read_rdf_header <- function(con, pos, end)
{
obj <- list()
repeat {
line <- con[pos, 1]
pos <- pos + 1 # advancing line to read
if(line == end) break
splitLine <- strsplit(line, ':', fixed = TRUE)[[1]]
name <- splitLine[1]
if (length(splitLine) > 1) {
if (substr(splitLine[2], 1, 1) == ' ') {
splitLine[2] <- substr(splitLine[2], 2, nchar(splitLine[2]))
}
contents <- paste(splitLine[2:length(splitLine)], collapse = ':')
} else {
contents <- NA
}
obj[[name]] <- contents
# 1 passed to this function sometimes; when it is, it forces it to read
# one line and parse
if (end == 1) break
}
#returns the object
return(list(data = obj, position = pos))
}
#' Read the initial meta data from the rdf file; this is the descriptor:pair
#' data up through the END_PACKAGE_PREAMBLE keyword. These are read once for
#' each rdf file and there is only one set of meta data regardless of the
#' number of traces.
#' @noRd
read_rdf_meta <- function(rdf.mat, rdf.obj)
{
rdf.tmp <- read_rdf_header(rdf.mat, rdf.obj$position, 'END_PACKAGE_PREAMBLE')
rdf.obj[['meta']] <- rdf.tmp$data
rdf.obj$position <- rdf.tmp$position
return(rdf.obj)
}
read_rdf_run <- function(rdf.mat, rdf.obj)
{
this.run <- length(rdf.obj$runs) + 1
rdf.tmp <- read_rdf_header(rdf.mat,rdf.obj$position,'END_RUN_PREAMBLE')
rdf.obj$runs[[this.run]] <- rdf.tmp$data
rdf.obj$position <- rdf.tmp$position
#time steps
nts <- as.integer(rdf.obj$runs[[this.run]]$time_steps)
#for non-mrm files
if (length(nts) == 0) {
nts <- as.integer(rdf.obj$runs[[this.run]]$timesteps)
}
rr <- rdf.obj$position:(rdf.obj$position + nts -1)
rdf.obj$runs[[this.run]][['times']] <- rdf.mat[rr, 1]
rdf.obj$position <- rdf.obj$position + nts
#Series
nob <- 0
repeat {
nob <- nob + 1
rdf.tmp <- read_rdf_header(rdf.mat,rdf.obj$position, 'END_SLOT_PREAMBLE')
rdf.obj$runs[[this.run]][['objects']][[nob]] <- rdf.tmp$data
rdf.obj$position <- rdf.tmp$position
# name the object after their object.slot name
obj.name <- rdf.obj$runs[[this.run]][['objects']][[nob]]$object_name
slot.name <- rdf.obj$runs[[this.run]][['objects']][[nob]]$slot_name
name <- paste(obj.name, slot.name, sep = '.')
names(rdf.obj$runs[[this.run]][['objects']])[nob] <- name
# read in the extr two header pieces
rdf.tmp <- read_rdf_header(rdf.mat,rdf.obj$position, 1)
rdf.obj$runs[[this.run]][['objects']][[nob]]$units <- rdf.tmp$data[[1]]
rdf.obj$position <- rdf.tmp$position
rdf.tmp <- read_rdf_header(rdf.mat,rdf.obj$position, 1)
rdf.obj$runs[[this.run]][['objects']][[nob]]$scale <- rdf.tmp$data[[1]]
rdf.obj$position <- rdf.tmp$position
# Figure out when the END_COLUMN keyword shows up
#rdf_tmp <- read_rdf_header(rdf.mat, rdf.obj$position, "END_COLUMN")
ec_pos <- Position(function(x) x > rdf.obj$position, rdf.obj$end_col_i)
ec_i <- rdf.obj$end_col_i[ec_pos] + 1
# remove the already used indeces so next Position call doesn't have to
# search for indeces that are already used
rdf.obj$end_col_i <- rdf.obj$end_col_i[
(ec_pos + 1):length(rdf.obj$end_col_i)
]
if (ec_i == rdf.obj$position + 2) {
# must be a scalar slot
row_nums <- rdf.obj$position
} else if (ec_i - rdf.obj$position - 1 == nts) {
row_nums <- rdf.obj$position:(ec_i - 2)
} else {
stop(
"rdf includes an unexpected number of data points.\n",
"`read.rdf()` expects the data entries to either be 1, or\n",
"the number of time steps."
)
}
rdf.obj$runs[[this.run]][['objects']][[nob]]$values <- as.numeric(
rdf.mat[row_nums, 1]
)
rdf.obj$position <- rdf.obj$position + length(row_nums)
#END_COLUMN,END_SLOT, table slots need support here
#dummy <- readLines(rdf.con,n=2) # just advances position by 2??
if (rdf.mat[rdf.obj$position+2,1] == 'END_RUN') {
rdf.obj$position <- rdf.obj$position + 3
break
} else {
rdf.obj$position <- rdf.obj$position + 2
}
}
return(rdf.obj)
}
#' Read an rdf file into R.
#'
#' `read.rdf()` reads an rdf file into R and formats it as a multi-level list
#' containing all of the metadata included in the rdf file. rdf files are
#' generated by RiverWare and are documented in the
#' [RiverWare documentation](http://www.riverware.org/HelpSystem/index.html).
#'
#' `read.rdf()`uses [data.table::fread()] to read in the file, which provides
#' performance benefits as compared to earlier versions of the function.
#'
#' `read.rdf2()` is deprecated and will be removed in a future release.
#'
#' @param iFile The input rdf file that will be read into R.
#' @param rdf Boolean; if `TRUE`, then an rdf object is returned. If `FALSE`,
#' then a character vector is returned.
#'
#' @return An rdf object or character vector.
#'
#' @examples
#' zz <- read_rdf(system.file(
#' 'extdata/Scenario/ISM1988_2014,2007Dems,IG,Most',
#' "KeySlots.rdf",
#' package = "RWDataPlyr"
#' ))
#'
#' @export
read.rdf <- function(iFile, rdf = TRUE)
{
check_rdf_file(iFile)
rdf.obj <- list()
# read entire file into memory
rdf.mat <- as.matrix(data.table::fread(
iFile,
sep = '\t',
header = FALSE,
data.table = FALSE
))
if (!rdf) {
return(rdf.mat)
}
rdf.obj$position <- 1 # initialize where to read from
rdf.obj <- read_rdf_meta(rdf.mat, rdf.obj)
rdf.obj$end_col_i <- which(rdf.mat == "END_COLUMN")
# Read each trace/run
for (i in 1:as.numeric(rdf.obj$meta$number_of_runs)) {
rdf.obj <- read_rdf_run(rdf.mat, rdf.obj)
}
rdf.obj$position <- NULL # remove position before returning
rdf.obj$end_col_i <- NULL
structure(
rdf.obj,
class = "rdf"
)
}
#' @describeIn read.rdf Deprecated version of `read.rdf()`
#' @export
read.rdf2 <- function(iFile)
{
.Deprecated("read.rdf")
read.rdf(iFile, rdf = TRUE)
}
#' @rdname read.rdf
#' @export
read_rdf <- read.rdf
check_rdf_file <- function(file)
{
if (tools::file_ext(file) != "rdf") {
stop(
file, " does not appear to be an rdf file.",
call. = FALSE
)
}
if (!file.exists(file)) {
stop(
file, " does not exist.",
call. = FALSE
)
}
invisible(file)
}
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