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SAE06.R
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### R code from vignette source 'SAE06.Rnw'
### Encoding: ISO8859-1
###################################################
### code chunk number 1: SAE06.Rnw:174-203
###################################################
library(maptools)
library(spdep)
library(rgdal)
#Read data from shapefile
nc <- readShapePoly(system.file("etc/shapes/sids.shp", package="spdep")[1],
ID="FIPSNO")#, proj4string=CRS("+proj=longlat +ellps=clrk66"))
rn <- sapply(slot(nc, "polygons"), function(x) slot(x, "ID"))
ncCC89nb <- read.gal(system.file("etc/weights/ncCC89.gal", package="spdep")[1],
region.id=rn)
nc.nb<-nb2WB(ncCC89nb)
#Prepare data set
nc$Observed<-nc$SID74
nc$Population<-nc$BIR74#Population at risk; number of births
r<-sum(nc$Observed)/sum(nc$Population)
nc$Expected<-nc$Population*r
N<-length(nc$Observed)
#Computed Standardised Mortality Ratio
nc$SMR<-nc$Observed/nc$Expected
#Proportion of non-white births
nc$nwprop<-nc$NWBIR74/nc$BIR74
d<-list(N=N, observed=nc$Observed, expected=nc$Expected,
nonwhite=nc$nwprop,#log(nwprop/(1-nwprop)),
adj=nc.nb$adj, weights=nc.nb$weights, num=nc.nb$num)
inits<-list(u=rep(0,N), v=rep(0,N), alpha=0, beta=0, precu=.001, precv=.001)
###################################################
### code chunk number 2: SAE06.Rnw:211-234
###################################################
library(R2WinBUGS)
bymmodelfile<-paste(getwd(), "/BYM-model.txt", sep="")
wdir<-paste(getwd(), "/BYM", sep="")
if(!file.exists(wdir)){dir.create(wdir)}
#BugsDir <- "/Users/virgiliogomezgislab/.wine/dosdevices/c:/Program Files/WinBUGS14"
BugsDir <- "/Users/virgil/.wine/dosdevices/c:/Program Files/WinBUGS14"
MCMCres<- bugs(data=d, inits=list(inits),
working.directory=wdir,
parameters.to.save=c("theta", "alpha", "beta", "u", "v", "sigmau", "sigmav"),
n.chains=1, n.iter=30000, n.burnin=20000, n.thin=10,
model.file=bymmodelfile,
bugs.directory=BugsDir,
WINEPATH="/usr/local/bin/winepath")
#Load the data obtained by running WinBUGS in Windows
nc$BYMmean<-MCMCres$mean$theta
nc$BYMumean<-MCMCres$mean$u
nc$BYMvmean<-NA
nc$BYMvmean[nc.nb$num>0]<-MCMCres$mean$v
###################################################
### code chunk number 3: coda (eval = FALSE)
###################################################
## library(coda)
## ncoutput<-read.coda("BYM/coda1.txt", "BYM/codaIndex.txt")
##
## #par(mfrow=c(2,4))
## #plot(ncoutput[,c("deviance", "alpha", "beta", "theta[94]")],auto.layout=FALSE)
## plot(ncoutput[,c("deviance", "beta")])
###################################################
### code chunk number 4: codaplot
###################################################
library(coda)
ncoutput<-read.coda("BYM/coda1.txt", "BYM/codaIndex.txt")
#par(mfrow=c(2,4))
#plot(ncoutput[,c("deviance", "alpha", "beta", "theta[94]")],auto.layout=FALSE)
plot(ncoutput[,c("deviance", "beta")])
###################################################
### code chunk number 5: sidsplot
###################################################
library(RColorBrewer)
brks<-quantile(nc$SMR, seq(0,1,1/5))
#Used method proposed by Nicky Best
logSMR<-log(nc$SMR[nc$SMR>0])
nsteps <- 5
step<-(max(logSMR)-min(logSMR))/nsteps
brks<-exp(min(logSMR)+(0:nsteps)*step)
brks[1]<-0
cols <- brewer.pal(5, "Oranges")
atcol<-(0:5)*max(nc$SMR)/5
colorkey<-list(labels=as.character(c(formatC(brks, format="f", dig=2))),
at=atcol, height=.5)
print(spplot(nc, c("SMR", "BYMmean"), at=brks, col.regions=cols,
axes=TRUE, colorkey=colorkey))
###################################################
### code chunk number 6: SAE06.Rnw:289-290 (eval = FALSE)
###################################################
## library(RColorBrewer)
## brks<-quantile(nc$SMR, seq(0,1,1/5))
##
## #Used method proposed by Nicky Best
## logSMR<-log(nc$SMR[nc$SMR>0])
## nsteps <- 5
## step<-(max(logSMR)-min(logSMR))/nsteps
## brks<-exp(min(logSMR)+(0:nsteps)*step)
## brks[1]<-0
##
## cols <- brewer.pal(5, "Oranges")
##
## atcol<-(0:5)*max(nc$SMR)/5
## colorkey<-list(labels=as.character(c(formatC(brks, format="f", dig=2))),
## at=atcol, height=.5)
##
## print(spplot(nc, c("SMR", "BYMmean"), at=brks, col.regions=cols,
## axes=TRUE, colorkey=colorkey))
###################################################
### code chunk number 7: SAE06.Rnw:363-383 (eval = FALSE)
###################################################
## dunemp<-source("Unemployment/WBdata/datasp.txt")$value
## dsp<-source("Unemployment/WBdata/spdata.txt")$value
##
## initsunemp1<-source("Unemployment/inits/initssp-1.txt")$value
## initsunemp2<-source("Unemployment/inits/initssp-2.txt")$value
##
## bymmodelfile<-paste(getwd(), "/Unemployment/models/modelsp.txt", sep="")
## wdir<-paste(getwd(), "/BYM-Unemp", sep="")
## if(!file.exists(wdir)){dir.create(wdir)}
##
## #BugsDir <- "/Users/virgiliogomezgislab/.wine/dosdevices/c:/Program Files/WinBUGS14"
## BugsDir <- "/Users/virgil/.wine/dosdevices/c:/Program Files/WinBUGS14"
## MCMCresunemp<- bugs(data=c(dunemp, dsp), inits=list(initsunemp1, initsunemp2),
## working.directory=wdir,
## parameters.to.save=c("p", "alpha", "bage", "bsex", "beduc"),
## n.chains=2, n.iter=3000, n.burnin=2000, n.thin=1,
## model.file=bymmodelfile,
## bugs.directory=BugsDir,
## WINEPATH="/usr/bin/winepath")
##
###################################################
### code chunk number 8: SAE06.Rnw:386-387
###################################################
load("MCMCresunemp.RData")
###################################################
### code chunk number 9: Sweden
###################################################
library(maptools)
Sweden<-readShapePoly(fn="Sweden_municipality")
Sweden<-unionSpatialPolygons(Sweden,Sweden$KOD83_91)
Sweden<-SpatialPolygonsDataFrame(Sweden,
data.frame(unemp=1-unique(MCMCresunemp$mean$p)), match.ID =FALSE )
print(spplot(Sweden, "unemp", cuts=20))
###################################################
### code chunk number 10: SAE06.Rnw:411-412 (eval = FALSE)
###################################################
## library(maptools)
## Sweden<-readShapePoly(fn="Sweden_municipality")
## Sweden<-unionSpatialPolygons(Sweden,Sweden$KOD83_91)
## Sweden<-SpatialPolygonsDataFrame(Sweden,
## data.frame(unemp=1-unique(MCMCresunemp$mean$p)), match.ID =FALSE )
##
## print(spplot(Sweden, "unemp", cuts=20))
##