% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/whittaker.R
\name{whittaker.raster}
\alias{whittaker.raster}
\title{Filter Vegetation Index with Modified Whittaker Approach}
\usage{
whittaker.raster(vi, w = NULL, t = NULL, timeInfo = orgTime(vi),
  lambda = 5000, nIter = 3, outputAs = "single", collapse = FALSE,
  prefixSuffix = c("MCD", "ndvi"), outDirPath = ".",
  outlierThreshold = NULL, mergeDoyFun = "max", ...)
}
\arguments{
\item{vi}{\code{Raster*} or \code{character} filenames, sorted VI. Use 
\code{\link{preStack}} functionality to ensure the right input.}

\item{w}{\code{Raster*} or \code{character} filenames. In case of MODIS 
composite, the sorted 'VI_Quality' layers.}

\item{t}{\code{Raster*} or \code{character} filenames. In case of MODIS 
composite, the sorted 'composite_day_of_the_year' layers. If missing, the 
date is determined using \code{timeInfo}.}

\item{timeInfo}{Output from \code{\link{orgTime}}.}

\item{lambda}{\code{character} or \code{integer}. Yearly lambda value passed 
to \code{\link{whit2}}. If set as \code{character} (i.e., 
\code{lambda = "600"}), it is not adapted to the time serie length, but used 
as a fixed value (see Details). High values = stiff/rigid spline.}

\item{nIter}{\code{integer}. Number of iteration for the upper envelope 
fitting.}

\item{outputAs}{\code{character}, organisation of output files. 
\code{"single"} (default) means each date one \code{RasterLayer}; 
\code{"yearly"} a \code{RasterBrick} for each year, and \code{"one"} one 
\code{RasterBrick} for the entire time series.}

\item{collapse}{\code{logical}. Collapse input data of multiple years into 
one single year before filtering.}

\item{prefixSuffix}{\code{character}, file naming. Names are composed 
dot-separated: \code{paste0(prefixSuffix[1], "YYYDDD", lambda, 
refixSuffix[2], ".defaultFileExtension")}.}

\item{outDirPath}{\code{character}, output path. Defaults to the current 
working directory.}

\item{outlierThreshold}{\code{numeric} in the same unit as \code{vi}, used 
for outlier removal (see Details).}

\item{mergeDoyFun}{Especially when using \code{collapse = TRUE}, multiple 
measurements for one day can be present. Here you can choose how those values 
are merged to one single value: \code{"max"} uses the highest value, 
\code{"mean"} or \code{"weighted.mean"} use the \code{\link{mean}} if no 
weighting \code{"w"} is available, and \code{\link{weighted.mean}} if it is.}

\item{...}{Arguments passed to \code{\link{writeRaster}} (except for 
\code{filename}).}
}
\value{
A Whittaker-smoothened \code{RasterStack}.
}
\description{
Use a modified Whittaker filter function (see References) from package 
\strong{ptw} to filter a vegetation index (VI) time serie of satellite data.
}
\details{
The argument \code{lambda} is passed to \code{MODIS:::miwhitatzb1}. You can 
set it as yearly \code{lambda}, which means that it doesn't matter how long 
the input time serie is because \code{lambda} is adapted to it with: 
\code{lambda*('length of input timeserie in days'/365)}. The input length can 
differ from the output because of the \code{pillow} argument in 
\code{orgTime}. But it can also be set as \code{character} (i.e., 
\code{lambda = "1000"}). In this case, the adaption to the time series length 
is not performed.\cr
}
\note{
Currently tested on MODIS and Landsat data. Using M*D13, it is also possible 
to use the 'composite_day_of_the_year' and the 'VI_Quality' layers. Note that 
this function is currently under heavy development.
}
\examples{
\dontrun{
# The following function will download bit more than 1 year of MOD13A1 (~180mB) and therefore
# take while to execute! Data will be downloaded to options("MODIS_localArcPath") and processed 
# to 'paste0(options("MODIS_outDirPath"),"fullCapa")'
# You need to extract: 'vegetation index', 'VI_Quality layer', and 'composite day of the year',
# this is expressed by the argument 'SDSstring'
runGdal(product="MOD13A2",begin="2004340",extent="irland",end="2006020", job="fullCapa",
SDSstring="101000000010")
path <- paste0(options("MODIS_outDirPath"),"fullCapa")

# the only obligatory dataset is the vegetatino index 
# get the 'vi' data in the source directory: 
vi <- preStack(path=path, pattern="*_NDVI.tif$")

# "orgTime" detects timing information of the input data and generates based on the arguments
# the output date information. 
# For spline functions (in general) the beginning and the end of the time series
# is always problematic. So there is the argument "pillow" (default 75 days) that adds
# (if available) some more layers on the two endings.
timeInfo <- orgTime(vi,nDays=16,begin="2005001",end="2005365",pillow=40)

# now re-run "preStack" with two differences, 'files' (output of the first 'preStack' call)
# and the 'timeInfo'
# Here only the data needed for the filtering is extracted:
vi <- preStack(files=vi,timeInfo=timeInfo)

whittaker.raster(vi,timeInfo=timeInfo,lambda=5000)

# if the files are M*D13 you can use also Quality layers and the composite day of the year:
wt <- preStack(path=path, pattern="*_VI_Quality.tif$", timeInfo=timeInfo)
# can also be already stacked:
inT <- preStack(path=path, pattern="*_composite_day_of_the_year.tif$", timeInfo=timeInfo)

whittaker.raster(vi=vi, wt=wt, inT=inT, timeInfo=timeInfo, lambda=5000, overwrite=TRUE)
}

}
\references{
Modified Whittaker smoother, according to Atzberger & Eilers 2011 
International Journal of Digital Earth 4(5):365-386.\cr
Implementation in R: Agustin Lobo 2012
}
\seealso{
\code{\link{smooth.spline.raster}}, \code{\link{raster}}.
}
\author{
Matteo Mattiuzzi and Agustin Lobo
}