R/calcIndices.R
In mqueinnec/foster: Forest Structure Extrapolation with R
Defines functions
calcIndices.list
calcIndices.SpatialPointsDataFrame
calcIndices.Raster
calcIndices
Documented in
calcIndices
#'Calculate spectral indices from multispectral data
#'
#'Calculate spectral indices (e.g. NDVI, tasseled cap coefficients etc.) from
#'multispectral data. Calculations are based on the functions
#'\code{\link[RStoolbox]{spectralIndices}} and
#'\code{\link[RStoolbox]{tasseledCap}}. Refer to the documentation of these
#'functions for more details.
#'
#'If x is a Raster* or list of Raster* objects, each layer should be one of the
#'spectral bands used to calculate the indices. If x is a SpatialPointsDataFrame
#'or list of spatialPointsDataFrame, each column should be a spectral band. When
#'calculating tasseledCap indices, bands should be provided in a specific order
#'specified in \code{\link[RStoolbox]{tasseledCap}}.
#'
#'Tasseled Cap Angle (TCA) and Distance (TCD) are calculated from greenness
#'(TCG) and brightness (TCB) as follows:
#'
#'\deqn{TCA = \arctan(\frac{TCG}{TCB})}
#'
#'\deqn{TCD = \sqrt{TCB^{2} + TCG^{2}}}
#'
#'If \code{x} is a list of Raster* objects, the processing can be parallelized
#'using \code{\link[raster]{cluster}}. In that case the user has to set
#'\code{par = TRUE} and provide the number of parallel threads \code{threads}.
#'You can control how many blocks will be processed by each thread by setting
#'\code{m} (see \code{\link[raster]{cluster}}).
#'
#'@param x Raster* or SpatialPointsDataFrame object or list of Raster* or
#' SpatialPointsDataFrame objects.
#'@param indices Character vector indicating Which indices are calculated.
#' Tasseled Cap indices are abbreviated as \code{TCB}, \code{TCW}, \code{TCG},
#' \code{TCA}, \code{TCD}. For a list of other supported indices see
#' \code{\link[RStoolbox]{spectralIndices}}
#'@param sat Character. If calculating tasseled cap indices, name of the sensor
#' needs to be provided. One of: c("Landsat4TM", "Landsat5TM", "Landsat7ETM",
#' "Landsat8OLI", "MODIS", "QuickBird", "Spot5", "RapidEye"). See
#' \code{\link[RStoolbox]{tasseledCap}}.
#'@param blue Integer. Blue band.
#'@param green Integer. Green band.
#'@param red Integer. Red band.
#'@param nir Integer. Near infrared band (700-1100 nm).
#'@param swir1 temporarily deprecated
#'@param swir2 Integer. Shortwave infrared band (1400-1800 nm)
#'@param swir3 Integer. Shortwave infrared band (2000-2500 nm)
#'@param coefs Coefficients necessary to calculate some of the spectral indices
#' (e.g. EVI). See \code{\link[RStoolbox]{spectralIndices}}.
#'@param filename Character. Output file name including path to directory and
#' eventually extension. If \code{x} is a list, \code{filename} must be a
#' vector of characters with one file name for each element of x. Default is
#' \code{""} (output not written to disk).
#'@param par Logical. Should the function be executed on parallel threads
#'@param threads Number of parallel threads used if par = TRUE
#'@param m tuning parameter to determine how many blocks will be used (m blocks
#' will be processed by each cluster)
#'@param progress Logical. If TRUE (default) a progress bar is displayed when
#' using parallel processing.
#'@param ... Other arguments passed to \code{\link[raster]{writeRaster}} or
#' \code{\link[rgdal]{writeOGR}}.
#'@seealso \code{\link[RStoolbox]{spectralIndices}},
#' \code{\link[RStoolbox]{tasseledCap}}, \code{\link[raster]{cluster}}
#'@return Raster* or SpatialPointsDataFrame object or list of Raster* or
#' SpatialPointsDataFrame objects.
#'@examples
#'\donttest{
#' library(raster)
#'
#' # Open Landsat BAP image
#' BAP_2006 <- stack(system.file("extdata/examples/Landsat_BAP_2006.tif",package =
#' "foster"))
#'
#' # Calculate NDVI
#' VI_2006 <- calcIndices(BAP_2006,
#' indices = "NDVI",
#' red=3,
#' nir=4)
#'}
#'@export
calcIndices <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
if (!is.character(indices)) {
stop("indices must be a vector of characters")
}
UseMethod("calcIndices", x)
}
#' @export
calcIndices.Raster <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
if (!(class(x) %in% c(
"SpatialPointsDataFrame", "RaterLayer", "RasterStack",
"RasterBrick"
))) {
stop("x must be a SpatialPointsDataFrame, RasterLayer, RasterStack or
RasterBrick object (or a list of these objects)")
}
if(progress) progress = "text" else progres = NULL
# Supported Tasseled Cap names
TC.names <- c("TCG", "TCB", "TCW", "TCA", "TCD")
if (any(indices %in% TC.names)) {
doTC <- TRUE
}else{
doTC <- FALSE
}
if (doTC && is.null(sat)) {
stop("The name of the satellite must be given to calculate Tasseled Cap
indices")
}
# Rename x to x_rast for use below
x_rast <- x
if (par) {
raster::beginCluster(threads)
if (doTC) {
out_tc <- raster::clusterR(x_rast, RStoolbox::tasseledCap,
args = list(sat = sat), filename = "", m = m, progress = progress, ...
)
names(out_tc) <- c("TCB", "TCG", "TCW")
}
out_ind <- raster::clusterR(x_rast, RStoolbox::spectralIndices,
args = list(
indices = setdiff(indices, TC.names), blue = blue,
green = green, red = red, nir = nir, swir1 = swir1, swir2 = swir2,
swir3 = swir3, coefs = coefs
), filename = "", m = m, progress = progress,
...
)
names(out_ind) <- setdiff(indices, TC.names)
on.exit(raster::endCluster())
if (doTC) {
out <- raster::stack(out_tc, out_ind)
} else {
out <- out_ind
}
if ("TCA" %in% indices) {
out$TCA <- atan(raster::subset(out, "TCG") /
raster::subset(out, "TCB"))
}
if ("TCD" %in% indices) {
out$TCD <- (raster::subset(out, "TCG")^2 +
raster::subset(out, "TCB")^2)^0.5
}
out <- raster::subset(out, indices)
temp_names <- names(out)
} else {
if (doTC) {
out_tc <- RStoolbox::tasseledCap(
img = x_rast, sat = sat, filename = "",
...
)
names(out_tc) <- c("TCB", "TCG", "TCW")
}
out_ind <- RStoolbox::spectralIndices(
img = x_rast,
indices = setdiff(indices, TC.names), blue = blue, green = green,
red = red, nir = nir, swir1 = swir1, swir2 = swir2, swir3 = swir3,
coefs = coefs, filename = "", ...
)
names(out_ind) <- setdiff(indices, TC.names)
if (doTC) {
out <- raster::stack(out_tc, out_ind)
} else {
out <- out_ind
}
if ("TCA" %in% indices) {
out$TCA <- atan(raster::subset(out, "TCG") /
raster::subset(out, "TCB"))
}
if ("TCD" %in% indices) {
out$TCD <- (raster::subset(out, "TCG")^2 +
raster::subset(out, "TCB")^2)^0.5
}
out <- raster::subset(out, indices)
temp_names <- names(out)
}
if (filename != "") {
out <- raster::writeRaster(out, filename = filename, ...)
names(out) <- temp_names
}
return(out)
}
#' @export
calcIndices.SpatialPointsDataFrame <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
if (!(class(x) %in% c(
"SpatialPointsDataFrame", "RaterLayer", "RasterStack",
"RasterBrick"
))) {
stop("x must be a SpatialPointsDataFrame, RaterLayer, RasterStack or
RasterBrick object")
}
if(progress) progress = "text" else progres = NULL
# Supported Tasseled Cap names
TC.names <- c("TCG", "TCB", "TCW", "TCA", "TCD")
if (any(indices %in% TC.names)) doTC <- TRUE else doTC <- FALSE
if (doTC && is.null(sat)) {
stop("The name of the satellite must be given to calculate Tasseled Cap
indices")
}
# We transform the spdf to a raster
x_df <- spdf2df(x, xy = TRUE)
# Store coordinates of x
coords <- x_df[, sp::coordnames(x)]
x_df <- x_df[, !(colnames(x_df) %in% sp::coordnames(x))]
# Transform x to a raster stack
x_rast <- raster::stack(lapply(as.list(x_df), function(x) {
raster::raster(matrix(x))
}))
if (doTC) {
out_tc <- RStoolbox::tasseledCap(
img = x_rast, sat = sat, filename = "",
...
)
names(out_tc) <- c("TCB", "TCG", "TCW")
}
out_ind <- RStoolbox::spectralIndices(
img = x_rast,
indices = setdiff(indices, TC.names), blue = blue, green = green,
red = red, nir = nir, swir1 = swir1, swir2 = swir2, swir3 = swir3,
coefs = coefs, filename = "", ...
)
names(out_ind) <- setdiff(indices, TC.names)
if (doTC) {
out <- raster::stack(out_tc, out_ind)
} else {
out <- out_ind
}
if ("TCA" %in% indices) {
out$TCA <- atan(raster::subset(out, "TCG") / raster::subset(out, "TCB"))
}
if ("TCD" %in% indices) {
out$TCD <- (raster::subset(out, "TCG")^2 + raster::subset(out, "TCB")^2)^0.5
}
out <- raster::subset(out, indices)
temp_names <- names(out)
# Transform back to spdf
out <- raster::rasterToPoints(out, spatial = FALSE)
out <- sp::SpatialPointsDataFrame(
coords = coords,
data = data.frame(out[, indices]), proj4string = raster::crs(x)
)
names(out) <- temp_names
if (filename != "") {
rgdal::writeOGR(out,
driver = "ESRI Shapefile",
layer = tools::file_path_sans_ext(basename(filename)),
dsn = dirname(filename), ...
)
}
return(out)
}
#' @export
calcIndices.list <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
# Check that there is a unique filename for each element of the list
if (length(filename) < length(x)) {
if (filename != "") {
warning("Number of filenames and processed objects don't match. Datasets with missing filename will be stored in memory or written to a temporary file")
}
# Append missing filenames
toAdd <- length(x) - length(filename)
filename = c(filename, rep("", toAdd))
}
# Check if filenames are unique (other than "")
filename_non_empty <- filename[filename != ""]
if (length(unique(filename_non_empty)) != length(filename_non_empty)) {
stop("filename must have unique values (other than \"\") for each element of the list x")
}
args <- c(as.list(environment()), list(...))
args <- args[ ! names(args) %in% c("x", "filename")]
mapply(calcIndices, x, filename, MoreArgs = args)
}
mqueinnec/foster documentation built on March 28, 2021, 4:27 p.m.
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Defines functions calcIndices.list calcIndices.SpatialPointsDataFrame calcIndices.Raster calcIndices
Documented in calcIndices
#'Calculate spectral indices from multispectral data
#'
#'Calculate spectral indices (e.g. NDVI, tasseled cap coefficients etc.) from
#'multispectral data. Calculations are based on the functions
#'\code{\link[RStoolbox]{spectralIndices}} and
#'\code{\link[RStoolbox]{tasseledCap}}. Refer to the documentation of these
#'functions for more details.
#'
#'If x is a Raster* or list of Raster* objects, each layer should be one of the
#'spectral bands used to calculate the indices. If x is a SpatialPointsDataFrame
#'or list of spatialPointsDataFrame, each column should be a spectral band. When
#'calculating tasseledCap indices, bands should be provided in a specific order
#'specified in \code{\link[RStoolbox]{tasseledCap}}.
#'
#'Tasseled Cap Angle (TCA) and Distance (TCD) are calculated from greenness
#'(TCG) and brightness (TCB) as follows:
#'
#'\deqn{TCA = \arctan(\frac{TCG}{TCB})}
#'
#'\deqn{TCD = \sqrt{TCB^{2} + TCG^{2}}}
#'
#'If \code{x} is a list of Raster* objects, the processing can be parallelized
#'using \code{\link[raster]{cluster}}. In that case the user has to set
#'\code{par = TRUE} and provide the number of parallel threads \code{threads}.
#'You can control how many blocks will be processed by each thread by setting
#'\code{m} (see \code{\link[raster]{cluster}}).
#'
#'@param x Raster* or SpatialPointsDataFrame object or list of Raster* or
#' SpatialPointsDataFrame objects.
#'@param indices Character vector indicating Which indices are calculated.
#' Tasseled Cap indices are abbreviated as \code{TCB}, \code{TCW}, \code{TCG},
#' \code{TCA}, \code{TCD}. For a list of other supported indices see
#' \code{\link[RStoolbox]{spectralIndices}}
#'@param sat Character. If calculating tasseled cap indices, name of the sensor
#' needs to be provided. One of: c("Landsat4TM", "Landsat5TM", "Landsat7ETM",
#' "Landsat8OLI", "MODIS", "QuickBird", "Spot5", "RapidEye"). See
#' \code{\link[RStoolbox]{tasseledCap}}.
#'@param blue Integer. Blue band.
#'@param green Integer. Green band.
#'@param red Integer. Red band.
#'@param nir Integer. Near infrared band (700-1100 nm).
#'@param swir1 temporarily deprecated
#'@param swir2 Integer. Shortwave infrared band (1400-1800 nm)
#'@param swir3 Integer. Shortwave infrared band (2000-2500 nm)
#'@param coefs Coefficients necessary to calculate some of the spectral indices
#' (e.g. EVI). See \code{\link[RStoolbox]{spectralIndices}}.
#'@param filename Character. Output file name including path to directory and
#' eventually extension. If \code{x} is a list, \code{filename} must be a
#' vector of characters with one file name for each element of x. Default is
#' \code{""} (output not written to disk).
#'@param par Logical. Should the function be executed on parallel threads
#'@param threads Number of parallel threads used if par = TRUE
#'@param m tuning parameter to determine how many blocks will be used (m blocks
#' will be processed by each cluster)
#'@param progress Logical. If TRUE (default) a progress bar is displayed when
#' using parallel processing.
#'@param ... Other arguments passed to \code{\link[raster]{writeRaster}} or
#' \code{\link[rgdal]{writeOGR}}.
#'@seealso \code{\link[RStoolbox]{spectralIndices}},
#' \code{\link[RStoolbox]{tasseledCap}}, \code{\link[raster]{cluster}}
#'@return Raster* or SpatialPointsDataFrame object or list of Raster* or
#' SpatialPointsDataFrame objects.
#'@examples
#'\donttest{
#' library(raster)
#'
#' # Open Landsat BAP image
#' BAP_2006 <- stack(system.file("extdata/examples/Landsat_BAP_2006.tif",package =
#' "foster"))
#'
#' # Calculate NDVI
#' VI_2006 <- calcIndices(BAP_2006,
#' indices = "NDVI",
#' red=3,
#' nir=4)
#'}
#'@export
calcIndices <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
if (!is.character(indices)) {
stop("indices must be a vector of characters")
}
UseMethod("calcIndices", x)
}
#' @export
calcIndices.Raster <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
if (!(class(x) %in% c(
"SpatialPointsDataFrame", "RaterLayer", "RasterStack",
"RasterBrick"
))) {
stop("x must be a SpatialPointsDataFrame, RasterLayer, RasterStack or
RasterBrick object (or a list of these objects)")
}
if(progress) progress = "text" else progres = NULL
# Supported Tasseled Cap names
TC.names <- c("TCG", "TCB", "TCW", "TCA", "TCD")
if (any(indices %in% TC.names)) {
doTC <- TRUE
}else{
doTC <- FALSE
}
if (doTC && is.null(sat)) {
stop("The name of the satellite must be given to calculate Tasseled Cap
indices")
}
# Rename x to x_rast for use below
x_rast <- x
if (par) {
raster::beginCluster(threads)
if (doTC) {
out_tc <- raster::clusterR(x_rast, RStoolbox::tasseledCap,
args = list(sat = sat), filename = "", m = m, progress = progress, ...
)
names(out_tc) <- c("TCB", "TCG", "TCW")
}
out_ind <- raster::clusterR(x_rast, RStoolbox::spectralIndices,
args = list(
indices = setdiff(indices, TC.names), blue = blue,
green = green, red = red, nir = nir, swir1 = swir1, swir2 = swir2,
swir3 = swir3, coefs = coefs
), filename = "", m = m, progress = progress,
...
)
names(out_ind) <- setdiff(indices, TC.names)
on.exit(raster::endCluster())
if (doTC) {
out <- raster::stack(out_tc, out_ind)
} else {
out <- out_ind
}
if ("TCA" %in% indices) {
out$TCA <- atan(raster::subset(out, "TCG") /
raster::subset(out, "TCB"))
}
if ("TCD" %in% indices) {
out$TCD <- (raster::subset(out, "TCG")^2 +
raster::subset(out, "TCB")^2)^0.5
}
out <- raster::subset(out, indices)
temp_names <- names(out)
} else {
if (doTC) {
out_tc <- RStoolbox::tasseledCap(
img = x_rast, sat = sat, filename = "",
...
)
names(out_tc) <- c("TCB", "TCG", "TCW")
}
out_ind <- RStoolbox::spectralIndices(
img = x_rast,
indices = setdiff(indices, TC.names), blue = blue, green = green,
red = red, nir = nir, swir1 = swir1, swir2 = swir2, swir3 = swir3,
coefs = coefs, filename = "", ...
)
names(out_ind) <- setdiff(indices, TC.names)
if (doTC) {
out <- raster::stack(out_tc, out_ind)
} else {
out <- out_ind
}
if ("TCA" %in% indices) {
out$TCA <- atan(raster::subset(out, "TCG") /
raster::subset(out, "TCB"))
}
if ("TCD" %in% indices) {
out$TCD <- (raster::subset(out, "TCG")^2 +
raster::subset(out, "TCB")^2)^0.5
}
out <- raster::subset(out, indices)
temp_names <- names(out)
}
if (filename != "") {
out <- raster::writeRaster(out, filename = filename, ...)
names(out) <- temp_names
}
return(out)
}
#' @export
calcIndices.SpatialPointsDataFrame <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
if (!(class(x) %in% c(
"SpatialPointsDataFrame", "RaterLayer", "RasterStack",
"RasterBrick"
))) {
stop("x must be a SpatialPointsDataFrame, RaterLayer, RasterStack or
RasterBrick object")
}
if(progress) progress = "text" else progres = NULL
# Supported Tasseled Cap names
TC.names <- c("TCG", "TCB", "TCW", "TCA", "TCD")
if (any(indices %in% TC.names)) doTC <- TRUE else doTC <- FALSE
if (doTC && is.null(sat)) {
stop("The name of the satellite must be given to calculate Tasseled Cap
indices")
}
# We transform the spdf to a raster
x_df <- spdf2df(x, xy = TRUE)
# Store coordinates of x
coords <- x_df[, sp::coordnames(x)]
x_df <- x_df[, !(colnames(x_df) %in% sp::coordnames(x))]
# Transform x to a raster stack
x_rast <- raster::stack(lapply(as.list(x_df), function(x) {
raster::raster(matrix(x))
}))
if (doTC) {
out_tc <- RStoolbox::tasseledCap(
img = x_rast, sat = sat, filename = "",
...
)
names(out_tc) <- c("TCB", "TCG", "TCW")
}
out_ind <- RStoolbox::spectralIndices(
img = x_rast,
indices = setdiff(indices, TC.names), blue = blue, green = green,
red = red, nir = nir, swir1 = swir1, swir2 = swir2, swir3 = swir3,
coefs = coefs, filename = "", ...
)
names(out_ind) <- setdiff(indices, TC.names)
if (doTC) {
out <- raster::stack(out_tc, out_ind)
} else {
out <- out_ind
}
if ("TCA" %in% indices) {
out$TCA <- atan(raster::subset(out, "TCG") / raster::subset(out, "TCB"))
}
if ("TCD" %in% indices) {
out$TCD <- (raster::subset(out, "TCG")^2 + raster::subset(out, "TCB")^2)^0.5
}
out <- raster::subset(out, indices)
temp_names <- names(out)
# Transform back to spdf
out <- raster::rasterToPoints(out, spatial = FALSE)
out <- sp::SpatialPointsDataFrame(
coords = coords,
data = data.frame(out[, indices]), proj4string = raster::crs(x)
)
names(out) <- temp_names
if (filename != "") {
rgdal::writeOGR(out,
driver = "ESRI Shapefile",
layer = tools::file_path_sans_ext(basename(filename)),
dsn = dirname(filename), ...
)
}
return(out)
}
#' @export
calcIndices.list <- function(x,
indices = "NDVI",
sat = NULL,
blue = NULL,
green = NULL,
red = NULL,
nir = NULL,
swir1 = NULL,
swir2 = NULL,
swir3 = NULL,
coefs = list(
L = 0.5, G = 2.5, L_evi = 1, C1 = 6,
C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL
),
filename = "",
par = FALSE,
threads = 2,
m = 2,
progress = TRUE,
...) {
# Check that there is a unique filename for each element of the list
if (length(filename) < length(x)) {
if (filename != "") {
warning("Number of filenames and processed objects don't match. Datasets with missing filename will be stored in memory or written to a temporary file")
}
# Append missing filenames
toAdd <- length(x) - length(filename)
filename = c(filename, rep("", toAdd))
}
# Check if filenames are unique (other than "")
filename_non_empty <- filename[filename != ""]
if (length(unique(filename_non_empty)) != length(filename_non_empty)) {
stop("filename must have unique values (other than \"\") for each element of the list x")
}
args <- c(as.list(environment()), list(...))
args <- args[ ! names(args) %in% c("x", "filename")]
mapply(calcIndices, x, filename, MoreArgs = args)
}
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