epi.conf(dat, ctype = "mean.single", method, N, design = 1,
   conf.level = 0.95)

## EXAMPLE 1:
dat <- rnorm(n = 100, mean = 0, sd = 1)
epi.conf(dat, ctype = "mean.single")

## EXAMPLE 2:
group <- c(rep("A", times = 5), rep("B", times = 5))
val = round(c(rnorm(n = 5, mean = 10, sd = 5), 
   rnorm(n = 5, mean = 7, sd = 5)), digits = 0)
dat <- data.frame(group = group, val = val)
epi.conf(dat, ctype = "mean.unpaired")

## EXAMPLE 3:
## Two paired samples (Altman et al. 2000, page 31):
## Systolic blood pressure levels were measured in 16 middle-aged men
## before and after a standard exercise test. The mean rise in systolic 
## blood pressure was 6.6 mmHg. The standard deviation of the difference
## was 6.0 mm Hg. The standard error of the mean difference was 1.49 mm Hg.

before <- c(148,142,136,134,138,140,132,144,128,170,162,150,138,154,126,116)
after <- c(152,152,134,148,144,136,144,150,146,174,162,162,146,156,132,126)
dat <- data.frame(before, after)
dat <- data.frame(cbind(before, after))
epi.conf(dat, ctype = "mean.paired", conf.level = 0.95)

## The 95% confidence interval for the population value of the mean 
## systolic blood pressure increase after standard exercise was 3.4 to 9.8
## mm Hg.

## EXAMPLE 4:
## Single sample (Altman et al. 2000, page 47):
## Out of 263 giving their views on the use of personal computers in 
## general practice, 81 thought that the privacy of their medical file
## had been reduced.

pos <- 81
neg <- (263 - 81)
dat <- as.matrix(cbind(pos, neg))
round(epi.conf(dat, ctype = "prop.single"), digits = 3)

## The 95% confidence interval for the population value of the proportion
## of patients thinking their privacy was reduced was from 0.255 to 0.366. 

## EXAMPLE 5:
## Two samples, unpaired (Altman et al. 2000, page 49):
## Goodfield et al. report adverse effects in 85 patients receiving either
## terbinafine or placebo treatment for dermatophyte onchomychois.
## Out of 56 patients receiving terbinafine, 5 patients experienced
## adverse effects. Out of 29 patients receiving a placebo, none experienced
## adverse effects.

grp1 <- matrix(cbind(5, 51), ncol = 2)
grp2 <- matrix(cbind(0, 29), ncol = 2)
dat <- as.matrix(cbind(grp1, grp2))
round(epi.conf(dat, ctype = "prop.unpaired"), digits = 3)

## The 95% confidence interval for the difference between the two groups is
## from -0.038 to +0.193.

## EXAMPLE 6:
## Two samples, paired (Altman et al. 2000, page 53):
## In a reliability exercise, 41 patients were randomly selected from those
## who had undergone a thalium-201 stress test. The 41 sets of images were
## classified as normal or not by the core thalium laboratory and, 
## independently, by clinical investigators from different centres.
## Of the 19 samples identified as ischaemic by clinical investigators 
## 5 were identified as ischaemic by the laboratory. Of the 22 samples 
## identified as normal by clinical investigators 0 were identified as 
## ischaemic by the laboratory. 

## Clinic       | Laboratory    |             |   
##              | Ischaemic     | Normal      | Total
## ---------------------------------------------------------
##  Ischaemic   | 14            | 5           | 19
##  Normal      | 0             | 22          | 22
## ---------------------------------------------------------
##  Total       | 14            | 27          | 41
## ---------------------------------------------------------

dat <- as.matrix(cbind(14, 5, 0, 22))
round(epi.conf(dat, ctype = "prop.paired", conf.level = 0.95), digits = 3)

## The 95% confidence interval for the population difference in 
## proportions is 0.011 to 0.226 or approximately +1% to +23%.

## EXAMPLE 7:
## A herd of 1000 cattle were tested for brucellosis. Four samples out of 200
## test returned a positive result. Assuming 100% test sensitivity and 
## specificity, what is the estimated prevalence of brucellosis in this 
## group of animals?

pos <- 4; pop <- 200
dat <- as.matrix(cbind(pos, pop))
epi.conf(dat, ctype = "prevalence", method = "exact", N = 1000, 
   design = 1, conf.level = 0.95) * 100

## The estimated prevalence of brucellosis in this herd is 2 cases
## per 100 cattle (95% CI 0.54 -- 5.0 cases per 100 cattle).

## EXAMPLE 8:
## The observed disease counts and population size in four areas are provided
## below. What are the the standardised morbidity ratios of disease for each
## area and their 95% confidence intervals?

obs <- c(5, 10, 12, 18); pop <- c(234, 189, 432, 812)
dat <- as.matrix(cbind(obs, pop))
round(epi.conf(dat, ctype = "smr"), digits = 2)

## EXAMPLE 9:
## A survey has been conducted to determine the proportion of broilers
## protected from a given disease following vaccination. We assume that 
## the intra-cluster correlation coefficient for protection (also known as the 
## rate of homogeneity, rho) is 0.4 and the average number of birds per
## flock is 30. A total of 5898 birds from a total of 10363 were identified
## as protected. What proportion of birds are protected and what is the 95%
## confidence interval for this estimate?

## Calculate the design effect, given rho = (design - 1) / (nbar - 1), where
## nbar equals the average number of individuals sampled per cluster:

D <- 0.4 * (30 - 1) + 1

## The design effect is 12.6. Now calculate the proportion protected:

dat <- as.matrix(cbind(5898, 10363))
epi.conf(dat, ctype = "prevalence", method = "fleiss", N = 1000000, 
   design = D, conf.level = 0.95)

## The estimated proportion of the population protected is 0.57 (95% CI
## 0.53 -- 0.60). If we had mistakenly assumed that data were a simple random 
## sample the confidence interval would have been 0.56 -- 0.58.