swh:1:snp:90d88b6f05096f57dd0a8e566e80f41cbfef6824
Tip revision: 12173496c6b934b4bc9d81609e19178b9675310f authored by Martin Schlather on 25 July 2014, 00:00:00 UTC
version 3.0.30
version 3.0.30
Tip revision: 1217349
RandomFields.Rd
\name{RandomFields-package}
\alias{RandomFields-package}
\alias{RandomFields}
\docType{package}
\title{Simulation and Analysis of Random Fields}
\description{
The package \code{RandomFields} offers various tools for
\enumerate{
\item{\bold{simulation}} of different kinds
of random fields, including
\itemize{
\item multivariate, spatial, spatio-temporal Gaussian random fields,
\item Poisson fields, binary fields, Chi2 fields and
\item max-stable fields.
}
It can also deal with non-stationarity and anisotropy of these
processes and conditional simulation (for Gaussian random fields,
currently).
\item{\bold{model estimation (ML) and inference (tests)
for regionalizd variables}} and data analysis,
\item{\bold{model estimation for (geostatistical) linear (mixed) models}}
}
}
\details{
The following features are provided by the package:
\enumerate{
\item \bold{Simulation}
\itemize{
\item \command{\link{RFsimulate}}: Simulation
of random fields,
including conditional simulation. For a list of all covariance
functions and variogram models see \command{\link{RMmodel}}.
Use \command{\link{plot}} for visualisation of the result.
\item \bold{ Estimation} of parameters
\itemize{
\item \command{\link{RFfit}} : general function for estimating
parameters;
\item \command{\link{RFhurst}} : estimation of the Hurst parameter
\item \command{\link{RFfractaldim}} : estimation of the fractal
dimension
\item \command{\link{RFempiricalvariogram}} : calculates
the empirical variogram
}
}
\item \bold{Prediction (for Gaussian random fields)}
\itemize{
\item \command{\link{RFinterpolate}} : kriging, including imputing
}
\item \bold{Inference (for Gaussian random fields)}
\itemize{
\item \command{\link{RFcrossvalidate}} : cross validation
\item \command{\link{RFratiotest}} : likelihood ratio test
\item \command{\link[=AIC.RF_fit]{AIC}},
\command{\link[=AICc.RF_fit]{AICc}},
\command{\link[=BIC.RF_fit]{BIC}}, \command{\link[=anova.RF_fit]{anova}},
\command{\link[=logLik.RFfit]{logLik}}
}
\item \bold{Models}
\itemize{
\item For a list of covariance and variogram models --e.g. for
\bold{geostatistical} purposes-- see \command{\link{RMmodel}}. More
sophisticated models
and covariance function operators are included.
\item To apply the offered package procedures to \bold{mixed models}
-- e.g. appearing in genetical data analysis-- see
\command{\link{RFformula}}.
\item models are evaluated by \command{\link{RFcov}},
\command{\link{RFvariogram}} and \command{\link{RFcovmatrix}}.
For a quick impression use \code{\link{plot}()model}.
}
\item \bold{Data and example studies}:
Some data sets and published code are provided to illustrate the
syntax and structure of the package functions.
\itemize{
\item \code{\link{soil}} : soil physical data
\item \code{\link{weather}} : UWME weather data
\item \code{\link{papers}} : code used in the papers published by
the author(s)
}
\item \bold{Graphics}
\itemize{
\item Fitting a covariance function manually
\command{\link{RFgui}}
\item the generic function \command{\link[graphics]{plot}}
}
\item \bold{S3 and S4 objects}
\itemize{
\item The functions return S4 objects
if \code{\link[=RFoptions]{spConform=TRUE}}.
This is the default.
If \code{\link[=RFoptions]{spConform=FALSE}},
simple objects as in version 2 are returned.
These simple objects are frequently provided with an S3 class
\item \command{\link[graphics]{plot}},
\command{\link[base]{print}}, \command{\link[base]{summary}},
sometimes also \command{\link[utils]{str}} recognise these S3 and S4
objects.
\item
Further generic functions are available for fitted models,
see \sQuote{Inference} above.
\item \bold{Note} that, in many cases, \command{print} will return
an invisible list. This list contains the main information of the
S4 object in an accessible way and is in many cases the
information obtained from \code{summary}. See examples below.
}
\item \bold{Advanced} users, package programmers
\itemize{
\item may use \sQuote{./configure
--with-tcl-config=/usr/lib/tcl8.5/tclConfig.sh
--with-tk-config=/usr/lib/tk8.5/tkConfig.sh} to configure R
\item might decide on a large variety of arguments of the
simulation and estimation procedures using the function
\command{\link{RFoptions}}
}
}
A list of changings from Version 2 to Version 3 can be found
in \link{MajorRevisions}.
}
% In the beta version, the following functionalities are currently
% not available:
% \itemize{
% \item \command{\link{ShowModels}}
% \item numerical evaluation of the covariance function in tbm2
% \item Harvard Rue's Markov fields
% }
\seealso{
See also \link{RC}, \link{RF}, \link{RM}, \link{RP}, \link{RR}
}
\note{
The following packages enable further
features in RandomFields:
\pkg{optimx}, \pkg{soma}, \pkg{GenSA}, \pkg{minqa}, \pkg{pso},
\pkg{DEoptim}, \pkg{nloptr}, \pkg{RColorBrewer}, \pkg{colorspace}
}
\section{Update}{
Current updates are available through \url{http://ms.math.uni-mannheim.de/de/publications/software}.
}
\author{Martin Schlather, \email{schlather@math.uni-mannheim.de}
\url{http://ms.math.uni-mannheim.de/de/publications/software}
}
\references{
\itemize{
\item
Singleton, R.C. (1979). In \emph{Programs for Digital Signal Processing}
Ed.: Digital Signal Processing Committee and IEEE Acoustics,
Speech, and Signal Processing Committe (1979)
IEEE press.
\item
Schlather, M., Malinowski, A., Menck, P.J., Oesting, M. and
Strokorb, K. (2013)
\R package \pkg{RandomFields}: Analysis and simulation of
multivariate random fields and more. \emph{Submitted to JSS}
}
}
\section{Contributions}{
\itemize{
\item Contributions to version 3.0 and following:\cr
Felix Ballani (TU Bergakademie Freiberg; Poisson Polygons, 2014) \cr
Daphne Boecker (Univ. Goettingen; RFgui, 2011)\cr
Katharina Burmeister (Univ. Goettingen; testing, 2012)\cr
Sebastian Engelke (Univ. Goettingen; RFempiricalvariogram, 2011-12)\cr
Sebastian Gross (Univ. Goettingen; tilde formulae, 2011)\cr
Alexander Malinowski (Univ. Mannheim; S3, S4 classes 2011-13)\cr
Juliane Manitz (Univ. Goettingen; testing, 2012)\cr
Johannes Martini (Univ. Goettingen; RFempiricalvariogram,
2011-12)\cr
Ulrike Ober (Univ. Goettingen; help pages, testing, 2011-12)\cr
Marco Oesting (Univ. Mannheim; Brown-Resnick processes, Kriging, Trend,
2011-13)\cr
Kirstin Strokorb (Univ. Mannheim; help pages, 2011-13)\cr
\item Contributions to version 2.0 and following:\cr
Peter Menck (Univ. Goettingen; multivariate circulant embedding)\cr
R Core Team, Richard Singleton (fft.c and advice)
\item Contributions to version 1 and following:\cr
Ben Pfaff, 12167 Airport Rd, DeWitt MI 48820, USA making available
an algorithm for AVL trees (avltr*)
}
}
\section{Thanks}{
Paulo Ribeiro : many comments on Version 3.0.27 and code delivered by
means of \pkg{geoR}\cr
Patrick Brown : comments on Version 3\cr
Paulo Riberio : comments on Version 1\cr
Martin Maechler : advice for Version 1
}
\section{Financial support}{
\itemize{
\item
V3.0 has been financially supported by the German Science Foundation
(DFG) through the Research Training Group 1953 \sQuote{Statistical
Modeling of Complex Systems and Processes --- Advanced Nonparametric
Approaches} (2013-2018).
\item
V3.0 has been financially supported by Volkswagen Stiftung within
the project \sQuote{WEX-MOP} (2011-2014).
\item
Alpha versions for V3.0 have been
financially supported by the German Science Foundation (DFG) through the
Research Training Groups 1644 \sQuote{Scaling problems in Statistics}
and 1023 \sQuote{Identification in Mathematical Models} (2008-13).
\item
V1.0 has been financially supported by
the German Federal Ministry of Research and Technology
(BMFT) grant PT BEO 51-0339476C during 2000-03.
\item
V1.0 has been financially supported by the EU TMR network
ERB-FMRX-CT96-0095 on
``Computational and statistical methods for the analysis of spatial
data'' in 1999.
}
}
\examples{
RFoptions(seed=0) ## *ANY* simulation will have the random seed 0; set
## RFoptions(seed=NA) to make them all random again
# Compare:
model <- RMexp(scale=2) + RMnugget(var=3)
str(model) ## S4 object
model <- summary(RMexp(scale=2) + RMnugget(var=3))
str(model) ## list style as in version 2 of RandomFields
\dontshow{FinalizeExample()}
}
\keyword{spatial}