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Commit ec5e78df authored by Christian Roever's avatar Christian Roever
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added baseline data to Karner (2014) example

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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: 2022-02-18 Date: 2022-02-21
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")),
......
...@@ -32,6 +32,19 @@ KarnerEtAl2014 <- cbind.data.frame("study" = c("Bateman2010a", "Bateman2010b", " ...@@ -32,6 +32,19 @@ KarnerEtAl2014 <- cbind.data.frame("study" = c("Bateman2010a", "Bateman2010b", "
1,1,1,1,1,1,1,1, 1,1,1,1,1,1,1,1,
1,1,1,1,1,2)]), 1,1,1,1,1,2)]),
################### ###################
"baseline.age" = c(65, 65, 62, 64, 65, 67, 65, 65, 65, 65, 62, 60,
64, 63, 68, 66, 62, 65, 64, 62, 60, 64),
"baseline.males" = c(0.78, 0.74, 0.76, 0.77, 0.64, 0.60, 0.77, NA,
0.88, NA, NA, 0.61, 0.95, 0.78, 0.98, NA,
NA, 0.75, 0.86, 0.69, 0.94, 0.70),
"baseline.fev1" = c(1.10, 1.06, 1.30, 1.10, 1.00, 0.97, 1.10, 1.00,
1.40, 1.30, 2.10, 1.50, 1.20, 1.30, 1.00, 1.30,
1.30, 1.10, 1.40, 2.00, 1.10, 1.10),
"baseline.fev1pp" = c(40, 38, 45, 39, 39, 39, 38, 39, 48, 49, 73, 53,
NA, 46, 36, 50, 47, 39, 44, 66, 35, 52),
"baseline.pyr" = c(45, 48, 36, 43, NA, 51, 52, 66, 43, 37, 31, 34,
NA, NA, 68, 55, NA, 49, 44, NA, 44, 52),
###################
"tiotropium.total" = c(1989, 1337, 1236, 402, 550, 608, 260, 100, 500, 200, "tiotropium.total" = c(1989, 1337, 1236, 402, 550, 608, 260, 100, 500, 200,
107, 228, 147, 123, 914, 69, 30, 2987, 266, 238, 107, 228, 147, 123, 914, 69, 30, 2987, 266, 238,
46, 360), 46, 360),
......
...@@ -10,20 +10,25 @@ ...@@ -10,20 +10,25 @@
\bold{year} \tab \code{numeric} \tab 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{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{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{baseline.age} \tab \code{numeric} \tab mean age at baseline \cr
\bold{tiotropium.exa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} exacerbation in the treatment group \cr \bold{baseline.males} \tab \code{numeric} \tab proportion of males among study participants \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{baseline.fev1} \tab \code{numeric} \tab mean FEV1 at baseline \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{baseline.fev1pp} \tab \code{numeric} \tab mean FEV1 (percent of predicted) at baseline \cr
\bold{tiotropium.deaths} \tab \code{numeric} \tab number of deaths in the treatment group\cr \bold{baseline.pyr} \tab \code{numeric} \tab mean number of pack-years (smoking history) \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.total} \tab \code{numeric} \tab total number of patients in the treatment group \cr
\bold{tiotropium.dropout} \tab \code{numeric} \tab number of withdrawals 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{placebo.total} \tab \code{numeric} \tab total number of patients in the control 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{placebo.exa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} exacerbation in the control 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{placebo.sexa} \tab \code{numeric} \tab number of patients with \eqn{\geq 1}{>=1} \emph{severe} exacerbation in the control group \cr \bold{tiotropium.deaths} \tab \code{numeric} \tab number of deaths in the treatment 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{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{placebo.deaths} \tab \code{numeric} \tab number of deaths in the control group\cr \bold{tiotropium.dropout} \tab \code{numeric} \tab number of withdrawals in the treatment 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.total} \tab \code{numeric} \tab total number of patients in the control group \cr
\bold{placebo.dropout} \tab \code{numeric} \tab number of withdrawals 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{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 \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
} }
...@@ -33,13 +38,15 @@ ...@@ -33,13 +38,15 @@
phases. Various treatment options are available, aimed at both phases. Various treatment options are available, aimed at both
providing relief during an acute exacerbation, and at delaying overall providing relief during an acute exacerbation, and at delaying overall
disease progression. A common drug used in the management of COPD is disease progression. A common drug used in the management of COPD is
\emph{tiotropium}, which is administered via an inhaler device. Karner \emph{tiotropium}, which is administered via an inhaler device.
\emph{et al.} (2014) conducted a systematic review in order to
Karner \emph{et al.} (2014) conducted a systematic review in order to
evaluate the evidence on the effects of tiotropium in comparison to evaluate the evidence on the effects of tiotropium in comparison to
placebo. 22 placebo-controlled studies were found, and a range of placebo. 22 placebo-controlled studies were found, and a range of
endpoints and subgroups were considered. The data reproduced here 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 relate to analyses 1.1, 1.9, 1.14, 1.15, 1.19, 1.26, 1.27 and 1.28 in
the original investigation. the original investigation. A number of study-level covariables are
also provided.
} }
\source{C. Karner, J. Chong, P. Poole. \source{C. Karner, J. Chong, P. Poole.
Tiotropium versus placebo for chronic obstructive pulmonary disease. Tiotropium versus placebo for chronic obstructive pulmonary disease.
...@@ -59,6 +66,16 @@ karner.exa <- escalc(measure="OR", ...@@ -59,6 +66,16 @@ karner.exa <- escalc(measure="OR",
forestplot(karner.exa, title="exacerbation", forestplot(karner.exa, title="exacerbation",
exponentiate=TRUE, xlog=TRUE, exponentiate=TRUE, xlog=TRUE,
xlab="odds ratio") xlab="odds ratio")
# derive St. George's Respiratory Questionnaire (SGRQ) effect sizes:
karner.sgrq <- escalc(measure="MD",
yi=sgrq.md, sei=sgrq.se,
slab=study, data=KarnerEtAl2014,
subset=is.finite(KarnerEtAl2014$sgrq.md))
# show forest plot:
forestplot(karner.sgrq, title="SGRQ",
xlab="mean difference")
} }
} }
\keyword{datasets} \keyword{datasets}
...@@ -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 2022-02-18\cr Date: \tab 2022-02-21\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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