| Benchmark {SUMMER} | R Documentation |
Benchmark posterior draws to national estimates
Description
Benchmark posterior draws to national estimates
Usage
Benchmark(
fitted,
national,
estVar,
sdVar,
timeVar = NULL,
weight.region = NULL,
method = c("MH", "Rejection")[2]
)
Arguments
fitted |
output from |
national |
a data frame of national level estimates that is benchmarked against, with at least two columns indicating national estimates (probability scale) and the associated standard error. If benchmarking over multiple time period, a third column indicating time period is needed. |
estVar |
column name in |
sdVar |
column name in |
timeVar |
column name in |
weight.region |
a data frame with a column 'region' specifying subnational regions, a column 'proportion' that specifies the proportion of population in each region. When multiple time periods exist, a third column 'years' is required and the population proportions are the population proportions of each region in the corresponding time period. |
method |
a string denoting the algorithm to use for benchmarking. Options include 'MH' for Metropolis-Hastings, and 'Rejection' for rejection sampler. Defaults to 'Rejection'. |
Value
Benchmarked object in S3 class SUMMERproj or SUMMERprojlist in the same format as the input object fitted.
Author(s)
Taylor Okonek, Zehang Richard Li
Examples
## Not run:
## ------------------------------------------ ##
## Benchmarking with smoothCluster output
## ------------------------------------------ ##
data(DemoData)
# fit unstratified cluster-level model
counts.all <- NULL
for(i in 1:length(DemoData)){
vars <- c("clustid", "region", "time", "age")
counts <- getCounts(DemoData[[i]][, c(vars, "died")],
variables = 'died',
by = vars, drop=TRUE)
counts$cluster <- counts$clustid
counts$years <- counts$time
counts$Y <- counts$died
counts$survey <- names(DemoData)[i]
counts.all <- rbind(counts.all, counts)
}
periods <- c("85-89", "90-94", "95-99", "00-04", "05-09", "10-14", "15-19")
fit.bb <- smoothCluster(data = counts.all, Amat = DemoMap$Amat,
family = "betabinomial",
year_label = periods,
survey.effect = TRUE)
est.bb <- getSmoothed(fit.bb, nsim = 1e4, CI = 0.95, save.draws=TRUE)
# construct a simple population weight data frame with equal weights
weight.region <- expand.grid(region = unique(counts.all$region),
years = periods)
weight.region$proportion <- 0.25
# construct a simple national estimates
national <- data.frame(years = periods,
est = seq(0.27, 0.1, length = 7),
sd = runif(7, 0.01, 0.03))
# benchmarking
est.bb.bench <- Benchmark(est.bb, national, weight.region = weight.region,
estVar = "est", sdVar = "sd", timeVar = "years")
# Sanity check: Benchmarking comparison
compare <- national
compare$before <- NA
compare$after <- NA
for(i in 1:dim(compare)[1]){
weights <- subset(weight.region, years == national$years[i])
sub <- subset(est.bb$overall, years == national$years[i])
sub <- merge(sub, weights)
sub.bench <- subset(est.bb.bench$overall, years == national$years[i])
sub.bench <- merge(sub.bench, weights)
compare$before[i] <- sum(sub$proportion * sub$median)
compare$after[i] <- sum(sub.bench$proportion * sub.bench$median)
}
plot(compare$est, compare$after, col = 2, pch = 10,
xlim = range(c(compare$est, compare$before, compare$after)),
ylim = range(c(compare$est, compare$before, compare$after)),
xlab = "External national estimates",
ylab = "Weighted posterior median after benchmarking",
main = "Sanity check: weighted average of area medians")
points(compare$est, compare$before)
abline(c(0, 1))
legend("topleft", c("Before benchmarking", "After benchmarking"), pch = c(1, 10), col = c(1, 2))
# construct a simple national estimates
national <- data.frame(years = periods,
est = seq(0.22, 0.1, length = 7),
sd = runif(7, 0.01, 0.03))
# national does not need to have all years
national_sub <- national[1:3,]
# benchmarking
est.bb.bench <- Benchmark(est.bb, national_sub,
weight.region = weight.region,
estVar = "est", sdVar = "sd", timeVar = "years")
# Sanity check: only benchmarked for three periods
compare <- national
compare$before <- NA
compare$after <- NA
for(i in 1:dim(compare)[1]){
weights <- subset(weight.region, years == national$years[i])
sub <- subset(est.bb$overall, years == national$years[i])
sub <- merge(sub, weights)
sub.bench <- subset(est.bb.bench$overall, years == national$years[i])
sub.bench <- merge(sub.bench, weights)
compare$before[i] <- sum(sub$proportion * sub$median)
compare$after[i] <- sum(sub.bench$proportion * sub.bench$median)
}
plot(compare$est, compare$after, col = 2, pch = 10,
xlim = range(c(compare$est, compare$before, compare$after)),
ylim = range(c(compare$est, compare$before, compare$after)),
xlab = "External national estimates",
ylab = "Weighted posterior median after benchmarking",
main = "Sanity check: weighted average of area medians")
points(compare$est, compare$before)
abline(c(0, 1))
legend("topleft", c("Before benchmarking", "After benchmarking"), pch = c(1, 10), col = c(1, 2))
# Another extreme benchmarking example, where almost all weights in central region
weight.region$proportion <- 0.01
weight.region$proportion[weight.region$region == "central"] <- 0.97
# benchmarking
est.bb.bench <- Benchmark(est.bb, national, weight.region = weight.region,
estVar = "est", sdVar = "sd", timeVar = "years")
# It can be seen the central region are pulled to the national benchmark
plot(national$est,
subset(est.bb.bench$overall, region == "central")$mean,
col = 2, pch = 10, xlab = "External national estimates",
ylab = "Central region estimates")
points(national$est,
subset(est.bb$overall, region == "central")$mean)
legend("topleft", c("Before benchmarking", "After benchmarking"), pch = c(1, 10), col = c(1, 2))
abline(c(0, 1))
# Example with the MH method
# Benchmarking with MH should be applied when customized priors are
# specified for fixed effects when fitting the model
fit.bb.new <- smoothCluster(data = counts.all, Amat = DemoMap$Amat,
family = "betabinomial",
year_label = periods,
survey.effect = TRUE,
control.fixed = list(
mean=list(`age.intercept0:1`=-4,
`age.intercept1-11:1`=-5,
`age.intercept12-23:1`=-8,
`age.intercept24-35:1`=-9,
`age.intercept36-47:1`=-10,
`age.intercept48-59:1`=-11),
prec=list(`age.intercept0:1`=10,
`age.intercept1-11:1`=10,
`age.intercept12-23:1`=10,
`age.intercept24-35:1`=10,
`age.intercept36-47:1`=10,
`age.intercept48-59:1`=10)))
est.bb.new <- getSmoothed(fit.bb.new, nsim = 10000, CI = 0.95, save.draws=TRUE)
# construct a simple national estimates
national <- data.frame(years = periods,
est = seq(0.22, 0.1, length = 7),
sd = runif(7, 0.01, 0.03))
weight.region <- expand.grid(region = unique(counts.all$region),
years = periods)
weight.region$proportion <- 0.25
est.bb.bench.MH <- Benchmark(est.bb.new, national,
weight.region = weight.region,
estVar = "est", sdVar = "sd", timeVar = "years",
method = "MH")
compare <- national
compare$before <- NA
compare$after <- NA
for(i in 1:dim(compare)[1]){
weights <- subset(weight.region, years == national$years[i])
sub <- subset(est.bb.new$overall, years == national$years[i])
sub <- merge(sub, weights)
sub.bench <- subset(est.bb.bench.MH$overall, years == national$years[i])
sub.bench <- merge(sub.bench, weights)
compare$before[i] <- sum(sub$proportion * sub$median)
compare$after[i] <- sum(sub.bench$proportion * sub.bench$median)
}
plot(compare$est, compare$after, col = 2, pch = 10,
xlim = range(c(compare$est, compare$before, compare$after)),
ylim = range(c(compare$est, compare$before, compare$after)),
xlab = "External national estimates",
ylab = "Weighted posterior median after benchmarking",
main = "Sanity check: weighted average of area medians")
points(compare$est, compare$before)
abline(c(0, 1))
legend("topleft", c("Before benchmarking", "After benchmarking"), pch = c(1, 10), col = c(1, 2))
## ------------------------------------------ ##
## Benchmarking with smoothDirect output
## ------------------------------------------ ##
years <- levels(DemoData[[1]]$time)
# obtain direct estimates
data_multi <- getDirectList(births = DemoData, years = years,
regionVar = "region", timeVar = "time", clusterVar = "~clustid+id",
ageVar = "age", weightsVar = "weights", geo.recode = NULL)
data <- aggregateSurvey(data_multi)
# subnational model
years.all <- c(years, "15-19")
fit2 <- smoothDirect(data = data, Amat = DemoMap$Amat,
year_label = years.all, year_range = c(1985, 2019),
time.model = "rw2", m = 5, type.st = 4)
out2a <- getSmoothed(fit2, joint = TRUE, nsim = 1e5, save.draws = TRUE)
##
## Benchmarking for yearly estimates
##
weight.region <- expand.grid(region = unique(data$region[data$region != "All"]),
years = 1985:2019)
weight.region$proportion <- 0.25
# construct a simple national estimates
national <- data.frame(years = 1985:2019,
est = seq(0.25, 0.15, length = 35),
sd = runif(35, 0.03, 0.05))
# Benchmarking to national estimates on the yearly scale
out2b <- Benchmark(out2a, national, weight.region = weight.region,
estVar = "est", sdVar = "sd", timeVar = "years")
plot(out2a$overall)
plot(out2b$overall)
# combine the point estimate and compare with the benchmark values
national.est <- aggregate(mean ~ years,
data = out2a$overall[out2a$overall$is.yearly, ], FUN = mean)
national.est.bench <- aggregate(mean ~ years,
data = out2b$overall[out2b$overall$is.yearly, ], FUN = mean)
plot(national$est, national.est$mean,
xlim = range(c(national$est, national.est$mean, national.est.bench$mean)),
ylim = range(c(national$est, national.est$mean, national.est.bench$mean)),
xlab = "External national estimates",
ylab = "Weighted posterior median after benchmarking",
main = "Sanity check: weighted average of area means")
points(national$est, national.est.bench$mean, col = 2, pch = 10)
abline(c(0, 1))
legend("topleft", c("Before benchmarking", "After benchmarking"), pch = c(1, 10), col = c(1, 2))
##
## Benchmarking for period estimates
##
weight.region <- expand.grid(region = unique(data$region[data$region != "All"]),
years = years.all)
weight.region$proportion <- 0.25
# construct a simple national estimates
national <- data.frame(years = years.all,
est = seq(0.25, 0.15, len = 7),
sd = runif(7, 0.01, 0.03))
# Benchmarking to national estimates on the period scale
out2c <- Benchmark(out2a, national, weight.region = weight.region,
estVar = "est", sdVar = "sd", timeVar = "years")
plot(out2a$overall)
plot(out2c$overall)
# combine the point estimate and compare with the benchmark values
national.est <- aggregate(mean ~ years,
data = out2a$overall[!out2a$overall$is.yearly, ], FUN = mean)
national.est.bench <- aggregate(mean ~ years,
data = out2c$overall[!out2b$overall$is.yearly, ], FUN = mean)
plot(national$est, national.est$mean,
xlim = range(c(national$est, national.est$mean, national.est.bench$mean)),
ylim = range(c(national$est, national.est$mean, national.est.bench$mean)),
xlab = "External national estimates",
ylab = "Weighted posterior median after benchmarking",
main = "Sanity check: weighted average of area means")
points(national$est, national.est.bench$mean, col = 2, pch = 10)
abline(c(0, 1))
legend("topleft", c("Before benchmarking", "After benchmarking"), pch = c(1, 10), col = c(1, 2))
## End(Not run)
[Package SUMMER version 1.4.0 Index]