[Stpp-commits] r51 - in pkg: . R man

[noreply at r-forge.r-project.org]

Author: gabriele
Date: 2012-04-25 16:13:59 +0200 (Wed, 25 Apr 2012)
New Revision: 51

Modified:
   pkg/DESCRIPTION
   pkg/R/plotK.R
   pkg/man/STIKhat.Rd
   pkg/man/animation.Rd
Log:


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-04-21 11:17:14 UTC (rev 50)
+++ pkg/DESCRIPTION	2012-04-25 14:13:59 UTC (rev 51)
@@ -3,7 +3,7 @@
 Title: Space-Time Point Pattern simulation, visualisation and analysis
 Version: 0.1
 Date: 2008-10-16
-Author: Edith Gabriel
+Authors: Edith Gabriel, Peter J Diggle, stan function by Barry Rowlingson
 Maintainer: Edith Gabriel <edith.gabriel at univ-avignon.fr>
 Depends: R (>= 2.10), splancs
 Suggests: rpanel, rgl

Modified: pkg/R/plotK.R
===================================================================
--- pkg/R/plotK.R	2012-04-21 11:17:14 UTC (rev 50)
+++ pkg/R/plotK.R	2012-04-25 14:13:59 UTC (rev 51)
@@ -23,7 +23,7 @@
   if (isTRUE(persp))
     {
       mask <- matrix(0,ncol=length(K$times),nrow=length(K$dist))
-      for(i in 1:length(K$dist)){ for(j in 1:length(K$times)){mask[i,j] <- COL[iplace(x=k[i,j],X=M,xinc=diff(range(M))/(n-1))]}}
+      for(i in 1:length(K$dist)){ for(j in 1:length(K$times)){mask[i,j] <- COL[.iplace(x=k[i,j],X=M,xinc=diff(range(M))/(n-1))]}}
       COL <- mask[1:(length(K$dist)-1),1:(length(K$times)-1)]
       
       if(isTRUE(legend))
@@ -33,8 +33,8 @@
           persp(x=K$dist, y=K$times, z=k, xlab="u",ylab="v", zlab="",expand=1, col=COL, ...)
           title(titl,cex.main=2)
           par(fig=c(0.825,1,0,1))
-          mini <- iplace(x=min(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
-          maxi <- iplace(x=max(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
+          mini <- .iplace(x=min(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
+          maxi <- .iplace(x=max(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
           legend("right",fill=colo(n)[maxi:mini],legend=M[maxi:mini],horiz=F,bty="n")
         }
       else
@@ -60,8 +60,8 @@
           axis(2,at=at[length(at)],labels="v",cex.axis=2)
           title(titl,cex.main=2)
           par(fig=c(0,1,0.1,1))
-          mini <- iplace(x=min(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
-          maxi <- iplace(x=max(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
+          mini <- .iplace(x=min(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
+          maxi <- .iplace(x=max(k,na.rm=T),X=M,xinc=diff(range(k))/(n-1))
           legend("right",fill=colo(n)[maxi:mini],legend=M[maxi:mini],horiz=F,bty="n")
         }
       else

Modified: pkg/man/STIKhat.Rd
===================================================================
--- pkg/man/STIKhat.Rd	2012-04-21 11:17:14 UTC (rev 50)
+++ pkg/man/STIKhat.Rd	2012-04-25 14:13:59 UTC (rev 51)
@@ -26,7 +26,7 @@
 \item{correction}{logical value. If \code{TRUE}, the Ripley's
 edge correction is used.} \item{infectious}{logical value. If
 \code{TRUE}, only future events
-  are considered. The estimate of the STIK function is thus the one given in Details.}
+  are considered. See Details.}
  }
 
 \details{Gabriel and Diggle (2009) propose the following
@@ -61,6 +61,13 @@
   \right\rbrace}}{K'(u,v) = |SxT|/(nv(n-1)) sum_{i=1,...,nv} sum_{j=1,...,nv; j>i} 1/wij 1{uij <=
   u} 1{tj - ti <= v}}
 
+If parameter \code{infectious = TRUE}, both future and past
+events are considered and the estimator is: \deqn{
+  \widehat K^*_{ST}(u,v) =  \frac{1}{|S \times T|} \sum_{i=1}^{n}
+  \sum_{j \neq j}^{n} \frac{1}{w_{ij}} \frac{1}{\lambda(x_i) \lambda(x_j)}{\bf 1}_{\left\lbrace u_{ij} \leq u
+  \right\rbrace} {\bf 1}_{\left\lbrace |t_j - t_i| \leq v \right\rbrace}}{K^*(u,v) = 1/|SxT| sum_{i=1,...,n}
+  sum_{j=1,...,n; j \neq j} 1/wij 1/(lambda(x_i)lambda(x_j)) 1{uij <=
+  u} 1{|tj - ti| <= v}}
 }
 
  \value{ A list containing:
@@ -68,8 +75,8 @@
  \item{Khat}{ndist x ntimes matrix containing values of \eqn{\hat
  K_{ST}(u,v)}{K(u,v)}.}
 \item{Ktheo}{ndist x ntimes matrix containing theoretical
-values for a Poisson process (\eqn{\pi u^2 v}{pi u^2 v} for K
-and \eqn{\pi u^2 v}{pi u^2 v}) for K'.}
+values for a Poisson process; \eqn{\pi u^2 v}{pi u^2 v} for K
+and \eqn{2 \pi u^2 v}{2 pi u^2 v}) for K^*.}
 
  \item{dist, times, infectious}{parameters passed in argument.}
  }
@@ -95,7 +102,7 @@
 data(northcumbria)
 FMD=as.3dpoints(fmd[,1]/1000,fmd[,2]/1000,fmd[,3])
 
-# estimation of the temporal intensity 
+# estimation of the temporal intensity
 M=density(FMD[,3],kernel="gaussian",n=200)
 mut=M$y[FMD[,3]]*dim(fmd)[1]
 

Modified: pkg/man/animation.Rd
===================================================================
--- pkg/man/animation.Rd	2012-04-21 11:17:14 UTC (rev 50)
+++ pkg/man/animation.Rd	2012-04-25 14:13:59 UTC (rev 51)
@@ -35,4 +35,4 @@
 None
 }
 
-\author{Peter Diggle, Edith Gabriel <edith.gabriel at univ-avignon.fr>.}
+\author{Peter J Diggle, Edith Gabriel <edith.gabriel at univ-avignon.fr>.}