% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/smoothSpline.R
\name{smooth.spline.raster}
\alias{smooth.spline.raster}
\title{Filter Time Series Imagery with a Cubic Spline}
\usage{
smooth.spline.raster(x, w = NULL, t = NULL, groupYears = TRUE,
  timeInfo = orgTime(x), df = 6, outDirPath = "./", ...)
}
\arguments{
\item{x}{\code{RasterBrick} (or \code{RasterStack}) or \code{character} vector 
of filenames, sorted 'Vegetation index'.}

\item{w}{\code{RasterBrick} (or \code{RasterStack}) with weighting 
information, e.g. derived from \code{\link{makeWeights}}.}

\item{t}{In case of MODIS composite, the corresponding 
'composite_day_of_the_year' \code{RasterBrick} (or \code{RasterStack}).}

\item{groupYears}{\code{logical}. If \code{TRUE}, output files are grouped by 
years.}

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

\item{df}{\code{numeric}, yearly degree of freedom value passed to 
\code{\link{smooth.spline}}. If set as \code{character} (i.e., \code{df = "6"}), 
it is not adapted to the time serie length but used as a fixed value (see 
Details).}

\item{outDirPath}{Output path, defaults to the current working directory.}

\item{...}{Arguments passed to \code{\link{writeRaster}}. Note that 
\code{filename} is created automatically.}
}
\value{
The filtered data and a text file with the dates of the output layers.
}
\description{
This function uses the \code{\link{smooth.spline}} function to filter a 
vegetation index time serie of satellite data.
}
\details{
\code{numeric} values of \code{df} (e.g., \code{df = 6)} are treated as 
yearly degrees of freedom. Here, the length of the input time series is not 
relevant since \code{df} is adapted to it with: 
\code{df*('length of _input_ timeserie in days'/365)}. The input length can 
differ from the output because of the \code{pillow} argument in 
\code{orgTime}. 

\code{character} values of \code{df} (e.g., \code{df = "6"}), on the other 
hand, are not adopted to the length of the input time series.

Currently tested on MODIS and Landsat data. Using M*D13 data, it is also 
possible to use the 'composite_day_of_the_year' layer and the 'VI_Quality' 
layer. This function is currently under heavy development and a lot of 
changes are expected to come soon.
}
\examples{
\dontrun{
# The full capacity of the following functions is currently avaliable only with M*D13 data.
# !! The function is very new, double check the result!!

# You need to extract the: 'vegetation index', 'VI_Quality layer', 
# and 'composite day of the year' layer.
# runGdal(product="MOD13A2",begin="2004340",extent="sicily",end="2006070",
# job="fullCapa",SDSstring="101000000010")
# Afterward extract it to: 
options("MODIS_outDirPath")

# the only obligatory dataset is "x" (vegetatino index), get the 'vi' data on the source directory: 
path <- paste0(options("MODIS_outDirPath"),"/fullCapa")
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 diferences, 'files' (output of the first 'preStack' call)
# and the 'timeInfo'.
# Here only the data needed for the filtering is extractet:
vi <- preStack(files=vi,timeInfo=timeInfo)

smooth.spline.raster(x=vi,timeInfo=timeInfo)

# Filter with weighting and time information:
# if the files are M*D13 you can use also Quality layers and the composite day of the year:
w <- stack(preStack(path=path, pattern="*_VI_Quality.tif$", timeInfo=timeInfo))
w <- makeWeights(w,bitShift=2,bitMask=15,threshold=6)
# you can also pass only the names
t <- preStack(path=path, pattern="*_composite_day_of_the_year.tif$", timeInfo=timeInfo)

smooth.spline.raster(x=vi,w=w,t=t,timeInfo=timeInfo)
}

}
\seealso{
\code{\link{whittaker.raster}}, \code{\link{raster}}.
}
\author{
Matteo Mattiuzzi
}