strate: Calculate Incidence Rates from time-to-event data

In myominnoo/mStats_beta: A tool for data management and statistical analysis

Description

strate calculates incidence rates of the cohort.

Usage

strate(
  data = NULL,
  time,
  status,
  by = NULL,
  fail = 1,
  per = 1,
  rnd = 4,
  plot = TRUE,
  print.table = TRUE
)

strate.calc(t, s, f, p, r, v)

Arguments

data	an optional data frame
time	specify the timer interval when the subject is at risk
status	event of interest to calculate incidence: 1 for event, 0 for censored
by	specify variable to calculate stratified rates
fail	failure event
per	units to be used in reported rates
rnd	Rounding of numbers
plot	logical value to display plots of rates across a categorical variable
print.table	logical value to display formatted outputs
t	time var
s	status var
f	failure var
p	person-time var
r	rnd var
v	vector

Details

Rates of event occurrences, known as incidence rates are outcome measures in longitudinal studies. In most longitudinal studies, follow-up times vary due to logistic resasons, different periods of recruitment, delay enrolment into the study, lost-to-follow-up, immigration or emigration and death.

Follow-up time in longitudinal studies

Period of observation (called as follow-up time) starts when individuals join the study and ends when they either have an outcome of interest, are lost-to- follow-up or the follow-up period ends, whichever happens first. This period is called person-year-at-risk. This is denoted by PY in strate function's output and numer of event by D.

Rate

is calcluated using the following formula:

λ = D / PY

Confidence interval of rate

is derived using the following formula:

95\% CI (rate) = rate x Error Factor

Error Factor (rate) = exp(1.96 / √{D})

plot, if TRUE, produces a graph of the rates against the numerical code used for categories of by.

References:

1. Essential Medical Statistics, Betty R. Kirkwood & Jonathan A.C. Sterne, Second Edition. Chapter 22, page 229 & 239

Author(s)

Myo Minn Oo (Email: [e-mail] | Website: https://myominnoo.github.io/)

See Also

stmh

Examples

## Not run: 
library(survival)
data(lung)

## incidence rates
strate(lung, time, status)
strate(lung, time, status, fail = 2)

## stratified incidence rates
strate(lung, time, status, by = sex)
strate(lung, time, status, by = sex, fail = 2)
strate(lung, time, status, by = sex, fail = 2, per = 1000)
strate(lung, time, status, by = sex, fail = 2, per = 100000, rnd = 1)
strate(time, status, data = lung, per = 100000)

## create ageband
lung1 <- egen(lung, age, c(56, 61, 71), new.var = ageband)
tab(ageband, lung1)

strate(lung1, time, status, by = ageband, per = 100000)

data(pbc)
str(pbc)
strate(pbc, time, status)
strate(pbc, time, status, trt)
strate(pbc, time, status, sex)
strate(pbc, time, status, stage, per = 100000)

## End(Not run)

myominnoo/mStats_beta documentation built on Feb. 29, 2020, 8:17 a.m.