epi.sscc {epiR}R Documentation

Sample size, power or minimum detectable odds ratio for an unmatched or matched case-control study

Description

Calculates the sample size, power or minimum detectable odds ratio for an unmatched or matched case-control study.

Usage

epi.sscc(OR, p0, n, power, r = 1, rho.cc = 0, design = 1, sided.test = 2, 
   nfractional = FALSE, conf.level = 0.95, method = "unmatched", fleiss = FALSE)

Arguments

OR

scalar, the expected study odds ratio.

p0

scalar, the prevalence of exposure amongst the controls.

n

scalar, the total number of subjects in the study (i.e. the number of cases plus the number of controls).

power

scalar, the required study power.

r

scalar, the number in the control group divided by the number in the case group.

rho.cc

scalar, the correlation between case and control exposures for matched pairs. Ignored when method = "unmatched".

design

scalar, the design effect.

sided.test

use a one- or two-sided test? Use a two-sided test if you wish to evaluate whether or not the odds of exposure in cases is greater than or less than the odds of exposure in controls. Use a one-sided test to evaluate whether or not the odds of exposure in cases is greater than the odds of exposure in controls.

nfractional

logical, return fractional sample size.

conf.level

scalar, the level of confidence in the computed result.

method

a character string defining the method to be used. Options are unmatched or matched.

fleiss

logical, indicating whether or not the Fleiss correction should be applied. This argument is ignored when method = "matched".

Details

This function implements the methodology described by Dupont (1988). A detailed description of sample size calculations for case-control studies (with numerous worked examples, many of them reproduced below) is provided by Woodward (2005), pp. 381 to 426.

Value

A list containing the following:

n.total

the total number of subjects required to estimate the specified odds ratio at the desired level of confidence and power (i.e. the number of cases plus the number of controls).

n.case

the total number of case subjects required to estimate the specified odds ratio at the desired level of confidence and power.

n.control

the total number of control subjects required to estimate the specified odds ratio at the desired level of confidence and power.

power

the power of the study given the number of study subjects, the specified odds ratio and the desired level of confidence.

OR

the expected detectable odds ratio given the number of study subjects, the desired power and desired level of confidence.

Note

The power of a study is its ability to demonstrate the presence of an association, given that an association actually exists.

See the documentation for epi.sscohortc for an example using the design facility implemented in this function.

References

Dupont WD (1988) Power calculations for matched case-control studies. Biometrics 44: 1157 - 1168.

Fleiss JL (1981). Statistical Methods for Rates and Proportions. Wiley, New York.

Kelsey JL, Thompson WD, Evans AS (1986). Methods in Observational Epidemiology. Oxford University Press, London, pp. 254 - 284.

Woodward M (2005). Epidemiology Study Design and Data Analysis. Chapman & Hall/CRC, New York, pp. 381 - 426.

Examples

## EXAMPLE 1 (from Woodward 2005 p. 412):
## A case-control study of the relationship between smoking and CHD is 
## planned. A sample of men with newly diagnosed CHD will be compared for
## smoking status with a sample of controls. Assuming an equal number of 
## cases and controls, how many study subject are required to detect an 
## odds ratio of 2.0 with 0.90 power using a two-sided 0.05 test? Previous 
## surveys have shown that around 0.30 of males without CHD are smokers.

epi.sscc(OR = 2.0, p0 = 0.30, n = NA, power = 0.90, r = 1, rho.cc = 0, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "unmatched", fleiss = FALSE)

## A total of 376 men need to be sampled: 188 cases and 188 controls.


## EXAMPLE 2 (from Woodward 2005 p. 414):
## Suppose we wish to determine the power to detect an odds ratio of 2.0 
## using a two-sided 0.05 test when 188 cases and 940 controls
## are available (that is, the ratio of controls to cases is 5:1). Assume 
## the prevalence of smoking in males without CHD is 0.30.

n <- 188 + 940
epi.sscc(OR = 2.0, p0 = 0.30, n = n, power = NA, r = 5, rho.cc = 0, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "unmatched", fleiss = TRUE)

## The power of this study, with the given sample size allocation is 0.99.


## EXAMPLE 3:
## The following statement appeared in a study proposal to identify risk 
## factors for campylobacteriosis in humans:

## `We will prospectively recruit 300 culture-confirmed Campylobacter cases 
## reported under the Public Health Act. We will then recruit one control per 
## case from general practices of the enrolled cases, using frequency matching 
## by age and sex. With exposure levels of 10% (thought to be realistic 
## given past foodborne disease case control studies) this sample size 
## will provide 80% power to detect an odds ratio of 2 at the 5% alpha 
## level.'

## Confirm the statement that 300 case subjects will provide 80% power in 
## this study.

epi.sscc(OR = 2.0, p0 = 0.10, n = 600, power = NA, r = 1, rho.cc = 0.01, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "matched", fleiss = TRUE)

## If the true odds ratio for Campylobacter in exposed subjects relative to 
## unexposed subjects is 2.0 we will be able to reject the null hypothesis 
## that this odds ratio equals 1 with probability (power) 0.826. The Type I 
# error probability associated with this test of this null hypothesis is 0.05.


## EXAMPLE 4:
## We wish to conduct a case-control study to assess whether bladder cancer 
## may be associated with past exposure to cigarette smoking. Cases will be 
## patients with bladder cancer and controls will be patients hospitalised 
## for injury. It is assumed that 20% of controls will be smokers or past 
## smokers, and we wish to detect an odds ratio of 2 with power 90%. 
## Three controls will be recruited for every case. How many subjects need 
## to be enrolled in the study?

epi.sscc(OR = 2.0, p0 = 0.20, n = NA, power = 0.90, r = 3, rho.cc = 0, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "unmatched", fleiss = FALSE)

## A total of 620 subjects need to be enrolled in the study: 155 cases and 
## 465 controls.

## An alternative is to conduct a matched case-control study rather than the 
## unmatched design outlined above. One case will be matched to one control 
## and the correlation between case and control exposures for matched pairs 
## (rho) is estimated to be 0.01 (low). Using the same assumptions as those
## described above, how many study subjects will be required?

epi.sscc(OR = 2.0, p0 = 0.20, n = NA, power = 0.90, r = 1, rho.cc = 0.01, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "matched", fleiss = FALSE)

## A total of 456 subjects need to be enrolled in the study: 228 cases and 
## 228 controls.


## EXAMPLE 5:
## Code to reproduce the isograph shown in Figure 2 in Dupont (1988):
r <- 1
p0 = seq(from = 0.05, to = 0.95, length = 50)
OR <- seq(from = 1.05, to = 6, length = 100)
dat.df05 <- expand.grid(p0 = p0, OR = OR)
dat.df05$n.total <- NA

for(i in 1:nrow(dat.df05)){
   dat.df05$n.total[i] <- epi.sscc(OR = dat.df05$OR[i], p0 = dat.df05$p0[i], 
   n = NA, power = 0.80, r = 1, rho.cc = 0, design = 1, sided.test = 2, 
   nfractional = FALSE, conf.level = 0.95, method = "unmatched", 
   fleiss = FALSE)$n.total
}  

grid.n <- matrix(dat.df05$n.total, nrow = length(p0))
breaks <- c(22:30,32,34,36,40,45,50,55,60,70,80,90,100,125,150,175,
   200,300,500,1000)

par(mar = c(5,5,0,5), bty = "n")
contour(x = p0, y = OR, z = log10(grid.n), add = FALSE, levels = log10(breaks), 
   labels = breaks, xlim = c(0,1), ylim = c(1,6), las = 1, method = "flattest", 
   xlab = 'Proportion of controls exposed', ylab = "Minimum OR to detect")

## Not run: 
## The same plot using ggplot2:
library(ggplot2); library(directlabels)

p <- ggplot(data = dat.df05, aes(x = p0, y = OR, z = n.total)) +
  geom_contour(aes(colour = ..level..), breaks = breaks) +
  scale_x_continuous(limits = c(0,1), name = "Proportion of controls exposed") +
  scale_y_continuous(limits = c(1,6), name = "Minimum OR to detect")

print(direct.label(p, list("far.from.others.borders", "calc.boxes", 
   "enlarge.box", hjust = 1, vjust = 1, box.color = NA, 
   fill = "transparent", "draw.rects")))

## End(Not run)


## EXAMPLE 6:
## From page 1164 of Dupont (1988). A matched case control study is to be 
## carried out to quantify the association between exposure A and an outcome B.
## Assume the prevalence of exposure in controls is 0.60 and the 
## correlation between case and control exposures for matched pairs (rho) is 
## 0.20 (moderate). Assuming an equal number of cases and controls, how many 
## subjects need to be enrolled into the study to detect an odds ratio of 3.0 
## with 0.80 power using a two-sided 0.05 test? 

epi.sscc(OR = 3.0, p0 = 0.60, n = NA, power = 0.80, r = 1, rho.cc = 0.2, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "matched", fleiss = FALSE)

## A total of 162 subjects need to be enrolled in the study: 81 cases and 
## 81 controls. 

## How many cases and controls are required if we select three 
## controls per case?

epi.sscc(OR = 3.0, p0 = 0.60, n = NA, power = 0.80, r = 3, rho.cc = 0.2, 
   design = 1, sided.test = 2, nfractional = FALSE, conf.level = 0.95, 
   method = "matched", fleiss = FALSE)

## A total of 204 subjects need to be enrolled in the study: 51 cases and 
## 153 controls.


[Package epiR version 2.0.31 Index]