[spcopula-commits] r115 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 20 16:27:22 CET 2013
Author: ben_graeler
Date: 2013-11-20 16:27:22 +0100 (Wed, 20 Nov 2013)
New Revision: 115
Removed:
pkg/man/getNeighbours.experimental.Rd
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/BB7copula.R
pkg/R/spatialPreparation.R
Log:
- made getNeighbours.experimental the "default"
- corrected boundaries for r270BB7Copula
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2013-11-20 09:20:38 UTC (rev 114)
+++ pkg/DESCRIPTION 2013-11-20 15:27:22 UTC (rev 115)
@@ -2,12 +2,12 @@
Type: Package
Title: copula driven spatial analysis
Version: 0.1-1
-Date: 2013-11-19
+Date: 2013-11-20
Authors at R: c(person("Benedikt", "Graeler", role = c("aut", "cre"), email =
"ben.graeler at uni-muenster.de"), person("Marius", "Appel",
role = "ctb"))
Maintainer: Benedikt Graeler <ben.graeler at uni-muenster.de>
-Description: This package provides a framework to analyse via copulas spatial and spatio-temporal data provided in the format of the spacetime package. Additionally, support for calculating different multivariate return periods is implemented.
+Description: This package provides a framework to analyse via copulas spatial and spatio-temporal data provided in the format of sp and spacetime package respectively. Additionally, support for calculating different multivariate return periods is implemented.
License: GPL-2
LazyLoad: yes
Depends: copula (>= 0.999-7), R (>= 2.15.0)
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2013-11-20 09:20:38 UTC (rev 114)
+++ pkg/NAMESPACE 2013-11-20 15:27:22 UTC (rev 115)
@@ -30,7 +30,7 @@
# export(setSizeLim)
# spatial
-export(getNeighbours,getNeighbours.experimental, getStNeighbours)
+export(getNeighbours, getStNeighbours)
export(calcBins)
export(calcSpTreeDists, dropSpTree)
Modified: pkg/R/BB7copula.R
===================================================================
--- pkg/R/BB7copula.R 2013-11-20 09:20:38 UTC (rev 114)
+++ pkg/R/BB7copula.R 2013-11-20 15:27:22 UTC (rev 115)
@@ -225,7 +225,7 @@
if (any(is.na(param) | param[1] > -1 | param[2] >= 0 | param <= c(-Inf,-Inf)))
stop(paste("Parameter values out of bounds: theta: (-Inf,-1], delta: (-Inf,0)."))
new("r270BB7Copula", dimension = as.integer(2), parameters = param,
- param.names = c("theta", "delta"), param.lowbnd = c(-Inf, -Inf), param.upbnd = c(-1, -1),
+ param.names = c("theta", "delta"), param.lowbnd = c(-Inf, -Inf), param.upbnd = c(-1, 0),
family=39, fullname = "270 deg rotated BB7 copula family. Number 39 in VineCopula.")
}
Modified: pkg/R/spatialPreparation.R
===================================================================
--- pkg/R/spatialPreparation.R 2013-11-20 09:20:38 UTC (rev 114)
+++ pkg/R/spatialPreparation.R 2013-11-20 15:27:22 UTC (rev 115)
@@ -58,49 +58,49 @@
# returns an neighbourhood object
##################################
-getNeighbours <- function(dataLocs, predLocs, var=names(dataLocs)[1], size=5,
- prediction=FALSE, min.dist=0.01) {
-
- stopifnot((!prediction && missing(predLocs)) || (prediction && !missing(predLocs)))
- stopifnot(min.dist>0 || prediction)
-
- if(missing(predLocs) && !prediction)
- predLocs=dataLocs
-
- stopifnot(is(predLocs,"Spatial"))
-
- if(any(is.na(match(var,names(dataLocs)))))
- stop("At least one of the variables is unkown or is not part of the data.")
+# getNeighbours <- function(dataLocs, predLocs, var=names(dataLocs)[1], size=5,
+# prediction=FALSE, min.dist=0.01) {
+#
+# stopifnot((!prediction && missing(predLocs)) || (prediction && !missing(predLocs)))
+# stopifnot(min.dist>0 || prediction)
+#
+# if(missing(predLocs) && !prediction)
+# predLocs=dataLocs
+#
+# stopifnot(is(predLocs,"Spatial"))
+#
+# if(any(is.na(match(var,names(dataLocs)))))
+# stop("At least one of the variables is unkown or is not part of the data.")
+#
+# nLocs <- length(predLocs)
+# size <- min(size, length(dataLocs)+prediction)
+#
+# allLocs <- matrix(NA,nLocs,size)
+# allDists <- matrix(NA,nLocs,size-1)
+# allData <- matrix(NA,nLocs,size)
+# for (i in 1:nLocs) {
+# tempDists <- spDists(dataLocs, predLocs[i, ])
+# tempDists[tempDists < min.dist] <- Inf
+# spLocs <- order(tempDists)[1:(size - 1)]
+#
+# allLocs[i,] <- c(i, spLocs)
+# allDists[i,] <- tempDists[spLocs]
+# allData[i,(prediction+1):size] <- dataLocs[c(i[!prediction],spLocs),
+# var, drop = F]@data[[1]]
+# }
+#
+# if (!prediction)
+# predLocs <- NULL
+# colnames(allData) <- paste(paste("N", rep(0:(size-1),
+# each=length(var)), sep=""),
+# rep(var,size),sep=".")
+# return(neighbourhood(allData, allDists, allLocs, dataLocs,
+# predLocs, prediction, var))
+# }
+#
- nLocs <- length(predLocs)
- size <- min(size, length(dataLocs)+prediction)
-
- allLocs <- matrix(NA,nLocs,size)
- allDists <- matrix(NA,nLocs,size-1)
- allData <- matrix(NA,nLocs,size)
- for (i in 1:nLocs) {
- tempDists <- spDists(dataLocs, predLocs[i, ])
- tempDists[tempDists < min.dist] <- Inf
- spLocs <- order(tempDists)[1:(size - 1)]
-
- allLocs[i,] <- c(i, spLocs)
- allDists[i,] <- tempDists[spLocs]
- allData[i,(prediction+1):size] <- dataLocs[c(i[!prediction],spLocs),
- var, drop = F]@data[[1]]
- }
-
- if (!prediction)
- predLocs <- NULL
- colnames(allData) <- paste(paste("N", rep(0:(size-1),
- each=length(var)), sep=""),
- rep(var,size),sep=".")
- return(neighbourhood(allData, allDists, allLocs, dataLocs,
- predLocs, prediction, var))
-}
-
-
-getNeighbours.experimental = function (dataLocs, predLocs, var = names(dataLocs)[1], size = 5,
+getNeighbours <- function (dataLocs, predLocs, var = names(dataLocs)[1], size = 5,
prediction = FALSE, min.dist = 0.01)
{
stopifnot((!prediction && missing(predLocs)) || (prediction &&
@@ -142,16 +142,6 @@
predLocs, prediction, var))
}
-
-
-
-
-
-
-
-
-
-
#############
## BINNING ##
#############
Deleted: pkg/man/getNeighbours.experimental.Rd
===================================================================
--- pkg/man/getNeighbours.experimental.Rd 2013-11-20 09:20:38 UTC (rev 114)
+++ pkg/man/getNeighbours.experimental.Rd 2013-11-20 15:27:22 UTC (rev 115)
@@ -1,49 +0,0 @@
-\name{getNeighbours.experimental}
-\alias{getNeighbours.experimental}
-
-\title{
-Creating Local Neighbourhoods
-}
-\description{
-This function calculates a local neighbourhood to be used for fitting of spatial/spatio-temporal vine copulas and for prediction using spatial/spatio-temporal vine copulas.
-}
-\usage{
-getNeighbours.experimental(dataLocs, predLocs, var = names(dataLocs)[1], size = 5,
-prediction=FALSE, min.dist = 0.01)
-}
-\arguments{
- \item{dataLocs}{
-some spatial data frame holding the data used for estimation/prediction
-}
- \item{predLocs}{
-A spatial object defining the prediction locations, might be missing if the neighbourhood is used for fitting.
-}
- \item{var}{
-the variable name of interest, by default the first variable is used.
-}
- \item{size}{
-The size of the neighbourhood including the location of interest (for fitting as well for prediction).
-}
- \item{prediction}{whether the neighbourhood should be used for prediction (TRUE) or spatial/Spatio-temporal vine copula fitting.}
- \item{min.dist}{
-the minimal distance for a location to be included. Must be larger than 0 for fitting purposes and might be 0 for prediction.
-}
-}
-\value{
-An object of \code{\linkS4class{neighbourhood}}.
-}
-\author{
-Benedikt Graeler
-}
-
-\seealso{
-See \code{\link{neighbourhood}} for the native constructor of a \code{\linkS4class{neighbourhood}} class.
-}
-\examples{
-library(sp)
-spdf <- data.frame(x=c(112,154,212,289,345),y=c(124,198,85,168,346),measure=rlnorm(5))
-coordinates(spdf) <- ~x+y
-
-getNeighbours.experimental(spdf,size=4)
-}
-\keyword{ spatial }
\ No newline at end of file
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