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Commit 0b257036 authored by Christian Roever's avatar Christian Roever
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added Karner (2014) example data

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DESCRIPTION
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...@@ -2,7 +2,7 @@ Package: bayesmeta ...@@ -2,7 +2,7 @@ Package: bayesmeta
Type: Package Type: Package
Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression
Version: 2.8 Version: 2.8
Date: 2021-11-04 Date: 2022-02-18
Authors@R: c(person(given="Christian", family="Roever", role=c("aut","cre"), Authors@R: c(person(given="Christian", family="Roever", role=c("aut","cre"),
email="christian.roever@med.uni-goettingen.de", email="christian.roever@med.uni-goettingen.de",
comment=c(ORCID="0000-0002-6911-698X")), comment=c(ORCID="0000-0002-6911-698X")),
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data/KarnerEtAl2014.R 0 → 100644
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#
# COPD data from:
#
# C. Karner, J. Chong, P. Poole.
# Tiotropium versus placebo for chronic obstructive pulmonary disease.
# Cochrane Database of Systematic Reviews, 7:CD009285, 2014.
# http://doi.org/10.1002/14651858.CD009285.pub3
#
# exacerbation: Analysis 1.9
# severe exacerbation: Analysis 1.14
# hospitalisation: Analysis 1.15
# mortality: Analysis 1.19
# serious adverse event: Analysis 1.27
# dropout (withdrawal): Analysis 1.28
# SGRQ: Analysis 1.1
# FEV_1: Analysis 1.26
#
KarnerEtAl2014 <- cbind.data.frame("study" = c("Bateman2010a", "Bateman2010b", "Beeh2006", "Brusasco2003",
"Casaburi2002", "Chan2007", "Cooper2010", "Covelli2005",
"Dusser2006", "Freeman2007", "Johansson2008", "Magnussen2008",
"Moita2008", "NCT00144326", "Niewoehner2005", "Powrie2007",
"Sun2007", "Tashkin2008", "Tonnel2008", "Trooster2011",
"Verkindre2006", "Voshaar2008"),
"year" = c(2010,2010,2006,2003,2002,2007,2010,2005,2006,2007,
2008,2008,2008,2005,2005,2007,2007,2008,2008,2011,
2006,2008),
"duration" = factor(c("up to 1 year","1 year or longer")[c(2,2,1,1,2,2,2,1,
2,1,1,1,1,1,1,2,
1,2,1,1,1,1)]),
"inhaler" = factor(c("dry powder","soft mist")[c(2,2,1,1,1,1,1,1,
1,1,1,1,1,1,1,1,
1,1,1,1,1,2)]),
###################
"tiotropium.total" = c(1989, 1337, 1236, 402, 550, 608, 260, 100, 500, 200,
107, 228, 147, 123, 914, 69, 30, 2987, 266, 238,
46, 360),
"tiotropium.exa" = c(685, 495, 180, 129, 198, 268, 112, 9, 213, 19,
2, 13, 6, 11, 255, 30, 0, 2001, 101, 11,
10, 43),
"tiotropium.sexa" = c(161, 78, 29, 48, 30, 51, 21, 2, 28, 2, 0, 4,
1, 2, 64, 2, 0, 759, 11, NA, 0, 2),
"tiotropium.hospi" = c(304, 198, 55, 48, 90, 105, 57, 5,
88, 7, 3, 9, 5, 6, NA, 15,
NA, 1369, 40, NA, 2, 11),
"tiotropium.deaths" = c(52, 34, 2, 1, 7, 13, 6, 0, 7, 1,
0, 0, 2, 0, 22, 1, 0, 381, 3, 0,
0, 2),
"tiotropium.sae" = c(342, 233, 63, 37, 99, 108, 63, 5, 86, 6, 3, 10,
4, 6, 140, 15, 0, 1541, 42, 10, 2, 12),
"tiotropium.dropout" = c(318, 251, 218, 62, 103, 135, 66, 10, 117, 18, 2, 5,
11, 10, 149, 21, 0, 1099, 39, 27, 1, 34),
###################
"placebo.total" = c(2002, 653, 403, 400, 371, 305, 259, 96, 510, 195,
117, 244, 164, 127, 915, 73, 30, 3006, 288, 219,
54, 181),
"placebo.exa" = c(842, 288, 80, 156, 156, 125, 102, 12, 272, 35,
4, 26, 6, 12, 296, 47, 2, 2049, 130, 24,
8, 21),
"placebo.sexa" = c(198, 44, 7, 90, 35, 19, 16, 1, 33, 1, 0, 0,
1, 0, 87, 3, 2, 811, 8, NA, 3, 0),
"placebo.hospi" = c(318, 99, 17, 90, 64, 39, 52, 5,
93, 10, 1, 3, 3, 4, NA, 13,
NA, 1357, 34, NA, 6, 5),
"placebo.deaths" = c(38, 10, 2, 5, 7, 2, 6, 0, 8, 4,
1, 2, 0, 0, 19, 2, 0, 411, 6, 0,
0, 0),
"placebo.sae" = c(336, 110,22, 52, 78, 42, 59, 5, 96, 10, 1, 5,
3, 4, 137, 11, 0, 1509, 38, 11, 6, 5),
"placebo.dropout" = c(373, 205, 90, 103, 103, 84, 96, 17, 147, 33, 4, 11,
11, 15, 245, 21, 3, 1358, 74, 21, 9, 22),
###################
"sgrq.md" = c(-2.90, -3.65, NA, -2.70, -3.44, -2.79, -4.03, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, -2.28, -4.18, NA,
-6.50, NA),
"sgrq.se" = c(0.49, 0.59, NA, 0.99, 0.92, 0.97, 1.5, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 0.38, 1.27, NA,
2.9, NA),
"fev1.md" = c(101, 141, 79, 120, 150, 100, 75, 184, 120, 60,
119, 98, 102, 70, 100, 190, 209, 107, 104, 166,
110, 134),
"fev1.se" = c(10, 6, 17, 7, 14, 20, 27, 37, 20, 23,
32, 23, 31, 56, 13, 88, 54, 7, 34, 29,
42, 19),
###################
stringsAsFactors=FALSE)
man/BaetenEtAl2013.Rd
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...@@ -57,7 +57,12 @@ ...@@ -57,7 +57,12 @@
\doi{10.1111/biom.12242}. \doi{10.1111/biom.12242}.
} }
\examples{ \examples{
# load data:
data("BaetenEtAl2013") data("BaetenEtAl2013")
# show data:
BaetenEtAl2013
\dontrun{ \dontrun{
# compute effect sizes (logarithmic odds) from the count data: # compute effect sizes (logarithmic odds) from the count data:
as <- escalc(xi=events, ni=total, slab=study, as <- escalc(xi=events, ni=total, slab=study,
...@@ -79,8 +84,8 @@ forestplot(bm, exponentiate=TRUE, xlab="odds", zero=NA) ...@@ -79,8 +84,8 @@ forestplot(bm, exponentiate=TRUE, xlab="odds", zero=NA)
# in terms of log-odds: # in terms of log-odds:
bm$summary[,"theta"] bm$summary[,"theta"]
# in terms of odds: # in terms of odds:
logodds <- bm$summary[c(2,5,6), "theta"] logodds <- exp(bm$summary[c(2,5,6), "theta"])
exp(logodds) logodds
# in terms of probabilities: # in terms of probabilities:
(exp(logodds) / (exp(logodds) + 1)) (exp(logodds) / (exp(logodds) + 1))
......
man/BucherEtAl1997.Rd
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...@@ -46,7 +46,7 @@ ...@@ -46,7 +46,7 @@
\emph{Cochrane handbook for systematic reviews of interventions}. \emph{Cochrane handbook for systematic reviews of interventions}.
Wiley and Sons, 2nd edition, 2019. Wiley and Sons, 2nd edition, 2019.
\doi{10.1002/9781119536604}. \doi{10.1002/9781119536604}.
\url{http://handbook.cochrane.org/}. \url{http://training.cochrane.org/handbook}.
C. Kiefer, S. Sturtz, R. Bender. C. Kiefer, S. Sturtz, R. Bender.
Indirect comparisons and network meta-analyses. Indirect comparisons and network meta-analyses.
......
man/KarnerEtAl2014.Rd 0 → 100644
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\name{KarnerEtAl2014}
\docType{data}
\alias{KarnerEtAl2014}
\title{COPD example data}
\description{Data on several endpoints from a systematic review in \emph{chronic obstructive pulmonary disease (COPD)}.}
\usage{data("KarnerEtAl2014")}
\format{The data frame contains the following columns:
\tabular{lll}{
\bold{study} \tab \code{character} \tab publication identifier (first author and publication year) \cr
\bold{year} \tab \code{numeric} \tab publication year \cr
\bold{duration} \tab \code{factor} \tab study duration (\eqn{<1} year vs. \eqn{\geq 1}{>=1} year) \cr
\bold{inhaler} \tab \code{factor} \tab type of inhaler investigated (\dQuote{dry powder} or \dQuote{soft mist}) \cr
\bold{tiotropium.total} \tab \code{numeric} \tab total number of patients in the treatment group\cr
\bold{tiotropium.exa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} exacerbation in the treatment group \cr
\bold{tiotropium.sexa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} \emph{severe} exacerbation in the treatment group \cr
\bold{tiotropium.hospi} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} hospitalisation (all-cause) in the treatment group \cr
\bold{tiotropium.deaths} \tab \code{numeric} \tab number of deaths in the treatment group\cr
\bold{tiotropium.sae} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} serious adverse event (non-fatal) in the treatment group \cr
\bold{tiotropium.dropout} \tab \code{numeric} \tab number of withdrawals in the treatment group \cr
\bold{placebo.total} \tab \code{numeric} \tab total number of patients in the control group \cr
\bold{placebo.exa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} exacerbation in the control group \cr
\bold{placebo.sexa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} \emph{severe} exacerbation in the control group \cr
\bold{placebo.hospi} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} hospitalisation (all-cause) in the control group \cr
\bold{placebo.deaths} \tab \code{numeric} \tab number of deaths in the control group\cr
\bold{placebo.sae} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} serious adverse event (non-fatal) in the control group \cr
\bold{placebo.dropout} \tab \code{numeric} \tab number of withdrawals in the control group \cr
\bold{sgrq.md}, \bold{sgrq.se} \tab \code{numeric} \tab mean difference and associated standard error for \emph{St. George's respiratory questionnaire (SGRQ)} total score \cr
\bold{fev1.md}, \bold{fev1.se} \tab \code{numeric} \tab mean difference and associated standard error for \emph{forced expiratory volume in 1 second (FEV1)} \cr
}
}
\details{Chronic obstructive pulmonary disease (COPD) is a chronic and
progressive condition characterized by recurrent exacerbation
phases. Various treatment options are available, aimed at both
providing relief during an acute exacerbation, and at delaying overall
disease progression. A common drug used in the management of COPD is
\emph{tiotropium}, which is administered via an inhaler device. Karner
\emph{et al.} (2014) conducted a systematic review in order to
evaluate the evidence on the effects of tiotropium in comparison to
placebo. 22 placebo-controlled studies were found, and a range of
endpoints and subgroups were considered. The data reproduced here
relate to analyses 1.1, 1.9, 1.14, 1.15, 1.19, 1.26, 1.27 and 1.28 in
the original investigation.
}
\source{C. Karner, J. Chong, P. Poole.
Tiotropium versus placebo for chronic obstructive pulmonary disease.
\emph{Cochrane Database of Systematic Reviews}, \bold{7}:CD009285, 2014.
\doi{10.1002/14651858.CD009285.pub3}.
}
\examples{
data("KarnerEtAl2014")
\dontrun{
# compute effect sizes (log odds ratios) from exacerbation count data
# (using the "metafor" package's "escalc()" function):
karner.exa <- escalc(measure="OR",
ai=tiotropium.exa, n1i=tiotropium.total,
ci=placebo.exa, n2i=placebo.total,
slab=study, data=KarnerEtAl2014)
# show forest plot:
forestplot(karner.exa, title="exacerbation",
exponentiate=TRUE, xlog=TRUE,
xlab="odds ratio")
}
}
\keyword{datasets}
man/bayesmeta-package.Rd
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...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
Package: \tab bayesmeta\cr Package: \tab bayesmeta\cr
Type: \tab Package\cr Type: \tab Package\cr
Version: \tab 2.8\cr Version: \tab 2.8\cr
Date: \tab 2021-11-04\cr Date: \tab 2022-02-18\cr
License: \tab GPL (>=2) License: \tab GPL (>=2)
} }
The main functionality is provided by the \code{\link{bayesmeta}()} The main functionality is provided by the \code{\link{bayesmeta}()}
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