probmap.Rd
The function returns a data frame of rates for counts in populations at risk with crude rates, expected counts of cases, relative risks, and Poisson probabilities.
probmap(n, x, row.names=NULL, alternative="less")
a numeric vector of counts of cases
a numeric vector of populations at risk
row names passed through to output data frame
default “less”, may be set to “greater”
The function returns a data frame, from which rates may be mapped after class intervals have been chosen. The class intervals used in the examples are mostly taken from the referenced source.
raw (crude) rates
expected counts of cases assuming global rate
relative risks: ratio of observed and expected counts of cases multiplied by 100
Poisson probability map values: probablility of getting a more ``extreme'' count than actually observed - one-tailed, default alternative observed “less” than expected
Bailey T, Gatrell A (1995) Interactive Spatial Data Analysis, Harlow: Longman, pp. 300--303.
auckland <- st_read(system.file("shapes/auckland.shp", package="spData")[1], quiet=TRUE)
res <- probmap(auckland$M77_85, 9*auckland$Und5_81)
rt <- sum(auckland$M77_85)/sum(9*auckland$Und5_81)
ppois_pmap <- numeric(length(auckland$Und5_81))
for (i in seq(along=ppois_pmap)) {
ppois_pmap[i] <- poisson.test(auckland$M77_85[i], r=rt,
T=(9*auckland$Und5_81[i]), alternative="less")$p.value
all.equal(ppois_pmap, res$pmap)
}
res$id <- 1:nrow(res)
auckland$id <- res$id <- 1:nrow(res)
auckland_res <- merge(auckland, res, by="id")
plot(auckland_res[, "raw"], main="Crude (raw) estimates")
plot(auckland_res[, "relRisk"], main="Standardised mortality ratios")
plot(auckland_res[, "pmap"], main="Poisson probabilities",
breaks=c(0, 0.05, 0.1, 0.5, 0.9, 0.95, 1))