getAdjusted {SUMMER}

Adjust direct estimates and their associated variances

Description

Adjust direct estimates and their associated variances

Usage

getAdjusted(
  data,
  ratio,
  time = "years",
  region = "region",
  est = "mean",
  logit = "logit.est",
  logit.var = "var.est",
  logit.prec = "logit.prec",
  logit.lower = "lower",
  logit.upper = "upper",
  prob.lower = NULL,
  prob.upper = NULL,
  adj = "ratio",
  verbose = FALSE,
  lower = NULL,
  upper = NULL
)

Arguments

data

data frame of the adjusted estimates and the associated uncertainties, see the arguments below for specific columns.

ratio

the ratio of unadjusted mortality rates to the true mortality rates. It can be either a data frame with the following three columns (region, time, and adj) if adjustment factor differ by region; or a data frame with the following two columns (time and adj) if adjustment factor only varies over time. The column names specifying region, time, and adjustment are specified by the arguments in the function call.

time

the column name for time in the data and adjustment ratio.

region

the column name for region in the data and adjustment ratio.

est

the column name for unadjusted mortality rates in the data

logit

the column name for the logit of the unadjusted mortality rates in the data

logit.var

the column name for the variance of the logit of the unadjusted mortality rates in the data

logit.prec

the column name for the precision of the logit of the unadjusted mortality rates in the data

logit.lower

the column name for the 95% lower bound of the logit of the unadjusted mortality rates in the data

logit.upper

the column name for the 95% lower bound of the logit of the unadjusted mortality rates in the data

prob.lower

the column name for the 95% lower bound of the unadjusted mortality rates in the data. If this is provided instead of logit.lower, the logit scale lower bound will be created.

prob.upper

the column name for the 95% lower bound of the unadjusted mortality rates in the data. if this is provided instead of logit.upper, the logit scale upper bound will be created.

adj

the column name for the adjustment ratio

verbose

logical indicator for whether to print out unadjusted row index

lower

previous argument name for prob.lower. Will be removed in the next update

upper

previous argument name for prob.upper. Will be removed in the next update

Value

adjusted dataset of the same columns.

Author(s)

Zehang Richard Li

Examples

## Not run: 
years <- levels(DemoData[[1]]$time)

# obtain direct estimates
data <- getDirectList(births = DemoData, 
years = years,  
regionVar = "region", timeVar = "time", 
clusterVar = "~clustid+id", 
ageVar = "age", weightsVar = "weights", 
geo.recode = NULL)
# 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)

# randomly simulate adjustment factor
adj <- expand.grid(region = unique(data$region), years = years)
adj$ratio <- runif(dim(adj)[1], min = 0.5, max = 0.8)
data.adj <- getAdjusted(data = data, ratio = adj)
 
## End(Not run)