%% Document started, Sat Jul  3 19:30:52 CEST 2004, my 37th birthday,
%% while being stuck for 24 hours at Philadelphia airport, on my way 
%% back from the joint TIES/Accuracy 2004 symposium in Portland, ME.
%% Continued, Oct 28, during the Apmosphere mid-term review. Oh, shame.

% \VignetteIndexEntry{ Spatio-temporal geostatistics using gstat }

\documentclass[a4paper]{article}
\usepackage[colorlinks=true,urlcolor=blue]{hyperref}

\newcommand{\code}[1]{{\tt #1}}

\SweaveOpts{echo=TRUE}

\title{Spatio-temporal geostatistics using {\tt gstat}}

\author{ \includegraphics[width=.4\columnwidth]{ifgi-logo_int}\\
\href{mailto:edzer.pebesma@uni-muenster.de}{Edzer Pebesma},
\href{mailto:ben.graeler@uni-muenster.de}{Benedikt Gr\"{a}ler}
}
\date{\small \today }

\begin{document}
\setkeys{Gin}{width=0.9\textwidth}

\maketitle

\section{Introduction}

Since \code{gstat} package version 1.0-0, a dependency of gstat on
the R package \code{spacetime} was introduced, allowing the code in
\code{gstat} to exploit spatio-temporal data structures from that
package. This vignette describes the possibilities and limitations
of the package for spatio-temporal geostatistics.

To understand some of the possibilities and limitations, some
knowledge of the history of the software is needed. The original
\code{gstat} software (Pebesma and Wesseling, 1998) was a standalone
computer {\em program} written in around 25,000 lines of C code, and
would do geostatistical modelling, prediction and simulation. The
\code{gstat} R package (Pebesma, 2004) consisted mostly of an R
interface to this C code, together with convenience functions to
use R's modelling interface (formula's, see \code{?lm}) and graphic
capabilities (trellis graphics in package \code{lattice} to show
cross variogram as matrix plots; interaction with variogram clouds
using base plots).

Starting 2003, a group of programmers developed a set of classes
and methods for dealing with spatial data in R (points, lines,
polygons, grids), which was supported by the publications
of the well-known ASDAR book (Bivand et al. 2008; see also
\url{http://www.asdar-book.org/}) and helped convergence in the user
community, with in 2011 over 2000 subscribers on the {\tt r-sig-geo}
mailing list.  Package \code{gstat} was one of the first packages
that adopted and benefited from these classes.

To realize a particular idea, writing code in C typically takes
about 10-20 times as long as writing it in R. C code can be more
efficient, gives more control over memory usage, but is also more
error prone--mistakes in C code make an R session crash, something
that is hard to do when writing R code.

The original C code of \code{gstat} (Pebesma and Wesseling, 1998)
provides all kriging varieties (universal, ordinary, simple;
univariable, or multivariable as in cokriging) for two- or
three-dimensional data. When the spatial domain is constrained to
two dimensions (and this might cover over 99\% of the use cases!),
the third dimension might be used to represent time. As such, the
{\em metric} variogram model, which allows for geometric anisotropy
definition in three dimensions, can be used for spatio-temporal
kriging. When defining the three-dimensional variogram as the
sum of 2 or more nested variogram (summed) models, one can choose
anisotropy coefficients for a single model such that this model is
{\em effectively} zero in some directions, e.g. in space {\em or}
in time; this allows one to approximate the so-called space-time sum
model. It should be noted that at the C code there is no knowledge
whether a third dimension represents space, or time. As such,
particular characteristics of time cannot be taken care of.

Since the second half of 2010, the development of an R package
\code{spacetime} started. It provides methods and classes for
spatio-temporal data, and builds on the spatial data classes in
\code{sp} and time series classes in \code{xts}. This document will
explain how data in this form, and methods provided by this package,
can be used for spatio-temporal geostatistics.

We will work with a data set with air quality (PM10) measurements over
germany, taken from rural background stations available in the data
sets provided by the European Environmental Agency.
<<>>=
library(spacetime)
rm(list = ls())
data(air)
ls()
@

\section{Variography}

\subsection{Temporal autocorrelation and cross correlation}

We will look into a subset of the data, ranging from 2005 to 2010, and
remove stations that have only missing values in this period:
<<>>=
if (!exists("rural"))
	rural = STFDF(stations, dates, data.frame(PM10 = as.vector(air)))
rr = rural[,"2005::2010"]
unsel = which(apply(as(rr, "xts"), 2, function(x) all(is.na(x))))
r5to10 = rr[-unsel,]
summary(r5to10)
@
Next, we will (rather arbitrarily) select four stations, which have the
following labels:
<<>>=
rn = row.names(r5to10@sp)[4:7]
rn
@

In the following, autocorrelation functions are computed and plotted.
The resulting plot is shown in Figure~\ref{fig:acf}.
<<fig=FALSE,eval=FALSE>>=cf(na.omit(as(r5to10[rn,], "xts")))
par(mfrow=c(2,2))
# select 4, 5, 6, 7
for(i in rn) 
	acf(na.omit(r5to10[i,]), main = i)
par(mfrow=c(1,1))
@

\begin{figure}[hbt]
\begin{center}
<<fig=TRUE>>=
par(mfrow=c(2,2))
# select 4, 5, 6, 7
rn = row.names(r5to10@sp)[4:7]
for(i in rn) 
	acf(na.omit(r5to10[i,]), main = i)
@
\end{center}
\caption{Autocorrelations for PM10; time lag unit in days.}
\label{fig:acf}
\end{figure}

Auto- and cross correlations can be computed when a multivariate time
series object is passed to {\tt acf}: 
<<fig=FALSE,echo=TRUE,eval=FALSE>>=
acf(na.omit(as(r5to10[rn,], "xts")))
@
The resulting plot is shown in Figure~\ref{fig:ccf}.
\begin{figure}[hbt]
\begin{center}
<<fig=TRUE,echo=FALSE>>=
acf(na.omit(as(r5to10[rn,], "xts")))
@
\end{center}
\caption{autocorrelations (diagonal) and cross correlations (off-diagonal) for
the four stations selected; time lag unit in days. }
\label{fig:ccf}
\end{figure}
From these graphs one should be able to observe the following
\begin{itemize}
\item autocorrelations for lag 0 are always 1
\item cross correlations for lag 0 are not always 1
\item cross correlations can be asymmetric, meaning that when
$\rho_{AB}(h)$ is the correlation between $Z(s_A,t)$ and $Z(s_B,t+h)$,
$$\rho_{AB}(h) = \rho_{BA}(-h) \ne \rho_{AB}(-h)$$
with $s_A$ and $s_B$ the two stations between which a cross correlation
is computed, and $h$ the (directional!) lag between the series.
\end{itemize}
The plot further more shows that for these four stations the
asymmetry is not very strong, but that cross correlations are fairly
strong and of a similar form of autocorrelations.

This kind of plot does not work very well in layouts of e.g. 10 x 10
sub-plots; {\tt acf} automatically chooses 4 x 4 as the maximum a
single plot. To try this out, do a 7 x 7 plot
<<eval=FALSE>>=
acf(na.omit(as(r5to10[4:10,], "xts")))
@
and note that here we see in the last figure (DESH \& DESN04) a pair
of plots with nearly no cross correlation. This might have to do with
the spatial distance between these two stations:
<<>>=
library(sp)
print(spDists(r5to10[4:10,]@sp), digits=3)
@
(What is the spatial distance between stations DESH and DESN04?)

\subsection{Spatial correlation, variograms}

In the next steps, we will sample 100 time instances randomly,
<<>>=
rs = sample(dim(r5to10)[2], 100)
@
we select these instances as a {\tt SpatialPointsDataFrame} and add a
time index to them. After this we bind them together in a single
{\tt SpatialPointsDataFrame} which has a time index {\tt ti}:
<<>>=
lst = lapply(rs, function(i) { x = r5to10[,i]; x$ti = i; x} )
pts = do.call(rbind, lst)
@
Then, we can compute the pooled variogram
<<>>=
library(gstat)
v = variogram(PM10~ti, pts[!is.na(pts$PM10),], dX=0)
@
and plot it (Figure~\ref{fig:vgm}):
<<eval=FALSE>>=
# plot(v, fit.variogram(v, vgm(1, "Exp", 200, 1)))
vmod = fit.variogram(v, vgm(1, "Exp", 200, 1))
plot(v, vmod)
@
\begin{figure}[hbt]
\begin{center}
<<fig=TRUE,echo=FALSE>>=
# plot(v, fit.variogram(v, vgm(1, "Exp", 200, 1)))
vmod = fit.variogram(v, vgm(1, "Exp", 200, 1))
print(plot(v, vmod))
@
\end{center}
\caption{sample spatial variogram, averaged over 100 randomly
chosen time steps}
\label{fig:vgm}
\end{figure}
The fitted model is this:
<<>>=
vmod
@
One should note that the fit is rather poor, and not forget that
we only have 53 stations selected. The time resolution is rich
(1862 days) but the number of stations is small:
<<>>=
dim(r5to10)
@

We can fit a spatio-temporal variogram the usual way, by passing an
object of class {\tt STFDF} (Pebesma, 2012):
<<eval=FALSE>>=
vv = variogram(PM10~1, r5to10, width=20, cutoff = 200, tlags=0:5)
@
Alternatively, if 
this takes too long, a temporal subset can be taken, e.g.
using the first 200 days:
<<eval=FALSE>>=
vv = variogram(PM10~1, r5to10, width=20, cutoff = 200, tlags=0:5)
@
taking random days from the full period will lead to the a wrong
assumption that every time index increment reflect a constant
lag increase. As an alternative, we will here load the precomputed 
S/T variogram:
<<>>=
data(vv)
@
% remove the model column to keep text and figures in line.
<<echo=FALSE>>=
vv <- vv[c("np", "dist", "gamma", "id", "timelag", "spacelag")]
@
Plotting this object can be done in several ways, two 2D-plots are 
shown in Figure~\ref{fig:map} and a 3D wireplot is shown in 
Figure~\ref{fig:wire}:
<<eval=FALSE>>=
plot(vv)
plot(vv, map = FALSE)
@
\begin{figure}[hbt]
\begin{center}
<<fig=TRUE,echo=FALSE>>=
print(plot(vv), split = c(1,1,1,2), more = TRUE)
print(plot(vv, map = FALSE), split = c(1,2,1,2))
@
\end{center}
\caption{Spatio-temporal sample variogram map (top) and sample 
variograms for each time lag (bottom); both figures depict the 
information of object {\tt vv}.}
\label{fig:map}
\end{figure}

\subsection{Fitting a spatio-temporal variogram model}

At first, we try to fit a metric model with spatio-temporal anisotropy:
<<>>==
metricVgm <- vgmST("metric",
                   joint=vgm(50,"Exp",100,0),
                   stAni=50)

metricVgm <- fit.StVariogram(vv, metricVgm)
@
As numerical criterion to judge the goodness of fit of model and 
sample variogram, the root-mean-squared-difference between the 
surfaces can be obtained by:
<<>>=
attr(metricVgm, "optim")$value
@

The final model can be plotted with the sample variogram (Figure~\ref{fig:mm}):

<<eval=FALSE>>=
plot(vv, metricVgm)
@

\begin{figure}[hbt]
\begin{center}
<<fig=TRUE,echo=FALSE,width=8, height=4>>=
print(plot(vv, metricVgm))
@
\end{center}
\caption{Sample variogram map (left) and fitted metric model (right).}
\label{fig:mm}
\end{figure}

\pagebreak 

Now, let us try to fit and plot a separable model (Figure~\ref{fig:sm}):
<<>>==
sepVgm <- vgmST("separable",
                space=vgm(0.9,"Exp", 123, 0.1),
                time =vgm(0.9,"Exp", 2.9, 0.1),
                sill=100)

sepVgm <- fit.StVariogram(vv, sepVgm, method = "L-BFGS-B",
                          lower = c(10,0,0.01,0,1),
                          upper = c(500,1,20,1,200))
@

To compare this model with the previous one, we look at the optimized 
root-mean-squared-differences between the two surfaces and plot sample
and both models:
<<>>=
attr(sepVgm, "optim")$value
plot(vv, list(sepVgm, metricVgm))
@

\begin{figure}[hbt]
\begin{center}
<<fig=TRUE,echo=FALSE,width=8,height=4>>=
print(plot(vv, list(sepVgm, metricVgm)))
@
\end{center}
\caption{Sample variogram map (left), fitted separable model (middle)
and fittted metric model (right).}
\label{fig:sm}
\end{figure}
A wireframe (3D) plot of sample variogram and fitted variogram models can be obtained e.g. by
<<eval=FALSE>>=
library(lattice)
plot(vv, list(sepVgm, metricVgm), all=T, wireframe=T, zlim=c(0,120),
     zlab=NULL,
     xlab=list("distance (km)", rot=30),
     ylab=list("time lag (days)", rot=-35),
     scales=list(arrows=F, z = list(distance = 5)))
@
which is shown in Figure~\ref{fig:wire}. Further spatio-temporal model
definitions can be found in the help pages of {\tt fit.StVariogram} 
and {\tt variogramSurface}. The demo {\tt stkrige} presents further 
examples and illustrates an interactive 3D-plot of sample variogram 
and the fitted variogram model. An interactive variogram exploration
web-tool is avaialble at 
\url{http://giv-graeler.uni-muenster.de:3838/spacetime/}.
\begin{figure}[hbt]
\begin{center}
<<fig=TRUE,echo=FALSE,width=8,height=8>>=
library(lattice)
print(plot(vv, list(sepVgm, metricVgm), all=T, wireframe=T, zlim=c(0,120),
           zlab=NULL,
           xlab=list("distance (km)", rot=30),
           ylab=list("time lag (days)", rot=-35),
           scales=list(arrows=F, z = list(distance = 5))))
@
\end{center}
\caption{Wireframe plots of sample and fitted space-time variograms.}
\label{fig:wire}
\end{figure}

\clearpage 

\section{Spatio-temporal prediction}

The vignette in package \code{spacetime} gives an example of using
the gstat function \code{krigeST} for spatio-temporal kriging of
the Irish wind data. The \code{krigeST} function uses global kriging,
but only needs to invert the purely spatial and purely time covariance
matrices in the separable case.

For more generic spatio-temporal kriging where space is
two-dimensional, one could use \code{krige}, defining the
observations and prediction locations as three-dimensional data sets,
see for an example
<<eval=FALSE>>=
demo(gstat3D)
@
It needs to be pointed out that in that case, the time (typically
the third dimension) needs to be numeric, and three-dimensional
anisotropy needs to be defined properly (see \code{?vgm}).

In case the data set is too large for global kriging, one could
try to use local kriging, and select data within some distance, or
by specifying \code{nmax} (the nearest $n$ observations).  In both
cases, it is advisable to transform time such that one can use an
{\em isotropic} variogram model in the three dimensions, as only
in that case the nearest $n$ observations correspond to the $n$
most correlated observations. \code{krigeST} provides a solution 
where a \code{bufferNmax}-times larger neighbourhood is evaluated 
within the covariance model and the strongest correlated \code{nmax}
neighbours are selected.

An additional consideration is that in space-time, observations may
not be regularly spaced. In some cases, the nearest $n$ observations
may come from a single measurement location, which may lead to sharp
jumps/boundaries in the interpolated values. This might be solved
by using larger neighbourhoods, or by setting the \code{omax}
in \code{krige} or \code{gstat} calls to the neighbourhood size
to select {\em per octant} (this should be combined with specifying
\code{maxdist}).

%\section{Spatio-temporal simulation}

\section*{References}
\begin{itemize}
\item Bivand, R., E. Pebesma and V. Gomez-Rubio, 2008. Applied
Spatial Data Analysis with R. Springer.

\item Cressie, N.A.C., 1993. Statistics for Spatial Data. Wiley.

\item Cressie, N. and C. Wikle, 2011. Statistics for Spatio-temporal
Data. Wiley.

\item Pebesma, E., 2012. spacetime: Spatio-Temporal Data
in R. Journal of Statistical Software, volume 51, issue 7;
\href{http://www.jstatsoft.org/v51/i07/}{1-30}.

\item Pebesma, E.J., Wesseling, C.G., 1998. Gstat, a program for
geostatistical modelling, prediction and simulation. Computers \&
Geosciences, 24 (1), pp. 17--31.

\item Pebesma, E.J., 2004.  Multivariable geostatistics
in S: the gstat package.  Computers \& Geosciences
\href{http://www.sciencedirect.com/science/journal/00983004}{30:
683-691}

\item Ver Hoef, J.M., Cressie, N.A.C, 1993. Multivariable Spatial
Prediction.  Mathematical Geology, 25 (2), pp. 219--240.
\end{itemize}

\end{document}
