Nothing
# install.packages("Pmisc", repos='http://r-forge.r-project.org')
library("Pmisc")
# rates
lungRates = diseasemapping::cancerRates(
'usa', 2000, 'F', 'Lung'
)
# table of counties and fips codes
countyTable = read.table(
url('http://www2.census.gov/geo/docs/reference/codes/files/national_county.txt'),
header=FALSE, stringsAsFactors=FALSE, sep=',', quote="\"",
col.names=c('ab1','id1','subId2','name2','junk'),
colClasses=rep('character',5)
)
countyTable$id2 = paste(
'USA',countyTable$id1,
'_0', countyTable$subId2,
sep=''
)
# Kentucky tract
kentuckyTract = gcensus(
country = 'USA',
year = 2000,
subset = c(name1='Kentucky'),
level = 4, income=TRUE,
simplifyTolerance=0.002,
crs='EPSG:3088'
)
# expected
kentuckyTract = diseasemapping::getSMR(
kentuckyTract,
5*lungRates
)
kentuckyTract = kentuckyTract[,grep("^(m|f)_", names(kentuckyTract), invert=TRUE)]
save(kentuckyTract,
file='/home/patrick/workspace/localem/pkg/localem/data/kentuckyTract.RData',
compress='xz')
file.info('/home/patrick/workspace/localem/pkg/localem/data/kentuckyTract.RData')['size']
if(FALSE) {
library(raster)
kMapSmall = mapmisc::openmap(kentuckyTract[1,], buffer=10000)
mapmisc::map.new(kMapSmall)
plot(kMapSmall, add=TRUE)
plot(kentuckyTract, add=TRUE, border='#0000FF50',lwd=3)
}
# Background map
kMapOrig = mapmisc::openmap(kentuckyTract, path='stamen-toner')
kMap = mapmisc::tonerToTrans(kMapOrig)
save(kMap,
file='/home/patrick/workspace/localem/pkg/localem/data/kMap.RData',
compress='xz')
file.info('/home/patrick/workspace/localem/pkg/localem/data/kMap.RData')['size']
# kentucky cases
kentuckyCases = diseasemapping:::usCancer(
site = 'Lung',
sex = 'F',
state = 'Kentucky',
year = c(2003, 2007)
)
kentuckyCases$ab1 = toupper(kentuckyCases$stateCode)
kentuckyCases$name2 = paste(kentuckyCases$County, "County", sep=' ')
kentuckyCases = merge(
kentuckyCases,
countyTable[,c('ab1','id2','name2')],
all.x=TRUE, all.y=FALSE
)
table(is.na(kentuckyCases$id2))
# Kentucky counties
kentuckyCounty = gcensus(
country = 'USA',
year = 2000,
subset = c(name1='Kentucky'),
level = 2, income=TRUE,
simplifyTolerance=0.002,
crs='EPSG:3088'
)
kentuckyCounty = sp::merge(
kentuckyCounty,
kentuckyCases
)
kentuckyCounty = kentuckyCounty[,
grep("^(id|name|cases)", names(kentuckyCounty), ignore.case=TRUE)]
kentuckyCounty = sp::spTransform(
kentuckyCounty,
kentuckyTract@proj4string
)
if(FALSE) {
library('raster')
kCol = mapmisc::colourScale(
kentuckyCounty$Cases,
breaks=9, dec=-1,style='quantile'
)
mapmisc::map.new(kentuckyCounty)
plot(kentuckyCounty, add=TRUE,
col=kCol$plot)
plot(kMap, add=TRUE)
mapmisc::legendBreaks("topleft", kCol)
}
save(kentuckyCounty,
file='/home/patrick/workspace/localem/pkg/localem/data/kentuckyCounty.RData',
compress='xz')
file.info('/home/patrick/workspace/localem/pkg/localem/data/kentuckyCounty.RData')['size']
# California, tract
californiaTract = gcensus(
country = 'USA',
year = 2000,
subset = c(name1='California'),
level = 4, income=TRUE,
simplifyTolerance=0.002,
crs='EPSG:3310'
)
californiaTract = diseasemapping::getSMR(
californiaTract,
lungRates
)
californiaTract = californiaTract[,grep("^(m|f)_", names(californiaTract), invert=TRUE)]
save(californiaTract,
file='/home/patrick/workspace/localem/sandbox/californiaTract.RData',
compress='xz')
file.info('/home/patrick/workspace/localem/sandbox/californiaTract.RData')['size']
if(FALSE) {
library(raster)
cMapSmall = mapmisc::openmap(californiaTract[1,], buffer=10000)
mapmisc::map.new(cMapSmall)
plot(cMapSmall, add=TRUE)
plot(californiaTract, add=TRUE, border='#0000FF50',lwd=3)
}
# california cases
californiaCases = diseasemapping:::usCancer(
site = 'Lung',
sex = 'F',
state = 'California',
year = 2003
)
californiaCases$ab1 = toupper(californiaCases$stateCode)
californiaCases$name2 = paste(californiaCases$County, "County", sep=' ')
# California counties
californiaCounty = gcensus(
country = 'USA',
year = 2000,
subset = c(name1='California'),
level = 2, income=TRUE,
simplifyTolerance=0.002,
crs='EPSG:3310'
)
calTable = countyTable[countyTable$ab1 == 'CA',]
calTable$name2Combined = calTable$name2
multiCounties = grep("-", californiaCases$County, value=TRUE)
for(D in multiCounties) {
DnoSp = gsub("[[:space:]]", "", D)
toGrep = paste("^(", gsub("-", "|", DnoSp), ")County", sep='')
cHere = grep(toGrep, gsub("[[:space:]]", "", calTable$name2))
calTable[cHere, 'name2Combined'] = paste(D, 'County')
}
californiaCounty = sp::merge(
californiaCounty,
calTable[,c('id2','name2Combined')]
)
californiaMerged = rgeos::gUnaryUnion(
californiaCounty,
californiaCounty$name2Combined
)
rownames(californiaCases) = gsub("[[:space:]]", "", californiaCases$name2)
californiaMerged = sp::spChFIDs(californiaMerged, gsub("[[:space:]]", "", names(californiaMerged) ))
californiaCases2 = californiaCases[match(
gsub("[[:space:]]", "", names(californiaMerged)),
gsub("[[:space:]]", "", californiaCases$name2)
), ]
californiaMerged = sp::SpatialPolygonsDataFrame(
californiaMerged, californiaCases2[,c('name2','Cases')]
)
californiaMerged = sp::spTransform(
californiaMerged,
californiaTract@proj4string
)
californiaCounty = sp::spTransform(
californiaCounty,
californiaTract@proj4string
)
if(FALSE) {
cMapOrig = mapmisc::openmap(californiaMerged, path='stamen-toner', fact=3)
cMap = mapmisc::tonerToTrans(cMapOrig)
library('raster')
cCol = mapmisc::colourScale(
californiaMerged$Cases,
breaks=9, dec=-1,style='quantile'
)
mapmisc::map.new(californiaCounty)
plot(californiaMerged, add=TRUE,
col=cCol$plot)
plot(californiaCounty, border='blue',add=TRUE)
plot(californiaMerged, border='grey',add=TRUE, lwd=2)
plot(cMap, add=TRUE)
mapmisc::legendBreaks("topright", cCol)
}
save(californiaMerged,
file='/home/patrick/workspace/localem/sandbox/californiaMerged.RData',
compress='xz')
file.info('/home/patrick/workspace/localem/sandbox/californiaMerged.RData')['size']
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