warning(reply, call. = FALSE)
}
print(unlist(sapply(ans, class)))
names(ans) <- gsub("..", replacement = "", names(ans), fixed = TRUE)
ans
}
###############
##daughter
##simplifyNamesADMS
#kr v0.5
#08 nov 2010
#notes
################
#two handlers: fun.temp and fun.temp.2
################
#fun.temp(x,y,z)
#replaces full term y with full term z in x
################
#fun.temp.2(x,y,z, y.names)
#replaces partial term y with partial term 2 in x
#if y.names = TRUE makes y r-friend first
#[make.names(y)...]
#
simplifyNamesADMS <- function(names=NULL){
#simplify.names lookup table for import.adms functions
#v0.2 kr
#handles as inputs (don't use after drop.case option)
#names=NULL returns simplification operation summary
if(is.null(names)) {
message("Simplification operation summary")
message("[ADMS => R => OPENAIR]:")
fun.temp <- function(x,y,z){
temp <- c(y, make.names(y), z)
message(paste("\t", paste(temp, collapse=" => "), sep=""))
temp <- data.frame(cbind(adms.input = temp[1], r.handling = temp[2], simplify.names = temp[3]),
stringsAsFactors = FALSE)
x <- rbind(x,temp)
x
}
fun.temp.2 <- function(x,y,z, y.name) x
} else {
names <- make.names(names)
fun.temp <- function(x,y,z){
x[which(x == make.names(y))] <- z
x
}
fun.temp.2 <- function(x,y,z, y.name) {
x <- if(y.name) gsub(make.names(y),z,x) else (gsub(y,z,x))
}
}
############
#update list
############
#1/LMO
names <- fun.temp(names, "1/LMO", "RECIP.LMO")
#1/MONIN-OBUKHOV LENGTH
names <- fun.temp(names, "1/MONIN-OBUKHOV LENGTH", "RECIP.LMO")
#ALBEDO(D)
names <- fun.temp(names, "ALBEDO(D)", "ALBEDO.DISP")
names <- fun.temp(names, "ALBEDO (D)", "ALBEDO.DISP")
#ALBEDO(DISP)
names <- fun.temp(names, "ALBEDO(DISP)", "ALBEDO.DISP")
names <- fun.temp(names, "ALBEDO (DISP)", "ALBEDO.DISP")
#ALBEDO (DISPERSION AREA)
names <- fun.temp(names, "ALBEDO (DISPERSION AREA)", "ALBEDO.DISP")
#ALBEDO(M)
names <- fun.temp(names, "ALBEDO(M)", "ALBEDO.MET")
names <- fun.temp(names, "ALBEDO (M)", "ALBEDO.MET")
#ALBEDO(MET)
names <- fun.temp(names, "ALBEDO(MET)", "ALBEDO.MET")
names <- fun.temp(names, "ALBEDO (MET)", "ALBEDO.MET")
#ALBEDO (MET SITE)
names <- fun.temp(names, "ALBEDO (MET SITE)", "ALBEDO.MET")
#ALPHA
##########
##conflict
##########
##both alpha.disp and alpha.met seem to have been abbrev. to alpha
#ALPHA(D)
names <- fun.temp(names, "ALPHA(D)", "ALPHA.DISP")
names <- fun.temp(names, "ALPHA (D)", "ALPHA.DISP")
#ALPHA(DISP)
names <- fun.temp(names, "ALPHA(DISP)", "ALPHA.DISP")
names <- fun.temp(names, "ALPHA (DISP)", "ALPHA.DISP")
#ALPHA(M)
names <- fun.temp(names, "ALPHA(M)", "ALPHA.MET")
names <- fun.temp(names, "ALPHA (M)", "ALPHA.MET")
#ALPHA(MET)
names <- fun.temp(names, "ALPHA(MET)", "ALPHA.MET")
names <- fun.temp(names, "ALPHA (MET)", "ALPHA.MET")
#BL DEPTH
names <- fun.temp(names, "BL DEPTH", "H")
#BOUNDARY LAYER DEPTH
names <- fun.temp(names, "BOUNDARY LAYER DEPTH", "H")
#BUOYANCY FREQUENCY ABOVE BOUNDARY LAYER
names <- fun.temp(names, "BUOYANCY FREQUENCY ABOVE BOUNDARY LAYER", "NU")
#BUTADIENE
#CL
#CLOUD
names <- fun.temp(names, "CLOUD", "CL")
#CLOUD AMOUNT (OKTAS)
names <- fun.temp(names, "CLOUD AMOUNT (OKTAS)", "CL")
#Conc|ppb|NAME|All sources|-| 1hr
names <- fun.temp(names, "Conc|ppb|NAME|SOURCES|-| RESOLUTION", "NAME.SOURCES.RESOLUTION")
#Conc|ppm|NAME|All sources|-| 1hr
names <- fun.temp(names, "Conc|ppm|NAME|SOURCES|-| RESOLUTION", "NAME.SOURCES.RESOLUTION")
#Conc|ug/m3|NAME|All sources|-| 1hr
names <- fun.temp(names, "Conc|ug/m3|NAME|SOURCES|-| RESOLUTION", "NAME.SOURCES.RESOLUTION")
#NAME.All.sources.1hr
names <- fun.temp(names, "NAME.All.sources.1hr", "NAME")
#NAME.All.sources.RESOLUTION
names <- fun.temp(names, "NAME.All.sources.RESOLUTION", "NAME.RESOLUTION")
#NAME.SOURCE.1hr
names <- fun.temp(names, "NAME.SOURCE.1hr", "NAME.SOURCE")
#general for above
names <- fun.temp.2(names, "Conc|ppb|", "", TRUE)
names <- fun.temp.2(names, "Conc|ppm|", "", TRUE)
names <- fun.temp.2(names, "Conc|.g/m.|", "", TRUE)
#above covers
##u, m and mu for 1st and
##3 and superscript3 for second
names <- fun.temp.2(names, "[.][.][.][.]", ".", FALSE)
names <- fun.temp.2(names, "[.][.][.]", ".", FALSE)
names <- fun.temp.2(names, "[.]All[.]sources", "", FALSE)
names <- fun.temp.2(names, "[.]1hr", "", FALSE)
#D(RELATIVE HUMIDITY)/DZ ABOVE BOUNDARY LAYER (PERCENT/M)
names <- fun.temp(names, "D(RELATIVE HUMIDITY)/DZ ABOVE BOUNDARY LAYER (PERCENT/M)", "DRHDZU")
#DAY
#DELTAPHI
names <- fun.temp(names, "DELTAPHI", "DELTA.WD")
#DELTAT
names <- fun.temp(names, "DELTAT", "DELTA.T")
names <- fun.temp(names, "DELTA T", "DELTA.T")
#DELTATHETA
names <- fun.temp(names, "DELTATHETA", "DELTA.THETA")
names <- fun.temp(names, "DELTA THETA", "DELTA.THETA")
#DIRN CHANGE
names <- fun.temp(names, "DIRN CHANGE", "DELTA.WD")
#DRH/DZ
names <- fun.temp(names, "DRH/DZ", "DRHDZU")
#DRHDZU
#FR
#FREQUENCY
#FTHETA0
#GEOSTROPHIC MINUS SURFACE WIND DIRECTION (DEGREES)
names <- fun.temp(names, "GEOSTROPHIC MINUS SURFACE WIND DIRECTION (DEGREES)", "DELTA.WD")
#H
#HEAT FLUX
names <- fun.temp(names, "HEAT FLUX", "FTHETA0")
#HOUR
#HOURS
#INCOMING SOLAR RADIATION
names <- fun.temp(names, "INCOMING SOLAR RADIATION", "K")
#INPUT_DATA:
#K
#LAMBDAE
#LATENT HEAT FLUX
names <- fun.temp(names, "LATENT HEAT FLUX", "LAMBDAE")
#LAT HT FLUX
names <- fun.temp(names, "LAT HT FLUX", "LAMBDAE")
#MODIFIED PRIESTLEY-TAYLOR PARAMETER (DISPERSION AREA)
names <- fun.temp(names, "MODIFIED PRIESTLEY-TAYLOR PARAMETER (DISPERSION AREA)", "ALPHA.DISP")
#MODIFIED PRIESTLEY-TAYLOR PARAMETER (MET SITE)
names <- fun.temp(names, "MODIFIED PRIESTLEY-TAYLOR PARAMETER (MET SITE)", "ALPHA.MET")
#MONTHS
#N ABOVE BL
names <- fun.temp(names, "N ABOVE BL", "NU")
#NO2
#NOx
#NU
#P
#PM10
#PM2.5
#O3
#Q0
#PHI
names <- fun.temp(names, "PHI", "WD")
#PHI0
names <- fun.temp(names, "PHI0", "WD.0")
#PHIG
names <- fun.temp(names, "PHIG", "WD.G")
#PHISEC
names <- fun.temp(names, "PHISEC", "WD.SEC")
#PRECIP
names <- fun.temp(names, "PRECIP", "P")
#PRECIPITATION RATE (MM/HOUR)
names <- fun.temp(names, "PRECIPITATION RATE (MM/HOUR)", "P")
#PROCESSED_DATA:
#R
names <- fun.temp(names, "R", "ALBEDO.MET")
#RECIPLMO
names <- fun.temp(names, "RECIPLMO", "RECIP.LMO")
#RELATIVE HUMIDITY ABOVE BOUNDARY LAYER (PERCENT)
names <- fun.temp(names, "RELATIVE HUMIDITY ABOVE BOUNDARY LAYER (PERCENT)", "RHU")
#RH ABOVE BL
names <- fun.temp(names, "RH ABOVE BL", "RHU")
#RHU
#RHUM
names <- fun.temp(names, "RHUM", "RHU")
#ROUGHNESS LENGTH (DISPERSION AREA)
names <- fun.temp(names, "ROUGHNESS LENGTH (DISPERSION AREA)", "Z0.DISP")
#ROUGHNESS LENGTH (MET SITE)
names <- fun.temp(names, "ROUGHNESS LENGTH (MET SITE)", "Z0.MET")
#RUN
#S HUMIDITY
names <- fun.temp(names, "S HUMIDITY", "SHU")
#SEA SURFACE TEMPERATURE (C)
names <- fun.temp(names, "SEA SURFACE TEMPERATURE (C)", "TSEA")
#SEA TEMP
names <- fun.temp(names, "SEA TEMP", "TSEA")
#SENSIBLE HEAT FLUX
names <- fun.temp(names, "SENSIBLE HEAT FLUX", "FTHETA0")
#SIGMATHETA
names <- fun.temp(names, "SIGMATHETA", "SIGMA.THETA")
names <- fun.temp(names, "SIGMA THETA", "SIGMA.THETA")
#SIGMA THETA (DEGREES)
names <- fun.temp(names, "SIGMA THETA (DEGREES)", "SIGMA.THETA")
#SO2
#SOLAR RAD
names <- fun.temp(names, "SOLAR RAD", "K")
#SPECIFIC HUMIDITY
names <- fun.temp(names, "SPECIFIC HUMIDITY", "SHU")
#T0C
names <- fun.temp(names, "T0C", "TEMP")
#TDAY
#TEMPERATURE
names <- fun.temp(names, "TEMPERATURE", "TEMP")
#TEMPERATURE (C)
names <- fun.temp(names, "TEMPERATURE (C)", "TEMP")
#TEMPERATURE JUMP ACROSS BOUNDARY LAYER TOP
names <- fun.temp(names, "TEMPERATURE JUMP ACROSS BOUNDARY LAYER TOP", "DELTA.THETA")
#THOUR
#TEMPERATURE OVER LAND MINUS SEA SURFACE TEMPERATURE
names <- fun.temp(names, "TEMPERATURE OVER LAND MINUS SEA SURFACE TEMPERATURE", "DELTA.T")
#Time(s)
#X(m)
names <- fun.temp(names, "Time(s)", "Time")
#TSEA
#TYEAR
#U
names <- fun.temp(names, "U", "WS")
#UG
names <- fun.temp(names, "UG", "WS.G")
#UGSTAR
names <- fun.temp(names, "UGSTAR", "WS.GSTAR")
#USTAR
names <- fun.temp(names, "USTAR", "WS.STAR")
#WIND DIRN
names <- fun.temp(names, "WIND DIRN", "WD")
#WIND DIRECTION (DEGREES)
names <- fun.temp(names, "WIND DIRECTION (DEGREES)", "WD")
#WIND HEIGHT
names <- fun.temp(names, "WIND HEIGHT", "WIND.HEIGHT")
#WIND MEASUREMENT HEIGHT
names <- fun.temp(names, "WIND MEASUREMENT HEIGHT", "WIND.HEIGHT")
#WIND SPEED
names <- fun.temp(names, "WIND SPEED", "WS")
#WSTAR
#X(m)
names <- fun.temp(names, "X(m)", "X")
#Y(m)
names <- fun.temp(names, "Y(m)", "Y")
#YEAR
#Z(m)
names <- fun.temp(names, "Z(m)", "Z")
#Z0(D)
names <- fun.temp(names, "Z0(D)", "Z0.DISP")
names <- fun.temp(names, "Z0 (D)", "Z0.DISP")
#Z0(DISP)
names <- fun.temp(names, "Z0(DISP)", "Z0.DISP")
names <- fun.temp(names, "Z0 (DISP)", "Z0.DISP")
#Z0(M)
names <- fun.temp(names, "Z0(M)", "Z0.MET")
names <- fun.temp(names, "Z0 (M)", "Z0.MET")
#Z0(MET)
names <- fun.temp(names, "Z0(MET)", "Z0.MET")
names <- fun.temp(names, "Z0 (MET)", "Z0.MET")
########
#outputs
########
invisible(names)
}
davidcarslaw/ggopenair documentation built on May 14, 2019, 10:37 p.m.
R Package Documentation
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##' CERC Atmospheric Dispersion Modelling System (ADMS) data import function(s) for openair
##'
##' Function(s) to import various ADMS file types into openair. Currently
##' handles ".met", ".bgd", ".mop" and ".pst" file structures. Uses
##' \code{read.csv} (in \code{utils}) to read in data, format for R and openair
##' and apply some file structure testing.
##'
##' The \code{importADMS} function were developed to help import various ADMS
##' file types into openair. In most cases the parent import function should
##' work in default configuration, e.g. \code{mydata <- importADMS()}. The
##' function currently recognises four file formats: \code{.bgd}, \code{.met},
##' \code{.mop} and \code{.pst}. Where other file extensions have been set but
##' the file structure is known, the import call can be forced by, e.g,
##' \code{mydata <- importADMS(file.type="bgd")}. Other options can be adjusted
##' to provide fine control of the data structuring and renaming.
##'
##' @aliases importADMS importADMSBgd importADMSMet importADMSMop importADMSPst
##' @param file The ADMS file to be imported. Default, \code{file.choose()}
##' opens browser. Use of \code{read.csv} (in \code{utils}) also allows this
##' to be a readable text-mode connection or url (although these options are
##' currently not fully tested).
##' @param file.type Type of ADMS file to be imported. With default, "unknown",
##' the import uses the file extension to identify the file type and, where
##' recognised, uses this to identify the file structure and import method to
##' be applied. Where file extension is not recognised the choice may be
##' forced by setting \code{file.type} to one of the known \code{file.type}
##' options: "bgd", "met", "mop" or "pst".
##' @param drop.case Option to convert all data names to lower case. Default,
##' \code{TRUE}. Alternative, \code{FALSE}, returns data with name cases as
##' defined in file.
##' @param drop.input.dates Option to remove ADMS "hour", "day", and "year"
##' data columns after generating openair "date" timeseries. Default,
##' \code{TRUE}. Alternative, \code{FALSE}, returns both "date" and the
##' associated ADMS data columns as part of openair data frame.
##' @param keep.units Option to retain ADMS data units. Default, \code{TRUE},
##' retains units (if recoverable) as character vector in data frame comment
##' if defined in \code{file}. Alternative, \code{FALSE}, discards units.
##' (NOTE: currently, only \code{.bgd} and \code{.pst} files assign units.
##' So, this option is ignored when importing \code{.met} or \code{.mop}
##' files.)
##' @param simplify.names Option to simplify data names in accordance with
##' common \code{openair} practices. Default, \code{TRUE}. Alternative,
##' \code{FALSE}, returns data with names as interpreted by standard R.
##' (NOTE: Some ADMS file data names include symbols and structures that R
##' does not allow as part of a name, so some renaming is automatic
##' regardless of \code{simplify.names} setting. For example, brackets or
##' symbols are removed from names or repaced with ".", and names in the form
##' "1/x" may be returned as "X1.x" or "recip.x".)
##' @param test.file.structure Option to test file structure before trying to
##' import. Default, \code{TRUE}, tests for expected file structure and halts
##' import operation if this is not found. Alternative, \code{FALSE},
##' attempts import regardless of structure.
##' @param drop.delim Option to remove delim columns from the data frame. ADMS
##' .mop files include two columns, "INPUT_DATA:" and "PROCESSED_DATA:", to
##' separate model input and output types. Default, \code{TRUE}, removes
##' these. Alternative, \code{FALSE}, retains them as part of import. (Note:
##' Option ignored when importing \code{.bgd}, \code{.met} or \code{.pst}
##' files.)
##' @param add.prefixes Option to add prefixes to data names. ADMS .mop files
##' include a number of input and process data types with shared names.
##' Prefixes can be automatically added to these so individual data can be
##' readily identified in the R/openair environment. Default, \code{TRUE},
##' adds "process." as a prefix to processed data. Other options include:
##' \code{FALSE} which uses no prefixes and leave all name rationalisation to
##' R, and character vectors which are treated as the required prefixes. If
##' one vector is sent, this is treated as processed data prefix. If two (or
##' more) vectors are sent, the first and second are treated as the input and
##' processed data prefixes, respectively. For example, the argument
##' (\code{add.prefixes="out"}) would add the "out" prefix to processed data
##' names, while the argument (\code{add.prefixes=c("in","out")}) would add
##' "in" and "out" prefixes to input and output data names, respectively.
##' (Note: Option ignored when importing \code{.bgd}, \code{.met} or
##' \code{.pst} files.)
##' @param names Option applied by \code{simplifyNamesADMS} when
##' \code{simplify.names} is enabled. All names are simplified for the
##' default setting, \code{NULL}.
##' @param ... Additional arguments, passed to \code{read.csv} as part of
##' import operation.
##' @export
##' @return In standard use \code{importADMS()} returns a data frame for use in
##' openair. By comparison to the original file, the resulting data frame is
##' modified as follows:
##'
##' Time and date information will combined in a single column "date",
##' formatted as a conventional timeseries (\code{as.POSIX*}). If
##' \code{drop.input.dates} is enabled data series combined to generated the
##' new "date" data series will also be removed.
##'
##' If \code{simplify.names} is enabled common chemical names may be
##' simplified, and some other parameters may be reset to openair standards
##' (e.g. "ws", "wd" and "temp") according to operations defined in
##' \code{simplifyNamesADMS}. A summary of simplfication operations can be
##' obtained using, e.g., the call \code{importADMS(simplify.names)}.
##'
##' If \code{drop.case} is enabled all upper case characters in names will be
##' converted to lower case.
##'
##' If \code{keep.units} is enabled data units information may also be retained
##' as part of the data frame comment if available.
##'
##' With \code{.mop} files, input and processed data series names may also been
##' modified on the basis of \code{drop.delim} and \code{add.prefixes}
##' settings
##' @note Times are assumed to be in GMT. Zero wind directions reset to 360 as
##' part of \code{.mop} file import.
##' @author Karl Ropkins, David Carslaw and Matthew Williams (CERC).
##' @seealso Generic import function \code{\link{import}}, for possible
##' alternative import methods. Other dedicated import functions available
##' for other file types, including \code{\link{importKCL}},
##' \code{\link{importAURN}}, etc.
##' @keywords methods
##' @examples
##'
##'
##' ##########
##' #example 1
##' ##########
##' #To be confirmed
##'
##'
##' #all current simplify.names operations
##' importADMS(simplify.names)
##'
##' #to see what simplify.names does to adms data series name PHI
##' new.name <- importADMS(simplify.names, names="PHI")
##' new.name
##'
##'
importADMS <- function(file=file.choose(), file.type="unknown",
drop.case = TRUE, drop.input.dates = TRUE, keep.units = TRUE,
simplify.names = TRUE, test.file.structure = TRUE,
drop.delim = TRUE, add.prefixes = TRUE,
names = NULL,
...)
{
#importADMS
#v0.2 kr
#parent with four daughters (below)
#Bgd, Mop and Met import methods and simplifyNamesADMS
if(substitute(file)=="simplify.names") { return(simplifyNamesADMS(names)) }
if(file.type=="unknown"){
file.type <- tolower(substr(file, nchar(file)-3, nchar(file)))
if(substr(file.type,1,1)=="."){
file.type <- substr(file.type,2,4)
} else {
stop("File extension not recognised\n [If valid ADMS file, try setting file.type to one of: bgd, mop or met]",
call. = FALSE)
}
}
if(file.type=="bgd") {
return(importADMSBgd(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
if(file.type=="mop") {
return(importADMSMop(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
if(file.type=="met") {
return(importADMSMet(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
if(file.type=="pst") {
return(importADMSPst(
file=file, drop.case = drop.case, drop.input.dates = drop.input.dates,
keep.units = keep.units, simplify.names = simplify.names,
test.file.structure = test.file.structure,
drop.delim = drop.delim, add.prefixes = add.prefixes,
...
))
}
stop("File extension not recognised\n [If valid ADMS file, try setting file.type to one of: bgd, mop, met or pst]",
call. = FALSE)
}
###############
##daughter
##importADMSBgd
importADMSBgd <- function(file=file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
bgd <- readLines(file, n = -1)
bgd <- sub('[[:space:]]+$', '', bgd) #strip out tail spaces
loc.start <- which(tolower(bgd) == "backgroundversion2")
if(test.file.structure){
if(length(loc.start)==0){
stop("File not recognised ADMS.bgd structure\n [please contact openair if valid]",
call. = FALSE)
}
}
if(length(loc.start) > 1){
warning("Multiple possible variable starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
loc.start <- loc.start[length(loc.start)]
}
no.var <- suppressWarnings(as.numeric(bgd[loc.start + 1]))[1]
if(test.file.structure & is.na(no.var)) {
stop("File not recognised ADMS.bgd structure\n [please contact openair if valid]",
call. = FALSE)
}
variables <- bgd[(loc.start + 2) : (loc.start + 1 + no.var)]
if(simplify.names) {variables <- simplifyNamesADMS(variables)}
#drop messy name handling
variables <- gsub("[.][.]", ".", variables)
variables <- gsub("^[.]", "", variables)
if(drop.case) { variables <- tolower(variables) }
units.start <- which(substr(bgd, 1, 6) == "UNITS:")
if(length(units.start)==0){
warning("Data units not extracted from ADMS.bgd\n [please contact file structure if problems encountered]",
call. = FALSE)
units <- "units: undefined"
}
if(length(units.start) > 1){
warning("Multiple possible unit starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
units.start <- units.start[length(units.start)]
}
units <- bgd[(units.start + 1) : (units.start + no.var)]
if(length(units)==0){
units <- "units: undefined"
} else {
units <- paste("units: ",paste(units, sep = "", collapse = ", "), sep="")
}
data.start <- which(substr(bgd, 1, 5) == "DATA:")
if(length(data.start)==0){
stop("Data start not not located ADMS.bgd\n [please contact file structure if problems encountered]",
call. = FALSE)
}
if(length(data.start) > 1){
warning("Multiple possible data starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
data.start <- data.start[length(data.start)]
}
ans <- read.csv(file, header = FALSE, skip = data.start
, na.strings = c("", "NA", "-999", "-999.0")
, ...)
ans[] <- lapply(ans, function(x) { replace(x, x == -999, NA) })
########################
#screening for missing data
#confirm formats, if they get any with bgd files, etc.
#might not be necessary
date<- paste(ans[,1], ans[,2], ans[,3], sep = "-")
date <- as.POSIXct(strptime(date, format = "%Y-%j-%H"), "GMT")
ans <- cbind(date = date, ans)
if(length(variables) != ncol(ans) - 4){
warning("Variable data mismatch, taking shortest\n [please contact if openair problems encountered]",
call. = FALSE)
variables <- variables[1: min(c(length(variables), ncol(ans) - 4), na.rm = TRUE)]
ans <- ans[, 1:(length(variables) + 4)]
}
names(ans) <- c("date", "bgd.year", "bgd.day", "bgd.hour", variables)
if(drop.input.dates==TRUE){
ans <- ans[, c(1, 5:ncol(ans))]
}
if(keep.units) {
comment(ans) <- c(comment(ans), units)
}
#error handling for bad days
ids <- which(is.na(ans$date))
if (length(ids) > 0) {
if(length(ids)==nrow(ans)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]"
, call. = FALSE)
}
ans <- ans[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids), "line", sep=" ")
if(length(ids) > 1) { reply <- paste(reply, "s", sep = "") }
warning(reply, call. = FALSE)
}
print(unlist(sapply(ans, class)))
ans
}
###############
##daughter
##importADMSMet
importADMSMet <- function (file = file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
met <- readLines(file, n = -1)
met <- sub('[[:space:]]+$', '', met) #strip out tail spaces
loc.start <- which(met == "VARIABLES:")
if(test.file.structure){
if(length(loc.start)==0){
stop("File not recognised ADMS.met structure\n [please contact openair if valid]",
call. = FALSE)
}
}
if(length(loc.start) > 1){
warning("Multiple possible variable starts, taking last\n [please contact openair problems encountered]",
call. = FALSE)
loc.start <- loc.start[length(loc.start)]
}
variables <- suppressWarnings(as.numeric(met[loc.start + 1]))[1]
if(test.file.structure & is.na(variables)) {
stop("File not recognised ADMS.met structure\n [please contact openair if valid]",
call. = FALSE)
}
variables <- met[(loc.start + 2) : (loc.start + 1 + variables)]
data.start <- which(met == "DATA:")
if(test.file.structure){
if(length(data.start)==0){
stop("File not recognised ADMS.met structure\n [please contact openair if valid]",
call. = FALSE)
}
}
if(length(data.start) > 1){
warning("Multiple possible data starts, taking last\n [please contact openair if problems encountered]",
call. = FALSE)
data.start <- data.start[length(data.start)]
}
met <- read.csv(file, skip = data.start, header = FALSE, na.strings = c("-999",
"-999.0"))
met[] <- lapply(met, function(x) {
replace(x, x == -999, NA)
})
## met <- met[, sapply(met, function(x) !all(is.na(x)))]
if(length(variables) != ncol(met)){
warning("Variable data mismatch, taking shortest\n [please contact if openair problems encountered]",
call. = FALSE)
variables <- variables[1: min(c(length(variables), ncol(met)), na.rm = TRUE)]
met <- met[, 1:length(variables)]
}
names(met) <- make.names(variables, unique = TRUE)
#multiple year day hour name options
fun.temp <- function(x, y, z){
if(all(!y %in% names(x))){
stop(paste(z,
" not extracted\n [please contact openair if valid file]",
sep = ""), call. = FALSE)
}
ans <- x[, y[y %in% names(x)]]
if(!is.null(ncol(ans))) { ans <- ans[, 1] }
ans
}
year <- fun.temp(met, c("YEAR"), "year")
day <- fun.temp(met, c("DAY", "TDAY"), "day")
hour <- fun.temp(met, c("HOUR", "THOUR"), "hour")
met <- cbind(date = paste(year, day, hour, sep = "-"), met)
met$date <- as.POSIXct(strptime(met$date, format = "%Y-%j-%H"),
"GMT")
if (drop.input.dates) {
met <- met[, !names(met) %in%
c("YEAR", "TDAY", "THOUR", "DAY", "HOUR", "MONTH", "DAY.OF.MONTH")]
}
if (simplify.names) {
names(met) <- simplifyNamesADMS(names(met))
}
#drop messy name handling
names(met) <- gsub("[.][.]", ".", names(met))
names(met) <- gsub("^[.]", "", names(met))
if (drop.case) {
names(met) <- tolower(names(met))
}
met[] <- lapply(met, function(x) {
replace(x, x == -999, NA)
})
ids <- which(is.na(met$date))
if (length(ids) > 0) {
if (length(ids) == nrow(met)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]",
call. = FALSE)
}
met <- met[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids),
"line", sep = " ")
if (length(ids) > 1) {
reply <- paste(reply, "s", sep = "")
}
warning(reply, call. = FALSE)
}
print(unlist(sapply(met, class)))
met
}
###############
##daughter
##importADMSMop
importADMSMop <- function(file=file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
#problem
#mismatch in file header line end with lr; data lines end with comma then lr
#########
#written a catch for this
#problem
#no obvious file structure for testing
########
#provisional tester based on delim names
#problem
#r handling of x(y) names and x: names is messy
############
#added tidy to correct for this
#might need to rationalise names
#problem
#file contains lots of same names, input and processed
##############
#added an add.prefixes option to handle this
#problem
#no keep.units options
##############
#no option to use
######################
#code
#read top line/data headers
check.names <- read.csv(file, header=FALSE, nrow=1, ...)
check.names <- make.names(as.vector(apply(check.names, 1, as.character)))
##tidy () handling; renaming x(y) as x.y. is messy
check.names <- ifelse(
substr(check.names,nchar(check.names),nchar(check.names))=="."
, substr(check.names,1,nchar(check.names)-1)
, check.names
)
##tidy 1/LMN
check.names <- gsub("X1.LMO", "RECIP.LMO", check.names)
x.1 <- which(check.names=="INPUT_DATA")
x.2 <- which(check.names=="PROCESSED_DATA")
if(test.file.structure){
#check for delim columns
if(length(x.1)==0 | length(x.2)==0){
stop("File not recognised ADMS.mop structure\n [please contact openair if valid]"
, call. = FALSE
)
}
}
#read in data
ans <- read.csv(file, header=FALSE, skip=1
, na.strings = c("", "NA", "-999", "-999.0")
, ...
)
ans[] <- lapply(ans, function(x) { replace(x, x == -999, NA) })
##check for extra empty column
if(length(ans[,ncol(ans)][!is.na(ans[,ncol(ans)])])==0) {
ans <- ans[,1:(ncol(ans)-1)]
}
if(ncol(ans)!=length(check.names)){
warning("Unexpected name/data mismatch, handled pragmatically\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
if(simplify.names) check.names <- simplifyNamesADMS(check.names)
##restructure names and data according to arguments and put together
if(is.logical(add.prefixes)==TRUE){
if(add.prefixes==TRUE){
check.names[(x.2[1]+1): length(check.names)] <- paste("PROCESS", check.names[(x.2[1]+1): length(check.names)], sep=".")
}
} else {
if(length(add.prefixes)==1){
check.names[(x.2[1]+1): length(check.names)] <- paste(add.prefixes[1], check.names[(x.2[1]+1): length(check.names)], sep=".")
} else {
if(length(add.prefixes)>1){
check.names[(x.1[1]+4): (x.2[1]-1)] <- paste(add.prefixes[1], check.names[(x.1[1]+4): (x.2[1]-1)], sep=".")
check.names[(x.2[1]+1): length(check.names)] <- paste(add.prefixes[2], check.names[(x.2[1]+1): length(check.names)], sep=".")
} else {
warning("Unexpected add.prefixes option, option treated as FALSE\n [check openair import settings]"
, call. = FALSE)
}
}
}
names(ans) <- make.names(check.names, unique=TRUE)
##reset wd 0 to 360
##get current PHI terminology
temp <- if(simplify.names) simplifyNamesADMS("PHI") else "PHI"
temp <- if(length(add.prefixes)>1) paste(add.prefixes[1], temp, sep=".") else temp
if(temp %in% names(ans)) {
ans[, temp][ans[, temp]==0] <- 360
warning("Zero wind directions encountered, resetting to 360"
, call. = FALSE)
}
#if(simplify.names){
# names(ans) <- simplifyNamesADMS(names(ans))
#}
#drop messy name handling
names(ans) <- gsub("[.][.]", ".", names(ans))
names(ans) <- gsub("^[.]", "", names(ans))
date <- paste(ans$TYEAR, ans$TDAY, ans$THOUR, sep = "-")
date <- as.POSIXct(strptime(date, format = "%Y-%j-%H"), "GMT")
if(drop.input.dates==TRUE){
ans <- ans[,!names(ans) %in% c("TYEAR", "TDAY", "THOUR")]
}
if(drop.delim==TRUE){
ans <- ans[,!names(ans) %in% c("PROCESSED_DATA", "INPUT_DATA")]
}
ans <- cbind(date=date,ans)
if(drop.case==TRUE) {
names(ans) <- tolower(names(ans))
}
#error handling for bad days
ids <- which(is.na(ans$date))
if (length(ids) > 0) {
if(length(ids)==nrow(ans)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
ans <- ans[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids), "line", sep=" ")
if(length(ids)>1) { reply <- paste(reply,"s",sep="") }
warning(reply, call. = FALSE)
}
print(unlist(sapply(ans, class)))
ans
}
###############
#daughter
#importADMSPst
#kr v0.2
#08 nov 2010
importADMSPst <- function(file=file.choose()
, drop.case=TRUE, drop.input.dates=TRUE
, keep.units=TRUE, simplify.names=TRUE
, test.file.structure=TRUE
, drop.delim = TRUE, add.prefixes = TRUE
, ...
){
#notes
#########
#used the header/data dimension mismatcher handler from importADMSMop
#maybe not be needed.
#########
#no obvious file structure for testing
#provisional tester checks Hour, Day, Year and Receptor.name in file names
#########
#units are recovered from names row
#########
#drops Time(s) if empty
#problems
#########
#my name simplifications on Conc terms may need work
#due to compiler can't catch mu.g/m3 units
#talk to Matt/David re mug, ug and mg
######################
#code
#read top line/data headers
check.names <- read.csv(file, header=FALSE, nrow=1, ...)
check.names <- as.vector(apply(check.names, 1, as.character))
check.names <- sub('[[:space:]]+$', '', check.names) #strip out tail spaces
check.names <- sub('^[[:space:]]{1,}', '', check.names) #strip leading space (safer?)
check.names <- make.names(check.names) #after removing front spaces or X.m. conflict
#test structure
if(test.file.structure){
temp <- c("Hour", "Day", "Year", "Receptor.name")
test <- temp[temp %in% check.names]
if(!identical(temp, test))
stop("File not recognised ADMS.pst structure\n [please contact openair if valid]"
, call. = FALSE)
}
#read in data
ans <- read.csv(file, header=FALSE, skip=1
, na.strings = c("", "NA", "-999", "-999.0")
, ...
)
ans[] <- lapply(ans, function(x) { replace(x, x == -999, NA) })
#match up data and names
if(ncol(ans)!=length(check.names)){
warning("Unexpected name/data mismatch, handled pragmatically\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
names(ans) <- make.names(check.names, unique=TRUE)
#setup date/time
date <- paste(ans$Year, ans$Day, ans$Hour, sep = "-")
date <- as.POSIXct(strptime(date, format = "%Y-%j-%H"), "GMT")
if(drop.input.dates==TRUE)
ans <- ans[,!names(ans) %in% c("Year", "Day", "Hour")]
#drop Time.s. if empty
if(all(is.na(ans$Time.s.)))
ans <- ans[,!names(ans) %in% c("Time.s.")]
#recover units from names
units <- rep(NA, ncol(ans))
units[grep("[.]s[.]", names(ans))] <- "s"
units[grep("^.[.]m", names(ans))] <- "m"
units[grep("[.]ug.m.", names(ans))] <- "ug/m3" #both 3 and superscript 3
units[grep("[.]ppb", names(ans))] <- "ppb"
units[grep("[.]ppm", names(ans))] <- "ppm"
if(length(na.omit(units))==0)
units <- "units: unknown" else
units <- paste("units: ",paste(units, sep = "", collapse = ", "), sep="")
if(simplify.names){
names(ans) <- simplifyNamesADMS(names(ans))
}
ans <- cbind(date=date,ans)
if(drop.case==TRUE) {
names(ans) <- tolower(names(ans))
}
comment(ans) <- c(comment(ans), units)
#error handling for bad days
ids <- which(is.na(ans$date))
if (length(ids) > 0) {
if(length(ids)==nrow(ans)) {
stop("Invalid date (and time) format requested\n [compare openair import settings and data structure]"
, call. = FALSE
)
}
ans <- ans[-ids, ]
reply <- paste("Missing dates detected, removing", length(ids), "line", sep=" ")
if(length(ids)>1) { reply <- paste(reply,"s",sep="") }
warning(reply, call. = FALSE)
}
print(unlist(sapply(ans, class)))
names(ans) <- gsub("..", replacement = "", names(ans), fixed = TRUE)
ans
}
###############
##daughter
##simplifyNamesADMS
#kr v0.5
#08 nov 2010
#notes
################
#two handlers: fun.temp and fun.temp.2
################
#fun.temp(x,y,z)
#replaces full term y with full term z in x
################
#fun.temp.2(x,y,z, y.names)
#replaces partial term y with partial term 2 in x
#if y.names = TRUE makes y r-friend first
#[make.names(y)...]
#
simplifyNamesADMS <- function(names=NULL){
#simplify.names lookup table for import.adms functions
#v0.2 kr
#handles as inputs (don't use after drop.case option)
#names=NULL returns simplification operation summary
if(is.null(names)) {
message("Simplification operation summary")
message("[ADMS => R => OPENAIR]:")
fun.temp <- function(x,y,z){
temp <- c(y, make.names(y), z)
message(paste("\t", paste(temp, collapse=" => "), sep=""))
temp <- data.frame(cbind(adms.input = temp[1], r.handling = temp[2], simplify.names = temp[3]),
stringsAsFactors = FALSE)
x <- rbind(x,temp)
x
}
fun.temp.2 <- function(x,y,z, y.name) x
} else {
names <- make.names(names)
fun.temp <- function(x,y,z){
x[which(x == make.names(y))] <- z
x
}
fun.temp.2 <- function(x,y,z, y.name) {
x <- if(y.name) gsub(make.names(y),z,x) else (gsub(y,z,x))
}
}
############
#update list
############
#1/LMO
names <- fun.temp(names, "1/LMO", "RECIP.LMO")
#1/MONIN-OBUKHOV LENGTH
names <- fun.temp(names, "1/MONIN-OBUKHOV LENGTH", "RECIP.LMO")
#ALBEDO(D)
names <- fun.temp(names, "ALBEDO(D)", "ALBEDO.DISP")
names <- fun.temp(names, "ALBEDO (D)", "ALBEDO.DISP")
#ALBEDO(DISP)
names <- fun.temp(names, "ALBEDO(DISP)", "ALBEDO.DISP")
names <- fun.temp(names, "ALBEDO (DISP)", "ALBEDO.DISP")
#ALBEDO (DISPERSION AREA)
names <- fun.temp(names, "ALBEDO (DISPERSION AREA)", "ALBEDO.DISP")
#ALBEDO(M)
names <- fun.temp(names, "ALBEDO(M)", "ALBEDO.MET")
names <- fun.temp(names, "ALBEDO (M)", "ALBEDO.MET")
#ALBEDO(MET)
names <- fun.temp(names, "ALBEDO(MET)", "ALBEDO.MET")
names <- fun.temp(names, "ALBEDO (MET)", "ALBEDO.MET")
#ALBEDO (MET SITE)
names <- fun.temp(names, "ALBEDO (MET SITE)", "ALBEDO.MET")
#ALPHA
##########
##conflict
##########
##both alpha.disp and alpha.met seem to have been abbrev. to alpha
#ALPHA(D)
names <- fun.temp(names, "ALPHA(D)", "ALPHA.DISP")
names <- fun.temp(names, "ALPHA (D)", "ALPHA.DISP")
#ALPHA(DISP)
names <- fun.temp(names, "ALPHA(DISP)", "ALPHA.DISP")
names <- fun.temp(names, "ALPHA (DISP)", "ALPHA.DISP")
#ALPHA(M)
names <- fun.temp(names, "ALPHA(M)", "ALPHA.MET")
names <- fun.temp(names, "ALPHA (M)", "ALPHA.MET")
#ALPHA(MET)
names <- fun.temp(names, "ALPHA(MET)", "ALPHA.MET")
names <- fun.temp(names, "ALPHA (MET)", "ALPHA.MET")
#BL DEPTH
names <- fun.temp(names, "BL DEPTH", "H")
#BOUNDARY LAYER DEPTH
names <- fun.temp(names, "BOUNDARY LAYER DEPTH", "H")
#BUOYANCY FREQUENCY ABOVE BOUNDARY LAYER
names <- fun.temp(names, "BUOYANCY FREQUENCY ABOVE BOUNDARY LAYER", "NU")
#BUTADIENE
#CL
#CLOUD
names <- fun.temp(names, "CLOUD", "CL")
#CLOUD AMOUNT (OKTAS)
names <- fun.temp(names, "CLOUD AMOUNT (OKTAS)", "CL")
#Conc|ppb|NAME|All sources|-| 1hr
names <- fun.temp(names, "Conc|ppb|NAME|SOURCES|-| RESOLUTION", "NAME.SOURCES.RESOLUTION")
#Conc|ppm|NAME|All sources|-| 1hr
names <- fun.temp(names, "Conc|ppm|NAME|SOURCES|-| RESOLUTION", "NAME.SOURCES.RESOLUTION")
#Conc|ug/m3|NAME|All sources|-| 1hr
names <- fun.temp(names, "Conc|ug/m3|NAME|SOURCES|-| RESOLUTION", "NAME.SOURCES.RESOLUTION")
#NAME.All.sources.1hr
names <- fun.temp(names, "NAME.All.sources.1hr", "NAME")
#NAME.All.sources.RESOLUTION
names <- fun.temp(names, "NAME.All.sources.RESOLUTION", "NAME.RESOLUTION")
#NAME.SOURCE.1hr
names <- fun.temp(names, "NAME.SOURCE.1hr", "NAME.SOURCE")
#general for above
names <- fun.temp.2(names, "Conc|ppb|", "", TRUE)
names <- fun.temp.2(names, "Conc|ppm|", "", TRUE)
names <- fun.temp.2(names, "Conc|.g/m.|", "", TRUE)
#above covers
##u, m and mu for 1st and
##3 and superscript3 for second
names <- fun.temp.2(names, "[.][.][.][.]", ".", FALSE)
names <- fun.temp.2(names, "[.][.][.]", ".", FALSE)
names <- fun.temp.2(names, "[.]All[.]sources", "", FALSE)
names <- fun.temp.2(names, "[.]1hr", "", FALSE)
#D(RELATIVE HUMIDITY)/DZ ABOVE BOUNDARY LAYER (PERCENT/M)
names <- fun.temp(names, "D(RELATIVE HUMIDITY)/DZ ABOVE BOUNDARY LAYER (PERCENT/M)", "DRHDZU")
#DAY
#DELTAPHI
names <- fun.temp(names, "DELTAPHI", "DELTA.WD")
#DELTAT
names <- fun.temp(names, "DELTAT", "DELTA.T")
names <- fun.temp(names, "DELTA T", "DELTA.T")
#DELTATHETA
names <- fun.temp(names, "DELTATHETA", "DELTA.THETA")
names <- fun.temp(names, "DELTA THETA", "DELTA.THETA")
#DIRN CHANGE
names <- fun.temp(names, "DIRN CHANGE", "DELTA.WD")
#DRH/DZ
names <- fun.temp(names, "DRH/DZ", "DRHDZU")
#DRHDZU
#FR
#FREQUENCY
#FTHETA0
#GEOSTROPHIC MINUS SURFACE WIND DIRECTION (DEGREES)
names <- fun.temp(names, "GEOSTROPHIC MINUS SURFACE WIND DIRECTION (DEGREES)", "DELTA.WD")
#H
#HEAT FLUX
names <- fun.temp(names, "HEAT FLUX", "FTHETA0")
#HOUR
#HOURS
#INCOMING SOLAR RADIATION
names <- fun.temp(names, "INCOMING SOLAR RADIATION", "K")
#INPUT_DATA:
#K
#LAMBDAE
#LATENT HEAT FLUX
names <- fun.temp(names, "LATENT HEAT FLUX", "LAMBDAE")
#LAT HT FLUX
names <- fun.temp(names, "LAT HT FLUX", "LAMBDAE")
#MODIFIED PRIESTLEY-TAYLOR PARAMETER (DISPERSION AREA)
names <- fun.temp(names, "MODIFIED PRIESTLEY-TAYLOR PARAMETER (DISPERSION AREA)", "ALPHA.DISP")
#MODIFIED PRIESTLEY-TAYLOR PARAMETER (MET SITE)
names <- fun.temp(names, "MODIFIED PRIESTLEY-TAYLOR PARAMETER (MET SITE)", "ALPHA.MET")
#MONTHS
#N ABOVE BL
names <- fun.temp(names, "N ABOVE BL", "NU")
#NO2
#NOx
#NU
#P
#PM10
#PM2.5
#O3
#Q0
#PHI
names <- fun.temp(names, "PHI", "WD")
#PHI0
names <- fun.temp(names, "PHI0", "WD.0")
#PHIG
names <- fun.temp(names, "PHIG", "WD.G")
#PHISEC
names <- fun.temp(names, "PHISEC", "WD.SEC")
#PRECIP
names <- fun.temp(names, "PRECIP", "P")
#PRECIPITATION RATE (MM/HOUR)
names <- fun.temp(names, "PRECIPITATION RATE (MM/HOUR)", "P")
#PROCESSED_DATA:
#R
names <- fun.temp(names, "R", "ALBEDO.MET")
#RECIPLMO
names <- fun.temp(names, "RECIPLMO", "RECIP.LMO")
#RELATIVE HUMIDITY ABOVE BOUNDARY LAYER (PERCENT)
names <- fun.temp(names, "RELATIVE HUMIDITY ABOVE BOUNDARY LAYER (PERCENT)", "RHU")
#RH ABOVE BL
names <- fun.temp(names, "RH ABOVE BL", "RHU")
#RHU
#RHUM
names <- fun.temp(names, "RHUM", "RHU")
#ROUGHNESS LENGTH (DISPERSION AREA)
names <- fun.temp(names, "ROUGHNESS LENGTH (DISPERSION AREA)", "Z0.DISP")
#ROUGHNESS LENGTH (MET SITE)
names <- fun.temp(names, "ROUGHNESS LENGTH (MET SITE)", "Z0.MET")
#RUN
#S HUMIDITY
names <- fun.temp(names, "S HUMIDITY", "SHU")
#SEA SURFACE TEMPERATURE (C)
names <- fun.temp(names, "SEA SURFACE TEMPERATURE (C)", "TSEA")
#SEA TEMP
names <- fun.temp(names, "SEA TEMP", "TSEA")
#SENSIBLE HEAT FLUX
names <- fun.temp(names, "SENSIBLE HEAT FLUX", "FTHETA0")
#SIGMATHETA
names <- fun.temp(names, "SIGMATHETA", "SIGMA.THETA")
names <- fun.temp(names, "SIGMA THETA", "SIGMA.THETA")
#SIGMA THETA (DEGREES)
names <- fun.temp(names, "SIGMA THETA (DEGREES)", "SIGMA.THETA")
#SO2
#SOLAR RAD
names <- fun.temp(names, "SOLAR RAD", "K")
#SPECIFIC HUMIDITY
names <- fun.temp(names, "SPECIFIC HUMIDITY", "SHU")
#T0C
names <- fun.temp(names, "T0C", "TEMP")
#TDAY
#TEMPERATURE
names <- fun.temp(names, "TEMPERATURE", "TEMP")
#TEMPERATURE (C)
names <- fun.temp(names, "TEMPERATURE (C)", "TEMP")
#TEMPERATURE JUMP ACROSS BOUNDARY LAYER TOP
names <- fun.temp(names, "TEMPERATURE JUMP ACROSS BOUNDARY LAYER TOP", "DELTA.THETA")
#THOUR
#TEMPERATURE OVER LAND MINUS SEA SURFACE TEMPERATURE
names <- fun.temp(names, "TEMPERATURE OVER LAND MINUS SEA SURFACE TEMPERATURE", "DELTA.T")
#Time(s)
#X(m)
names <- fun.temp(names, "Time(s)", "Time")
#TSEA
#TYEAR
#U
names <- fun.temp(names, "U", "WS")
#UG
names <- fun.temp(names, "UG", "WS.G")
#UGSTAR
names <- fun.temp(names, "UGSTAR", "WS.GSTAR")
#USTAR
names <- fun.temp(names, "USTAR", "WS.STAR")
#WIND DIRN
names <- fun.temp(names, "WIND DIRN", "WD")
#WIND DIRECTION (DEGREES)
names <- fun.temp(names, "WIND DIRECTION (DEGREES)", "WD")
#WIND HEIGHT
names <- fun.temp(names, "WIND HEIGHT", "WIND.HEIGHT")
#WIND MEASUREMENT HEIGHT
names <- fun.temp(names, "WIND MEASUREMENT HEIGHT", "WIND.HEIGHT")
#WIND SPEED
names <- fun.temp(names, "WIND SPEED", "WS")
#WSTAR
#X(m)
names <- fun.temp(names, "X(m)", "X")
#Y(m)
names <- fun.temp(names, "Y(m)", "Y")
#YEAR
#Z(m)
names <- fun.temp(names, "Z(m)", "Z")
#Z0(D)
names <- fun.temp(names, "Z0(D)", "Z0.DISP")
names <- fun.temp(names, "Z0 (D)", "Z0.DISP")
#Z0(DISP)
names <- fun.temp(names, "Z0(DISP)", "Z0.DISP")
names <- fun.temp(names, "Z0 (DISP)", "Z0.DISP")
#Z0(M)
names <- fun.temp(names, "Z0(M)", "Z0.MET")
names <- fun.temp(names, "Z0 (M)", "Z0.MET")
#Z0(MET)
names <- fun.temp(names, "Z0(MET)", "Z0.MET")
names <- fun.temp(names, "Z0 (MET)", "Z0.MET")
########
#outputs
########
invisible(names)
}
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