Merge pull request #29 from guido-s/master

Add some datasets used in Schwarzer et al. (2015).

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metadat
 Version: 1.3-0
-Date: 2024-01-08
+Date: 2024-01-22
 Title: Meta-Analysis Datasets
 Authors@R: c(
   person(given = "Thomas", family="White",

data-raw/.rfiles.txt

@@ -6,6 +6,7 @@
 "dat.baker2009.r"
 "dat.bangertdrowns2004.r"
 "dat.baskerville2012.r"
+"dat.bassler2004.r"
 "dat.bcg.r"
 "dat.begg1989.r"
 "dat.berkey1998.r"
@@ -20,23 +21,29 @@
 "dat.collins1985b.r"
 "dat.craft2003.r"
 "dat.crede2010.r"
+"dat.crisafulli2020.r"
+"dat.curtin2002.r"
 "dat.curtis1998.r"
 "dat.dagostino1998.r"
 "dat.damico2009.r"
 "dat.debruin2009.r"
 "dat.dogliotti2014.r"
 "dat.dong2013.r"
 "dat.dorn2007.r"
+"dat.dumouchel1994.r"
 "dat.egger2001.r"
 "dat.fine1993.r"
 "dat.franchini2012.r"
+"dat.frank2008.r"
+"dat.furukawa2003.r"
 "dat.gibson2002.r"
 "dat.graves2010.r"
 "dat.gurusamy2011.r"
 "dat.hackshaw1998.r"
 "dat.hahn2001.r"
 "dat.hannum2020.r"
 "dat.hart1999.r"
+"dat.hartmannboyce2018.r"
 "dat.hasselblad1998.r"
 "dat.hine1989.r"
 "dat.ishak2007.r"
@@ -71,8 +78,12 @@
 "dat.pritz1997.r"
 "dat.raudenbush1985.r"
 "dat.riley2003.r"
+"dat.roever2022.r"
 "dat.senn2013.r"
+"dat.spooner2002.r"
 "dat.stowe2010.r"
+"dat.tannersmith2016.r"
+"dat.ursino2021.r"
 "dat.vanhowe1999.r"
 "dat.viechtbauer2021.r"
 "dat.white2020.r"

data-raw/dat.bassler2004.r

@@ -0,0 +1,7 @@
+# Bassler D, Mitra A, Ducharme FM, J Forster J, Schwarzer G (2004).
+# Ketotifen alone or as additional medication for
+# long-term control of asthma and wheeze in children.
+# Cochrane Database of Systematic Reviews, CD001384.
+
+dat.bassler2004 <- read.csv("data-raw/dat.bassler2004.txt")
+save(dat.bassler2004, file = "data/dat.bassler2004.rda")

data-raw/dat.bassler2004.txt

@@ -0,0 +1,11 @@
+"study","Ee","Ne","Ec","Nc","blind"
+"1","Chay 1992",1,10,6,10,"Adequate blinding"
+"2","Rackham 1989",31,68,38,65,"Adequate blinding"
+"3","Van Asperen 1992",16,52,19,51,"Adequate blinding"
+"4","Croce 1995",19,39,17,36,"Method unclear"
+"5","de Benedictis 1990",7,34,35,41,"Method unclear"
+"6","Longo 1986",10,18,15,18,"Method unclear"
+"7","Montoya 1988",6,20,14,20,"Method unclear"
+"8","Mulhern 1982",6,16,8,15,"Method unclear"
+"9","Salmon",8,28,16,34,"Method unclear"
+"10","Spicak 1983",9,25,20,25,"Method unclear"

data-raw/dat.curtin2002.r

@@ -0,0 +1,7 @@
+# Curtin F, Altman DG, Elbourne D (2002).
+# Meta-analysis combining parallel and cross-over clinical trials. I:
+# Continuous outcomes.
+# Statistics in Medicine, 21, 2131-44.
+
+dat.curtin2002 <- read.csv("data-raw/dat.curtin2002.txt")
+save(dat.curtin2002, file = "data/dat.curtin2002.rda")

data-raw/dat.curtin2002.txt

@@ -0,0 +1,22 @@
+"author","year","N","mean","SE","corr"
+"1","Skrabal et al.","1981a",20,-4.5,2.1,0.49
+"2","Skrabal et al.","1981b",20,-0.5,1.7,0.54
+"3","MacGregor et al.","1982",23,-4,1.9,0.41
+"4","Khaw and Thom","1982",20,-2.4,1.1,0.83
+"5","Richards et al.","1984",12,-1,3.4,0.5
+"6","Smith et al.","1985",20,0,1.9,0.5
+"7","Kaplan et al.","1985",16,-5.8,1.6,0.65
+"8","Zoccali et al.","1985",23,-3,3,0.5
+"9","Matlou et al.","1986",36,-3,1.5,0.61
+"10","Barden et al.","1986",44,-1.5,1.4,0.44
+"11","Poulter and Sever","1986",19,2,2.2,0.36
+"12","Grobbee et al.","1987",40,-0.3,1.5,0.61
+"13","Krishna et al.","1989",10,-8,2.2,0.48
+"14","Mullen and O'Connor","1990a",24,3,2,0.5
+"15","Mullen and O'Connor","1990b",24,1.4,2,0.5
+"16","Patki et al.","1990",37,-13.1,0.7,0.53
+"17","Valdes et al.","1991",24,-3,2,0.5
+"18","Barden et al.","1991",39,-0.6,0.6,0.88
+"19","Overlack et al.","1991",12,3,2,0.5
+"20","Smith et al.","1992",22,-1.7,2.5,0.29
+"21","Fotherby and Potter","1992",18,-6,2.5,0.81

data-raw/dat.furukawa2003.r

@@ -0,0 +1,6 @@
+# Furukawa TA, McGuire H, Barbui C (2003).
+# Low dosage tricyclic antidepressants for depression.
+# Cochrane Database of Systematic Reviews, CD003197.
+
+dat.furukawa2003 <- read.csv("data-raw/dat.furukawa2003.txt")
+save(dat.furukawa2003, file = "data/dat.furukawa2003.rda")

data-raw/dat.furukawa2003.txt

@@ -0,0 +1,18 @@
+"author","Ne","Me","Se","Nc","Mc","Sc"
+"1","Blashki(75&150)",13,6.4,5.4,18,11.4,9.6
+"2","Hormazabal(86)",17,11,8.2,16,19,8.2
+"3","Jacobson(75-100)",10,17.5,8.8,6,23,8.8
+"4","Jenkins(75)",7,12.3,9.9,7,20,10.5
+"5","Lecrubier(100)",73,15.7,10.6,73,18.7,10.6
+"6","Murphy(100)",26,8.5,11,28,14.5,11
+"7","Nandi(97)",17,25.5,24,10,53.2,11.2
+"8","Petracca(100)",11,6.2,7.6,10,10,7.6
+"9","Philipp(100)",105,-8.1,3.9,46,-8.5,5.2
+"10","Rampello(100)",22,13.4,2.3,19,19.7,1.3
+"11","Reifler(83)",13,12.5,7.6,15,12.5,7.6
+"12","Rickels(70)",29,1.99,0.77,39,2.54,0.77
+"13","Robertson(75)",13,11,8.2,13,15,8.2
+"14","Rouillon(98)",78,15.8,6.8,71,17.1,7.2
+"15","Tan(70)",23,-8.5,8.6,23,-8.3,6
+"16","Tetreault(50-100)",11,51.9,18.5,11,74.3,18.5
+"17","Thompson(75)",11,8,8.1,18,10,9.7

data-raw/dat.spooner2002.csv

@@ -0,0 +1,18 @@
+"author","year","Ne","Me","Se","Nc","Mc","Sc","agegroup"
+"Boner","1988",13,13.54,13.85,13,20.77,21.46,"Children"
+"Novembre","1994f",24,15.42,8.35,24,28.46,13.84,"Children"
+"DeBenedictis","1994b",8,14.8,18.6,8,31.4,20.6,"Children"
+"Novembre","1994s",19,11,12.4,19,26.1,14.9,"Children"
+"DeBenedictis","1994a",17,14.4,11.1,17,27.4,17.3,"Children"
+"DeBenedictis","1995",13,15.7,16.8,13,29.6,18.9,"Children"
+"Boner","1989",20,15.7,13.1,20,22.7,16.47,"Children"
+"Henriksen","1988",12,17.5,13.1,12,47.2,16.47,"Children"
+"Chudry","1987",12,21.3,13.1,12,39.7,12.9,"Children"
+"Comis","1993",12,14.5,12.2,12,31.3,15.1,"Children"
+"Debelic","1986",12,29.83,15.95,12,48.08,15.08,"Children"
+"Morton","1992",16,15.83,13.43,16,38.36,18.01,"Adults"
+"Shaw","1985",8,10.27,7.02,8,34.43,10.96,"Adults"
+"Konig","1987",12,12,14.6,12,26.2,12.3,"Adults"
+"Todaro","1993",13,10.1,8.9,13,23.5,4,"Adults"
+"Roberts","1985",9,18.9,17.7,9,38.9,18.9,"Adults"
+"Oseid","1995",20,14.1,9.5,20,28.9,18,"Adults"

data-raw/dat.spooner2002.r

@@ -0,0 +1,10 @@
+# Spooner C, Saunders LD, Rowe BH (2002).
+# Nedocromil sodium for preventing exercise‐induced
+# bronchoconstriction.
+# Cochrane Database of Systematic Reviews, CD001183.
+
+dat.spooner2002 <- read.csv("data-raw/dat.spooner2002.csv")
+dat.spooner2002$agegroup <-
+  factor(dat.spooner2002$agegroup, levels = c("Children", "Adults"))
+#
+save(dat.spooner2002, file = "data/dat.spooner2002.rda")

man/dat.baker2009.Rd

@@ -26,18 +26,18 @@ The data frame contains the following columns:
    Baker, W. L., Baker, E. L., & Coleman, C. I. (2009). Pharmacologic treatments for chronic obstructive pulmonary disease: A mixed-treatment comparison meta-analysis. \emph{Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy}, \bold{29}(8), 891--905. \verb{https://doi.org/10.1592/phco.29.8.891}
 }
 \author{
-   Guido Schwarzer, \email{sc@imbi.uni-freiburg.de}, \url{https://github.com/guido-s/}
+   Guido Schwarzer, \email{guido.schwarzer@uniklinik-freiburg.de}, \url{https://github.com/guido-s/}
 }
 \examples{
 ### Show first 6 rows of the dataset
 head(dat.baker2009)
 
 \dontrun{
 ### Load netmeta package
-suppressPackageStartupMessages(library(netmeta))
+suppressPackageStartupMessages(library("netmeta"))
 
 ### Print odds ratios and confidence limits with two digits
-settings.meta(digits = 2)
+oldset <- settings.meta(digits = 2)
 
 ### Transform data from long arm-based format to contrast-based
 ### format. Argument 'sm' has to be used for odds ratio as summary
@@ -68,6 +68,9 @@ cnet
 ### Compare results of NMA and additive CNMA
 nb <- netbind(net, cnet, name = c("Standard NMA", "Additive CNMA"))
 forest(nb)
+
+### Use previous settings
+settings.meta(oldset)
 }
 }
 \seealso{

man/dat.bassler2004.Rd

@@ -0,0 +1,97 @@
+\name{dat.bassler2004}
+\docType{data}
+\alias{dat.bassler2004}
+
+\title{Studies on ketotifen alone or as additional medication for
+  long-term control of asthma and wheeze in children}
+
+\description{  
+Results from 10 trials reporting the physicians' judgement on the
+overall efficacy of ketotifen for long-term control of asthma and wheeze
+in children.
+}
+
+\usage{
+dat.bassler2004
+}
+
+\format{
+The data frame contains the following columns:
+\tabular{lll}{
+\bold{study} \tab \code{character} \tab study label \cr
+\bold{Ee} \tab \code{integer} \tab number of children with treament
+success (ketotifen group) \cr
+\bold{Ne} \tab \code{integer} \tab number of children (ketotifen group) \cr
+\bold{Ec} \tab \code{integer} \tab number of children with treament
+success (control group) \cr
+\bold{Nc} \tab \code{integer} \tab number of children (control group) \cr
+\bold{blind} \tab \code{character} \tab blinding of clinicians \cr
+}  
+}
+
+\details{
+Results from 10 trials reporting the physicians' judgement on the
+overall efficacy of Ketotifen for long-term control of asthma and wheeze
+in children. A prespecified subgroup analysis was conducted to evaluate
+whether the treatment effect is different in trials with adequate
+blinding compared to trials with inadequate / unclear blinding.
+
+This data set is used as an example in Schwarzer et al. (2015).
+}
+
+\source{
+Bassler D, Mitra A, Ducharme FM, J Forster J, Schwarzer G (2004).
+Ketotifen alone or as additional medication for long-term control of
+asthma and wheeze in children.
+\emph{Cochrane Database of Systematic Reviews}, CD001384.
+}
+
+\references{
+Schwarzer G, Carpenter JR and Rücker G (2015):
+\emph{Meta-Analysis with R (Use-R!)}.
+Springer International Publishing, Switzerland
+}
+
+\author{Guido Schwarzer, \email{guido.schwarzer@uniklinik-freiburg.de},
+  \url{https://github.com/guido-s/}}
+
+\examples{
+### Show full data set
+dat.bassler2004
+
+\dontrun{
+### Load meta package
+suppressPackageStartupMessages(library("meta"))
+
+### Use DerSimonian-Laird estimator (which was the default in meta in
+### the year 2015).
+### Furthermore, print meta-analysis results with two digits.
+oldset <- settings.meta(method.tau = "DL", digits = 2)
+
+### Calculate experimental and control event rates
+with(dat.bassler2004, summary(Ee / Ne))
+with(dat.bassler2004, summary(Ec / Nc))
+
+### Conduct meta-analysis using the inverse variance method
+mb3 <- metabin(Ee, Ne, Ec, Nc, method = "I",
+  data = dat.bassler2004, studlab = study)
+mb3
+
+### Conduct subgroup analysis comparing trials with adequate blinding
+### to trials with inadequate or unclear blinding
+mb3s <- update(mb3, subgroup = blind, print.subgroup.name = FALSE)
+mb3s
+
+### Conduct subgroup analysis assuming common between-study variance
+### in subgroups
+mb3s.c <- update(mb3s, tau.common = TRUE)
+mb3s.c
+
+### Use previous settings
+settings.meta(oldset)
+}
+}
+\keyword{datasets}
+\concept{risk ratio}
+\concept{medicine}
+\concept{subgroup analysis}

man/dat.curtin2002.Rd

@@ -0,0 +1,76 @@
+\name{dat.curtin2002}
+\docType{data}
+\alias{dat.curtin2002}
+
+\title{Studies on potassium supplementation to reduce diastolic blood
+pressure}
+
+\description{
+Results from 21 cross-over studies evaluating the effect of potassium
+supplementation to reduce diastolic blood pressure.
+}
+
+\usage{
+dat.curtin2002
+}
+
+\format{
+The data frame contains the following columns:
+\tabular{lll}{
+\bold{author} \tab \code{character} \tab first author \cr
+\bold{year} \tab \code{character} \tab year of publication \cr
+\bold{N} \tab \code{integer} \tab total sample size \cr
+\bold{mean} \tab \code{numeric} \tab mean difference in diastolic blood pressure  \cr
+\bold{SE} \tab \code{numeric} \tab standard error \cr
+\bold{corr} \tab \code{numeric} \tab within-patient correlation \cr
+}  
+}
+
+\details{
+Results from 21 cross-over studies evaluating the effect of potassium
+supplementation to reduce diastolic blood pressure (Curtin et al., 2002,
+Table II).
+
+This data set is used as an example in Schwarzer et al. (2015), Chapter
+2.}
+
+\source{
+Curtin F, Altman DG, Elbourne D (2002).
+Meta-analysis combining parallel and cross-over clinical trials. I:
+Continuous outcomes.
+\emph{Statistics in Medicine}, 21, 2131-44.
+}
+
+\references{
+Schwarzer G, Carpenter JR and Rücker G (2015):
+\emph{Meta-Analysis with R (Use-R!)}.
+Springer International Publishing, Switzerland
+}
+
+\author{Guido Schwarzer, \email{guido.schwarzer@uniklinik-freiburg.de},
+  \url{https://github.com/guido-s/}}
+
+\examples{
+### Show first five studies
+head(dat.curtin2002, 5)
+
+\dontrun{
+### Load meta package
+suppressPackageStartupMessages(library("meta"))
+
+### Use DerSimonian-Laird estimator (which was the default in meta in
+### the year 2015).
+### Furthermore, print meta-analysis results with two digits.
+oldset <- settings.meta(method.tau = "DL", digits = 2)
+
+### Conduct meta-analysis
+mg2 <- metagen(mean, SE, studlab = paste(author, year),
+  data = dat.curtin2002, sm = "MD")
+mg2
+
+### Use previous settings
+settings.meta(oldset)
+}
+}
+\keyword{datasets}
+\concept{mean difference}