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### R code from vignette source 'Ch_meta_analysis.Rnw'
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### code chunk number 1: setup
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rm(list = ls())
s <- search()[-1]
s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices",
"package:utils", "package:datasets", "package:methods", "Autoloads"), s)]
if (length(s) > 0) sapply(s, detach, character.only = TRUE)
if (!file.exists("tables")) dir.create("tables")
if (!file.exists("figures")) dir.create("figures")
set.seed(290875)
options(prompt = "R> ", continue = "+ ",
width = 63, # digits = 4,
SweaveHooks = list(leftpar = function()
par(mai = par("mai") * c(1, 1.05, 1, 1))))
HSAURpkg <- require("HSAUR")
if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR"))
rm(HSAURpkg)
a <- Sys.setlocale("LC_ALL", "C")
book <- TRUE
refs <- cbind(c("AItR", "SI", "CI", "ANOVA", "MLR", "GLM",
"DE", "RP", "SA", "ALDI", "ALDII", "MA", "PCA",
"MDS", "CA"), 1:15)
ch <- function(x, book = TRUE) {
ch <- refs[which(refs[,1] == x),]
if (book) {
return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
} else {
return(paste("Chapter~\\\\ref{", ch[2], "}", sep = ""))
}
}
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### code chunk number 2: MA-smoking-OR
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library("rmeta")
data("smoking", package = "HSAUR")
smokingOR <- meta.MH(smoking[["tt"]], smoking[["tc"]],
smoking[["qt"]], smoking[["qc"]],
names = rownames(smoking))
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### code chunk number 3: MA-smoking-OR-summary
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summary(smokingOR)
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### code chunk number 4: MA-smoking-OR-plot
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plot(smokingOR, ylab = "")
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### code chunk number 5: MA-smoking-random
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smokingDSL <- meta.DSL(smoking[["tt"]], smoking[["tc"]],
smoking[["qt"]], smoking[["qc"]],
names = rownames(smoking))
print(smokingDSL)
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### code chunk number 6: MA-BCG-odds
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data("BCG", package = "HSAUR")
BCG_OR <- meta.MH(BCG[["BCGVacc"]], BCG[["NoVacc"]],
BCG[["BCGTB"]], BCG[["NoVaccTB"]],
names = BCG$Study)
BCG_DSL <- meta.DSL(BCG[["BCGVacc"]], BCG[["NoVacc"]],
BCG[["BCGTB"]], BCG[["NoVaccTB"]],
names = BCG$Study)
###################################################
### code chunk number 7: MA-BCGOR-summary
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summary(BCG_OR)
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### code chunk number 8: MA-BCGDSL-summary
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summary(BCG_DSL)
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### code chunk number 9: BCG-studyweights
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studyweights <- 1 / (BCG_DSL$tau2 + BCG_DSL$selogs^2)
y <- BCG_DSL$logs
BCG_mod <- lm(y ~ Latitude + Year, data = BCG,
weights = studyweights)
###################################################
### code chunk number 10: MA-mod-summary
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summary(BCG_mod)
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### code chunk number 11: BCG-Latitude-plot
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plot(y ~ Latitude, data = BCG, ylab = "Estimated log-OR")
abline(lm(y ~ Latitude, data = BCG, weights = studyweights))
###################################################
### code chunk number 12: MA-funnel-ex
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set.seed(290875)
sigma <- seq(from = 1/10, to = 1, length.out = 35)
y <- rnorm(35) * sigma
gr <- (y > -0.5)
layout(matrix(1:2, ncol = 1))
plot(y, 1/sigma, xlab = "Effect size", ylab = "1 / standard error")
plot(y[gr], 1/(sigma[gr]), xlim = range(y),
xlab = "Effect size", ylab = "1 / standard error")
###################################################
### code chunk number 13: MA-smoking-funnel
###################################################
funnelplot(smokingDSL$logs, smokingDSL$selogs,
summ = smokingDSL$logDSL, xlim = c(-1.7, 1.7))
abline(v = 0, lty = 2)
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