[Stpp-commits] r28 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 12 16:12:49 CET 2010
Author: barryrowlingson
Date: 2010-02-12 16:12:49 +0100 (Fri, 12 Feb 2010)
New Revision: 28
Modified:
pkg/man/rinfec.Rd
pkg/man/rinter.Rd
pkg/man/rlgcp.Rd
pkg/man/rpcp.Rd
pkg/man/rpp.Rd
Log:
fixing examples in docs
Modified: pkg/man/rinfec.Rd
===================================================================
--- pkg/man/rinfec.Rd 2010-02-12 14:47:25 UTC (rev 27)
+++ pkg/man/rinfec.Rd 2010-02-12 15:12:49 UTC (rev 28)
@@ -50,7 +50,7 @@
\item{...}{additional parameters if \code{lambda} is a function.}
}
-value{
+\value{
A list containing:
\item{xyt}{matrix (or list of matrices if \code{nsim}>1)
containing the points (x,y,t) of the simulated point pattern.
@@ -70,7 +70,7 @@
\examples{
# inhibition; spatial distribution: uniform
inf1 = rinfec(npoints=100, alpha=0.2, beta=0.6, gamma=0.5, maxrad=c(0.075,0.5), t.region=c(0,50), s.distr="uniform", t.distr="uniform", h="step", p="min", recent="all", inhibition=TRUE)
-animation(inf1$xyt, cex=0.8, runtime=10)
+\dontrun{animation(inf1$xyt, cex=0.8, runtime=10)}
# contagion; spatial distribution: Poisson with intensity a given matrix
data(fmd)
@@ -79,6 +79,10 @@
h = h$h[which.min(h$mse)]
Ls = kernel2d(as.points(fmd[,1:2]), northcumbria, h, nx=50, ny=50)
inf2 = rinfec(npoints=100, alpha=4, beta=0.6, gamma=20, maxrad=c(12000,20), s.region=northcumbria, t.region=c(1,2000), s.distr="poisson", t.distr="uniform", h="step", p="min", recent=1, lambda=Ls$z, inhibition=FALSE)
+
+\dontrun{
image(Ls$x, Ls$y, Ls$z, col=grey((1000:1)/1000)); polygon(northcumbria,lwd=2)
animation(inf2$xyt, add=TRUE, cex=0.7, runtime=15)
}
+
+}
Modified: pkg/man/rinter.Rd
===================================================================
--- pkg/man/rinter.Rd 2010-02-12 14:47:25 UTC (rev 27)
+++ pkg/man/rinter.Rd 2010-02-12 15:12:49 UTC (rev 28)
@@ -45,7 +45,7 @@
generated. Otherwise, it is a contagious process. }
}
-value{
+\value{
A list containing:
\item{xyt}{matrix (or list of matrices if \code{nsim}>1)
containing the points (x,y,t) of the simulated point pattern.
@@ -65,7 +65,7 @@
\examples{
# simple inhibition process
inh1 = rinter(npoints=200,thetas=0,deltas=0.05,thetat=0,deltat=0.001,inhibition=TRUE)
-stani(inh1$xyt)
+\dontrun{stani(inh1$xyt)}
# inhibition process using hs and ht defined by the user
hs = function(d,theta,delta,mus=0.1)
@@ -100,12 +100,16 @@
legend("bottomright",col=1:2,lty=1,lwd=2,legend=c(expression(h[s]),expression(h[t])),bty="n",cex=2)
inh2 = rinter(npoints=100, hs=hs, gs="min", thetas=0.2, deltas=0.1, ht=ht, gt="min", thetat=0.1, deltat=0.05, inhibition=TRUE)
-animation(inh2$xyt, runtime=15, cex=0.8)
+\dontrun{animation(inh2$xyt, runtime=15, cex=0.8)}
# simple contagious process for given spatial and temporal regions
data(northcumbria)
cont1 = rinter(npoints=250, s.region=northcumbria, t.region=c(1,200), thetas=0,
deltas=5000, thetat=0, deltat=10, recent=1, inhibition=FALSE)
-animation(cont1$xyt, s.region=cont1$s.region, t.region=cont1$t.region,
+
+\dontrun{animation(cont1$xyt, s.region=cont1$s.region, t.region=cont1$t.region,
incident="darkgreen", prevalent="green3", runtime=15, cex=0.8)
-}
+}
+}
+
+
Modified: pkg/man/rlgcp.Rd
===================================================================
--- pkg/man/rlgcp.Rd 2010-02-12 14:47:25 UTC (rev 27)
+++ pkg/man/rlgcp.Rd 2010-02-12 15:12:49 UTC (rev 28)
@@ -142,14 +142,21 @@
# non separable covariance function:
lgcp1 <- rlgcp(npoints=200, nx=50, ny=50, nt=50, separable=FALSE, model="gneiting",
param=c(1,1,1,1,1,2), var.grf=1, mean.grf=0)
-N <- lgcp1$Lambda[,,1];for(j in 2:(dim(lgcp1$Lambda)[3])){N <- N+lgcp1$Lambda[,,j]}
+N <- lgcp1$Lambda[,,1];for(j in 2:(dim(lgcp1$Lambda)[3])){N <-
+N+lgcp1$Lambda[,,j]}
+\dontrun{
image(N,col=grey((1000:1)/1000));box()
animation(lgcp1$xyt, cex=0.8, runtime=10, add=TRUE, prevalent="orange")
-
+}
# separable covariance function:
lgcp2 <- rlgcp(npoints=200, nx=50, ny=50, nt=50, separable=TRUE, model="exponential",
param=c(1,1,1,1,1,2), var.grf=2, mean.grf=-0.5*2)
-N <- lgcp2$Lambda[,,1];for(j in 2:(dim(lgcp2$Lambda)[3])){N <- N+lgcp2$Lambda[,,j]}
+N <- lgcp2$Lambda[,,1];for(j in 2:(dim(lgcp2$Lambda)[3])){N <-
+N+lgcp2$Lambda[,,j]}
+\dontrun{
image(N,col=grey((1000:1)/1000));box()
-animation(lgcp2$xyt, cex=0.8, pch=20, runtime=10, add=TRUE, prevalent="orange")
+animation(lgcp2$xyt, cex=0.8, pch=20, runtime=10, add=TRUE,
+prevalent="orange")
}
+
+}
Modified: pkg/man/rpcp.Rd
===================================================================
--- pkg/man/rpcp.Rd 2010-02-12 14:47:25 UTC (rev 27)
+++ pkg/man/rpcp.Rd 2010-02-12 15:12:49 UTC (rev 28)
@@ -74,11 +74,15 @@
data(northcumbria)
pcp1 <- rpcp(nparents=50, npoints=500, s.region=northcumbria, t.region=c(1,365),cluster=c("normal","exponential"), maxrad=c(5000,5))
+\dontrun{
animation(pcp1$xyt, s.region=pcp1$s.region, t.region=pcp1$t.region,runtime=5)
-
+}
# inhomogeneous Poisson distribution of parents
lbda <- function(x,y,t,a){a*exp(-4*y) * exp(-2*t)}
pcp2 <- rpcp(nparents=50, npoints=500, cluster="normal", lambda=lbda, a=4000/((1-exp(-4))*(1-exp(-2))))
+\dontrun{
stani(pcp2$xyt)
}
+
+}
Modified: pkg/man/rpp.Rd
===================================================================
--- pkg/man/rpp.Rd 2010-02-12 14:47:25 UTC (rev 27)
+++ pkg/man/rpp.Rd 2010-02-12 15:12:49 UTC (rev 28)
@@ -64,21 +64,23 @@
# Homogeneous Poisson process
# ---------------------------
hpp1 <- rpp(lambda=200,replace=FALSE)
-stani(hpp1$xyt)
+\dontrun{stani(hpp1$xyt)}
+
# fixed number of points, discrete time, with time repeat.
data(northcumbria)
hpp2 = rpp(npoints=500, s.region=northcumbria, t.region=c(1,1000), discrete.time=TRUE)
+\dontrun{
polymap(northcumbria)
animation(hpp2$xyt, s.region=hpp2$s.region, t.region=hpp2$t.region, runtime=10, add=TRUE)
-
+}
# Inhomogeneous Poisson process
# -----------------------------
# intensity defined by a function
lbda1 = function(x,y,t,a){a*exp(-4*y) * exp(-2*t)}
ipp1 = rpp(lambda=lbda1, npoints=400, a=3200/((1-exp(-4))*(1-exp(-2))))
-stani(ipp1$xyt)
+\dontrun{stani(ipp1$xyt)}
# intensity defined by a matrix
data(fmd)
@@ -89,6 +91,8 @@
Lt = dim(fmd)[1]*density(fmd[,3], n=200)$y
ipp2 = rpp(lambda="m", Lambda=Ls$z, mut=Lt, s.region=northcumbria,
t.region=c(1,200), discrete.time=TRUE)
+\dontrun{
image(Ls$x, Ls$y, Ls$z, col=grey((1000:1)/1000)); polygon(northcumbria)
animation(ipp2$xyt, add=TRUE, cex=0.7, runtime=15)
}
+}
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