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%#
%# fields is a package for analysis of spatial data written for
%# the R software environment.
%# Copyright (C) 2024 Colorado School of Mines
%# 1500 Illinois St., Golden, CO 80401
%# Contact: Douglas Nychka, douglasnychka@gmail.edu,
%#
%# This program is free software; you can redistribute it and/or modify
%# it under the terms of the GNU General Public License as published by
%# the Free Software Foundation; either version 2 of the License, or
%# (at your option) any later version.
%# This program is distributed in the hope that it will be useful,
%# but WITHOUT ANY WARRANTY; without even the implied warranty of
%# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
%# GNU General Public License for more details.
%#
%# You should have received a copy of the GNU General Public License
%# along with the R software environment if not, write to the Free Software
%# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
%# or see http://www.r-project.org/Licenses/GPL-2
%##END HEADER
%##END HEADER
\name{compactToMat}
\alias{compactToMat}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
%% ~~function to do ... ~~
Convert Matrix from Compact Vector to Standard Form
}
\description{
%% ~~ A concise (1-5 lines) description of what the function does. ~~
\code{compactToMat} transforms a matrix from compact, vector form to
a standard matrix. Only symmetric matrices can be stored in this
form, since a compact matrix is stored as a vector with elements
representing the upper triangle of the matrix. This function assumes
the vector does not contain diagonal elements of the matrix.
An example of a matrix stored in compact form is any matrix
generated from the \code{rdist} function with \code{compact=TRUE}.
}
\usage{
compactToMat(compactMat, diagVal=0, lower.tri=FALSE, upper.tri=TRUE)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{compactMat}{
%% ~~Describe \code{compactMat} here~~
A symmetric matrix stored as a vector containing elements for the lower-triangular
portion of the true matrix (and none of the diagonal elements), as returned by
\code{rdist} with \code{compact=TRUE}.
}
\item{diagVal}{
%% ~~Describe \code{diagVal} here~~
A number to put in the diagonal entries of the output matrix.
}
\item{lower.tri}{
%% ~~Describe \code{diagVal} here~~
Whether or not to fill in the upper triangle of the output matrix
}
\item{upper.tri}{
%% ~~Describe \code{diagVal} here~~
Whether or not to fill in the lower triangle of the output matrix
}
}
\value{
%% ~Describe the value returned
%% If it is a LIST, use
%% \item{comp1 }{Description of 'comp1'}
%% \item{comp2 }{Description of 'comp2'}
%% ...
The standard form matrix represented by the input compact matrix
}
\author{
%% ~~who you are~~
John Paige
}
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
%% ~~objects to See Also as \code{\link{help}}, ~~~
\code{\link{rdist}}, \code{link{dist}}
}
\examples{
################
#Calculate distance matrix from compact form:
################
#make a distance matrix
distOut = rdist(1:5, compact=TRUE)
print(distOut)
#note that distOut is in compact form:
print(c(distOut))
#convert to standard matrix form:
distMat = compactToMat(distOut)
################
#fast computation of covariance matrix:
################
#generate 5 random points on [0,1]x[0,1] square
x = matrix(runif(10), nrow=5)
#get compact distance matrix
distOut = rdist(x, compact=TRUE)
#evaluate Exponential covariance with range=1. Note that
#Covariance function is only evaluated over upper triangle
#so time is saved.
diagVal = Exponential(0, range=1)
compactCovMat = Exponential(distOut, range=1)
upperCovMat = compactToMat(compactCovMat, diagVal)
lowerCovMat = compactToMat(compactCovMat, diagVal, lower.tri=TRUE, upper.tri=FALSE)
fullCovMat = compactToMat(compactCovMat, diagVal, lower.tri=TRUE, upper.tri=TRUE)
compactCovMat
lowerCovMat
upperCovMat
fullCovMat
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ compact }
\keyword{ matrix }% __ONLY ONE__ keyword per line
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