Berkey98: Five Published Trails from Berkey et al. (1998)

In metaSEM: Meta-Analysis using Structural Equation Modeling

Five Published Trails from Berkey et al. (1998)

Description

The data set includes five published trials, reported by Berkey et al. (1998), comparing surgical and non-surgical treatments for medium-severity periodontal disease, one year after treatment.

Usage

data(Berkey98)

Details

The variables are:

trial

Trial number

pub_year

Publication year

no_of_patients

Number of patients

PD

Patient improvements (mm) in probing depth

AL

Patient improvements (mm) in attachment level

var_PD

Sampling variance of PD

cov_PD_AL

Sampling covariance between PD and AD

var_AL

Sampling variance of AL

Source

Berkey, C. S., Hoaglin, D. C., Antczak-Bouckoms, A., Mosteller, F, & Colditz, G. A. (1998). Meta-analysis of multiple outcomes by regression with random effects. Statistics in Medicine, 17, 2537-2550.

Examples

data(Berkey98)

#### ML estimation method
## Multivariate meta-analysis
x <- meta(y=cbind(PD, AL), v=cbind(var_PD, cov_PD_AL, var_AL), data=Berkey98)
x <- rerun(x)
summary(x)
plot(x)

## Plot individual studies proportional to the weights
plot(x, study.weight.plot=TRUE)

## Include forest plot from the metafor package
library(metafor)
plot(x, diag.panel=TRUE, main="Multivariate meta-analysis",
     axis.label=c("PD", "AL"))
     forest( rma(yi=PD, vi=var_PD, data=Berkey98) )
     title("Forest plot of PD")
     forest( rma(yi=AL, vi=var_AL, data=Berkey98) )
     title("Forest plot of AL")

## Multivariate meta-analysis with "publication year-1979" as the predictor
summary( meta(y=cbind(PD, AL), v=cbind(var_PD, cov_PD_AL, var_AL),
              x=scale(pub_year, center=1979), data=Berkey98,
              RE.lbound=NA) )

## Multivariate meta-analysis with equality constraint on the regression coefficients
summary( meta(y=cbind(PD, AL), v=cbind(var_PD, cov_PD_AL, var_AL),
              x=scale(pub_year, center=1979), data=Berkey98,
              coef.constraints=matrix(c("0.3*Eq_slope", "0.3*Eq_slope"),
              nrow=2)) )

#### REML estimation method
## Multivariate meta-analysis
summary( reml(y=cbind(PD, AL), v=cbind(var_PD, cov_PD_AL, var_AL),
              data=Berkey98,
              model.name="Multivariate meta analysis with REML") )

## Multivariate meta-analysis with "publication year-1979" as the predictor
## Diagonal structure for the variance component
summary( reml(y=cbind(PD, AL), v=cbind(var_PD, cov_PD_AL, var_AL),
              RE.constraints=Diag(c("1e-5*Tau2_1_1", "1e-5*Tau2_2_2")),
              x=scale(pub_year, center=1979), data=Berkey98) )

metaSEM documentation built on Sept. 30, 2024, 9:21 a.m.