reconstitution: Reconstitution of blood-milk barrier after reconstitution

In parfm: Parametric Frailty Models

Description

When an udder quarter of a cow is infected (reconstitution), the blood-milk barrier is partially destroyed and particular ions can flow freely from blood to milk and vice versa, leading to higher concentrations of, for instance, the sodium concentration Na.

The objective of this study is to demonstrate that the local application of a drug based on corticosteroids decreases the time to reconstitution of the blood-milk barrier in dairy cows. We therefore consider as outcome the time until the Na concentration goes below a certain threshold (a concentration below the threshold value is considered to be normal again). Each udder quarter is separated from the three other quarters so that a quarter can be used as experimental unit to which a treatment is assigned. The Na concentration in each of the experimental units is followed up. The rear udder quarters of 100 cows are experimentally infected with Escherichia coli. After nine hours, one of the two infected udder quarters is treated locally with the active compound whereas the other is treated with placebo. Cows are followed up for 6.5 days, and are censored at that point in time if the Na concentration is still above the threshold level.

We further include parity in the study as covariate. The parity of a cow is the number of calvings (and therefore the number of lactation periods) that the cow has already experienced. Parity is often converted into a binary covariate, grouping all the cows with more than one calving in the group of multiparous cows (heifer=0) compared to the group of primiparous cows or heifers, cows with only one calving (heifer=1).

Usage

data(reconstitution)

Format

A dataframe containing 200 observations.

Cowid:

Cow's identifyier.

Time:

The time to reconstitution (in days).

Status:

Censored (0) or observed (1) event time.

Drug:

Drug or placebo application.

Heifer:

Multiparous cow (0) or primiparous cow (1).

Note

These data are downloaded from http://www.vetstat.ugent.be/research/frailty/datasets/. They are simulated data, with exactly the same structure as the real data used in the book, that could not be made publicly available.

Source

Example 1.3 of Duchateau an Janssen (2008) http://www.vetstat.ugent.be/research/frailty/datasets/

References

Duchateau L, Janssen P (2008). The frailty model. Springer. New York: Springer–Verlag.

Examples

data(reconstitution)
head(reconstitution)
                

################################################################################
# Example 3.1: The [...] frailty model for the time to blood-milk barrier      #
# reconstitution: the effect of treatment                                      #
# Duchateau and Janssen (2008, page 79)                                        #
################################################################################
pfmDrug <- parfm(Surv(Time, Status) ~ Drug,
                 cluster = "Cowid", dist = "exponential",
                 frailty = "gamma", data = reconstitution)
ci.parfm(pfmDrug)
                

################################################################################
# Example 3.2: The [...] frailty model for the time to blood-milk barrier      #
# reconstitution: the heifer effect                                            #
# Duchateau and Janssen (2008, page 82)                                        #
################################################################################
pfmHeifer <- parfm(Surv(Time, Status) ~ Heifer,
                   cluster = "Cowid", dist = "exponential",
                   frailty = "gamma", data = reconstitution)
ci.parfm(pfmHeifer)

parfm documentation built on May 2, 2019, 5 p.m.