From ec5e78df126a1b5872a10a9a2a4036e962549bc4 Mon Sep 17 00:00:00 2001
From: Christian Roever <christian.roever@med.uni-goettingen.de>
Date: Mon, 21 Feb 2022 12:27:26 +0100
Subject: [PATCH] added baseline data to Karner (2014) example
---
DESCRIPTION | 2 +-
data/KarnerEtAl2014.R | 13 ++++++++++
man/KarnerEtAl2014.Rd | 51 ++++++++++++++++++++++++++--------------
man/bayesmeta-package.Rd | 2 +-
4 files changed, 49 insertions(+), 19 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 605bb35..a1f8306 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: bayesmeta
Type: Package
Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression
Version: 2.8
-Date: 2022-02-18
+Date: 2022-02-21
Authors@R: c(person(given="Christian", family="Roever", role=c("aut","cre"),
email="christian.roever@med.uni-goettingen.de",
comment=c(ORCID="0000-0002-6911-698X")),
diff --git a/data/KarnerEtAl2014.R b/data/KarnerEtAl2014.R
index 2fbad20..343f7b0 100644
--- a/data/KarnerEtAl2014.R
+++ b/data/KarnerEtAl2014.R
@@ -32,6 +32,19 @@ KarnerEtAl2014 <- cbind.data.frame("study" = c("Bateman2010a", "Bateman2010b", "
1,1,1,1,1,1,1,1,
1,1,1,1,1,2)]),
###################
+ "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,
107, 228, 147, 123, 914, 69, 30, 2987, 266, 238,
46, 360),
diff --git a/man/KarnerEtAl2014.Rd b/man/KarnerEtAl2014.Rd
index 33f6e19..3030088 100644
--- a/man/KarnerEtAl2014.Rd
+++ b/man/KarnerEtAl2014.Rd
@@ -10,20 +10,25 @@
\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{baseline.age} \tab \code{numeric} \tab mean age at baseline \cr
+ \bold{baseline.males} \tab \code{numeric} \tab proportion of males among study participants \cr
+ \bold{baseline.fev1} \tab \code{numeric} \tab mean FEV1 at baseline \cr
+ \bold{baseline.fev1pp} \tab \code{numeric} \tab mean FEV1 (percent of predicted) at baseline \cr
+ \bold{baseline.pyr} \tab \code{numeric} \tab mean number of pack-years (smoking history) \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
}
@@ -33,13 +38,15 @@
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
+ \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.
+ the original investigation. A number of study-level covariables are
+ also provided.
}
\source{C. Karner, J. Chong, P. Poole.
Tiotropium versus placebo for chronic obstructive pulmonary disease.
@@ -59,6 +66,16 @@ karner.exa <- escalc(measure="OR",
forestplot(karner.exa, title="exacerbation",
exponentiate=TRUE, xlog=TRUE,
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}
diff --git a/man/bayesmeta-package.Rd b/man/bayesmeta-package.Rd
index d1f5f5e..b39c7df 100644
--- a/man/bayesmeta-package.Rd
+++ b/man/bayesmeta-package.Rd
@@ -17,7 +17,7 @@
Package: \tab bayesmeta\cr
Type: \tab Package\cr
Version: \tab 2.8\cr
- Date: \tab 2022-02-18\cr
+ Date: \tab 2022-02-21\cr
License: \tab GPL (>=2)
}
The main functionality is provided by the \code{\link{bayesmeta}()}
--
GitLab