Package directadjusting

Compute estimates and confidence intervals of weighted averages quickly and easily. Weighted averages are computed using data.table for speed. Confidence intervals are approximated using the delta method with either using known formulae or via algorithmic or numerical derivation.

Recommended installation

You can install this R package from CRAN.

install.packages("directadjusting")

Alternatively this installs the latest release.

devtools::install_github(
  "FinnishCancerRegistry/directadjusting@release"
)

Example

# suppose we have poisson rates that we want to adjust for by age group.
# they are stratified by sex.
set.seed(1337)
offsets <- rnorm(8, mean = 1000, sd = 100)
baseline <- 100
sex_hrs <- rep(1:2, each = 4)
age_group_hrs <- rep(c(0.75, 0.90, 1.10, 1.25), times = 2)
counts <- rpois(8, baseline * sex_hrs * age_group_hrs)

# raw estimates
my_stats <- data.table::data.table(
  sex = rep(1:2, each = 4),
  ag = rep(1:4, times = 2),
  e = counts / offsets
)
my_stats[, "v" := my_stats[["e"]] / offsets]
print(my_stats)
#      sex    ag          e            v
#    <int> <int>      <num>        <num>
# 1:     1     1 0.08928141 8.759527e-05
# 2:     1     2 0.10054601 1.175523e-04
# 3:     1     3 0.11987410 1.238776e-04
# 4:     1     4 0.09722692 8.365551e-05
# 5:     2     1 0.18043221 1.937844e-04
# 6:     2     2 0.14781448 1.227479e-04
# 7:     2     3 0.21747515 1.987203e-04
# 8:     2     4 0.21519746 1.781152e-04

# adjusted by age group
my_adj_stats <- directadjusting::directly_adjusted_estimates(
  stats_dt = my_stats,
  stat_col_nms = "e",
  var_col_nms = "v",
  conf_lvls = 0.95,
  conf_methods = "log",
  stratum_col_nms = "sex",
  adjust_col_nms = "ag",
  weights = c(200, 300, 400, 100)
)

print(my_adj_stats)
# Key: <sex>
#      sex         e            v       e_lo      e_hi
#    <int>     <num>        <num>      <num>     <num>
# 1:     1 0.1056924 3.474049e-05 0.09474912 0.1178996
# 2:     2 0.1889406 5.237509e-05 0.17527556 0.2036710