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.
herdA factor identifying the herd (1 to 15).
incidenceThe number of new serological cases for a
given herd and time period.
sizeA numeric vector describing herd size at the
beginning of a given time period.
periodA 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))
--
Dataset imported from https://www.r-project.org.