## Contagious bovine pleuropneumonia

### Description

Contagious bovine pleuropneumonia (CBPP) is a major
disease of cattle in Africa, caused by a mycoplasma.
This dataset describes the serological incidence of CBPP
in zebu cattle during a follow-up survey implemented in
15 commercial herds located in the Boji district of
Ethiopia. The goal of the survey was to study the
within-herd spread of CBPP in newly infected herds. Blood
samples were quarterly collected from all animals of
these herds to determine their CBPP status. These data
were used to compute the serological incidence of CBPP
(new cases occurring during a given time period). Some
data are missing (lost to follow-up).

### Format

A data frame with 56 observations on the following 4 variables.

`herd`

A factor identifying the herd (1 to 15).

`incidence`

The number of new serological cases for a
given herd and time period.

`size`

A numeric vector describing herd size at the
beginning of a given time period.

`period`

A factor with levels `1`

to `4`

.

### Details

Serological status was determined using a competitive
enzyme-linked immuno-sorbent assay (cELISA).

### Source

Lesnoff, M., Laval, G., Bonnet, P., Abdicho, S.,
Workalemahu, A., Kifle, D., Peyraud, A., Lancelot, R.,
Thiaucourt, F. (2004) Within-herd spread of contagious
bovine pleuropneumonia in Ethiopian highlands.
*Preventive Veterinary Medicine* **64**, 27–40.

### Examples

## response as a matrix
(m1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
family = binomial, data = cbpp))
## response as a vector of probabilities and usage of argument "weights"
m1p <- glmer(incidence / size ~ period + (1 | herd), weights = size,
family = binomial, data = cbpp)
## Confirm that these are equivalent:
stopifnot(all.equal(fixef(m1), fixef(m1p), tolerance = 1e-5),
all.equal(ranef(m1), ranef(m1p), tolerance = 1e-5))
## GLMM with individual-level variability (accounting for overdispersion)
cbpp$obs <- 1:nrow(cbpp)
(m2 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd) + (1|obs),
family = binomial, data = cbpp))