bacteria {MASS}

R Documentation

Presence of Bacteria after Drug Treatments

Description

Tests of the presence of the bacteria H. influenzae in children with otitis media in the Northern Territory of Australia.

Usage

bacteria

Format

This data frame has 220 rows and the following columns:

y

presence or absence: a factor with levels n and y.

ap

active/placebo: a factor with levels a and p.

hilo

hi/low compliance: a factor with levels hi amd lo.

week

numeric: week of test.

ID

subject ID: a factor.

trt

a factor with levels placebo, drug and drug+, a re-coding of ap and hilo.

Details

Dr A. Leach tested the effects of a drug on 50 children with a history of otitis media in the Northern Territory of Australia. The children were randomized to the drug or the a placebo, and also to receive active encouragement to comply with taking the drug.

The presence of H. influenzae was checked at weeks 0, 2, 4, 6 and 11: 30 of the checks were missing and are not included in this data frame.

Source

Dr Amanda Leach via Mr James McBroom.

References

Menzies School of Health Research 1999–2000 Annual Report. p.20. https://www.menzies.edu.au/icms_docs/172302_2000_Annual_report.pdf.

Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth edition. Springer.

Examples

contrasts(bacteria$trt) <- structure(contr.sdif(3),
     dimnames = list(NULL, c("drug", "encourage")))
## fixed effects analyses
## IGNORE_RDIFF_BEGIN
summary(glm(y ~ trt * week, binomial, data = bacteria))
summary(glm(y ~ trt + week, binomial, data = bacteria))
summary(glm(y ~ trt + I(week > 2), binomial, data = bacteria))
## IGNORE_RDIFF_END

# conditional random-effects analysis
library(survival)
bacteria$Time <- rep(1, nrow(bacteria))
coxph(Surv(Time, unclass(y)) ~ week + strata(ID),
      data = bacteria, method = "exact")
coxph(Surv(Time, unclass(y)) ~ factor(week) + strata(ID),
      data = bacteria, method = "exact")
coxph(Surv(Time, unclass(y)) ~ I(week > 2) + strata(ID),
      data = bacteria, method = "exact")

# PQL glmm analysis
library(nlme)
## IGNORE_RDIFF_BEGIN
summary(glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,
                family = binomial, data = bacteria))
## IGNORE_RDIFF_END

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