calculate_I_smooth: Estimate the incidence based on PPS data using monotone...

In prevtoinc: Prevalence to Incidence Calculations for Point-Prevalence Studies in a Nosocomial Setting

Estimate the incidence based on PPS data using monotone estimators for the distribution of A.

Description

Estimate incidence from PPS by the method proposed in the companion paper. 'data' should be supplied as a data frame with at least a column named 'A.loi' giving lengths of infection up to date of PPS. Values of zero for 'A.loi' indicate absence of a HAI. Optionally, the data frame can also contain a column 'A.los' supplying lengths of stay up to PPS to estimate x.los with the same method as well. If 'correct.one' is 'TRUE', the number infections on their first day will be augmented to be at least as high as the number of infections on their second day for the estimation of x.loi .

Usage

calculate_I_smooth(
  data,
  method = "gren",
  correct.one.loi = "no",
  correct.one.los = "no"
)

Arguments

data	data frame which contains a column 'A.loi' with lengths of nosocomial infections up to survey point ( zero if none) and possibly a column 'A.los' with length of stay up to survey point
method	method to use for smoothing ("gren" ( Grenander ) or "rear" (rearrangement))
correct.one.loi	use correction for underreporting of one day LOIs: "no" if none, "fill.ones" to set the one-day cases to be at least the number of two-day cases, "start.two" to only use P(A=2| A > 1) as a proxy for P(A=1)
correct.one.los	use correction for underreporting of one day LOSs: "no" if none, "fill.ones" to set the one-day cases to be at least the number of two-day cases, "start.two" to only use P(A=2| A > 1) as a proxy for P(A=1)

Value

one-row data frame with following columns

n	number of patients sampled
n.noso	number of HAIs
P.hat	estimate of prevalence P
I.hat	estimate of incidence rate I
I.pp.hat	estimate of incidence proportion per admission I.pp
x.loi.hat	estimate of x.loi
x.los.hat	estimate of x.los
method	name of the method

Examples

# create example data for PPS
example.dist <- create_dist_vec(function(x) dpois(x-1, 7), max.dist = 70)
example.dist.los <- create_dist_vec(function(x) dpois(x-1, lambda = 12),
                                    max.dist = 70)
data.pps.fast <- simulate_pps_fast(n.sample=200,
                                   P=0.05,
                                   dist.X.loi = example.dist,
                                   dist.X.los = example.dist.los)
head(data.pps.fast)

# estimate of incidence
calculate_I_smooth(data = data.pps.fast,
                   method = "gren")

prevtoinc documentation built on Sept. 3, 2026, 5:07 p.m.