##### GRAPHICS  ########################################################################

#### need to get polygon objects into R   and in a form usable by INLA
#### shapefiles can be imported to R
####  GeoBUGS format map files can b exported from WInbUGS and converted for INLA


#### getting polygons into R  #######################################################

### from shapefiles  ##################################################################

library(maptools)
polys<-readShapePoly("filename.shp")
plot(polys)

#example: 
setwd("C:/A_NEWER_FOLDER/A_NEW_FOLDER/A_courses/A_courses/Spatial Statistics _workshop (2013)/participant files/co45_d00_shp")
polySC<-readShapePoly("co45_d00.shp")
plot(polySC)



### from GeoBUGS map files ##########################################################

Export a map file in SPlus format into a text file. (adjacency tool: adj matrix).  I have done this already:
SCgeobugsSPlus.txt

setwd("C:/A_NEWER_FOLDER/A_NEW_FOLDER/A_courses/A_courses/Spatial Statistics _workshop (2013)/participant files")
polySC<-readSplus("SC_geobugsSPlus.txt")
plot(polySC)


polySC is a polygon object and can be used for mapping on R. 
However INLA requires that a special format is used when fitting models with spatial components. This format can be 
obtained via two routes:  
1) if adj and num vectors are available (already read into R) then the command

geobugs2inla(adj,num, graph.file="SC.poly.txt")
will create a valid spatial graph file for inla models

2) using library spdep

library(spdep)
adjpoly<-poly2nb(polySC)
nb2INLA("SC.poly.txt",adjpoly)

will create the graph file "SC.poly.txt"


### General purpose polygon mapping tool:fillmap.R  #################################
#### fillmap creates thematic maps based on data in vectors and polygons which have been 
#### created on R or imported  ########################################################

setwd(.....working directory.....)
source("fillmap.R")
polySC is a polygon object that can be used for mapping

a model fit is obtained in 'result1'
then we can map result1$summary.random[,2] by the following:

rand<-result1$summary.random[,2]
fillmap(polySC,"random effect",rand,n.col=6)