gemtc: Network Meta-Analysis Using Bayesian Methods
Version 0.8-2

Network meta-analyses (mixed treatment comparisons) in the Bayesian framework using JAGS. Includes methods to assess heterogeneity and inconsistency, and a number of standard visualizations.

AuthorGert van Valkenhoef, Joel Kuiper
Date of publication2016-12-23 11:56:29
MaintainerGert van Valkenhoef <gert@gertvv.nl>
LicenseGPL-3
Version0.8-2
URL http://github.com/gertvv/gemtc
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gemtc")

Getting started

Package overview

Popular man pages

blobbogram: Plot a blobbogram (AKA forest plot)
blocker: Beta blockers to prevent mortality after myocardial...
gemtc-package: GeMTC: Network meta-analysis in R
mtc.anohe: Analysis of heterogeneity (ANOHE)
mtc.model: Generate network meta-analysis models
parkinson: Mean off-time reduction in Parkinson's disease
rank.probability: Calculating rank-probabilities
See all...

All man pages Function index File listing

Man pages

atrialFibrillation: Prevention of stroke in atrial fibrillation patients
blobbogram: Plot a blobbogram (AKA forest plot)
blocker: Beta blockers to prevent mortality after myocardial...
certolizumab: Certolizumab Pegol (CZP) for Rheumatoid Arthritis
depression: Treatment response in major depression
dietfat: Effects of low-fat diets on mortality
gemtc-package: GeMTC: Network meta-analysis in R
hfPrevention: Statins versus placebo in primary and secondary prevention of...
ll.call: Call a likelihood/link-specific function
mtc.anohe: Analysis of heterogeneity (ANOHE)
mtc.data.studyrow: Convert one-study-per-row datasets
mtc.deviance: Inspect residual deviance
mtc.hy.prior: Set priors for the heterogeneity parameter
mtc.model: Generate network meta-analysis models
mtc.network: Create an mtc.network
mtc.nodesplit: Node-splitting analysis of inconsistency
mtc.run: Running an 'mtc.model' using an MCMC sampler
parkinson: Mean off-time reduction in Parkinson's disease
plotCovariateEffect: Plot treatment effects versus covariate values
rank.probability: Calculating rank-probabilities
read.mtc.network: Read mtc.network from legacy GeMTC XML files (.gemtc)
relative.effect: Calculating relative effects
relative.effect.table: Table of relative effects
smoking: Psychological treatments to aid smoking cessation
thrombolytic: Thrombolytic treatment after acute myocardial infarction

Functions

absolute.one.center Source code
add.group Source code
add.group.label Source code
all.pair.matrix Source code
alpha.ab Source code
arm.index.matrix Source code
arrayize Source code
as.character.mtc.hy.prior Source code
as.data.frame.mtc.relative.effect.table Man page Source code
as.mcmc.list.mtc.result Man page Source code
as.treatment.factor Source code
atrialFibrillation Man page
blobbogram Man page Source code
blobbogram.styles.default Source code
blocker Man page
certolizumab Man page
check.duplicated.treatments Source code
cob.matrix Source code
coerce.factor Source code
computeDeviance Source code
connect.mds.forest Source code
consistency.relative.effect.matrix Source code
correction.counts Source code
decompose.network Source code
decompose.trials Source code
decompose.variance Source code
depression Man page
devfit.ab Source code
devfit.re Source code
deviance.binom Source code
deviance.monitors Source code
deviance.monitors.fitted.ab Source code
deviance.monitors.fitted.re Source code
deviance.monitors.residuals.ab Source code
deviance.monitors.residuals.re Source code
deviance.normal Source code
deviance.poisson Source code
dietfat Man page
draw.page Source code
edge.length Source code
edges.create Source code
extract.comparisons Source code
filter.network Source code
fitted.values.parameter.binom Source code
fitted.values.parameter.normal Source code
fitted.values.parameter.poisson Source code
fix.network Source code
fixna Source code
forest Man page Source code
forest.mtc.relative.effect.table Man page Source code
forest.mtc.result Man page Source code
formatCI Source code
func.param.matrix.consistency Source code
func.param.matrix.nodesplit Source code
func.param.matrix.regression Source code
func.param.matrix.ume Source code
gemtc Man page
gemtc-package Man page
get.row.groups Source code
graph.create Source code
grob.ci Source code
guess.scale Source code
has.indirect.evidence Source code
hfPrevention Man page
i.squared Source code
inits.info.binom.cloglog Source code
inits.info.binom.log Source code
inits.info.binom.logit Source code
inits.info.normal.identity Source code
inits.info.poisson.log Source code
inits.to.monitors Source code
isRegressionControl Source code
likelihood.arm.list Source code
ll.call Man page Source code
ll.defined Source code
local.center Source code
minimum.diameter.spanning.tree Source code
mle.pooled.effect Source code
mtc Man page
mtc.anohe Man page Source code
mtc.arm.mle.binom.cloglog Source code
mtc.arm.mle.binom.log Source code
mtc.arm.mle.binom.logit Source code
mtc.arm.mle.normal.identity Source code
mtc.arm.mle.poisson.log Source code
mtc.basic.parameters Source code
mtc.build.syntaxModel Source code
mtc.code.likelihood.binom.cloglog Source code
mtc.code.likelihood.binom.log Source code
mtc.code.likelihood.binom.logit Source code
mtc.code.likelihood.normal.identity Source code
mtc.code.likelihood.poisson.log Source code
mtc.comparisons Source code
mtc.comparisons.baseline Source code
mtc.data.studyrow Man page Source code
mtc.deviance Man page Source code
mtc.devplot Man page Source code
mtc.hy.empirical.lor Man page Source code
mtc.hy.prior Man page Source code
mtc.init Source code
mtc.init.fixRegressionDimensions Source code
mtc.init.hy Source code
mtc.init.mle.baseline Source code
mtc.init.mle.basic Source code
mtc.init.mle.regression Source code
mtc.init.mle.relative Source code
mtc.levplot Man page Source code
mtc.linearModel.matrix Source code
mtc.merge.data Source code
mtc.model Man page Source code
mtc.model.call Source code
mtc.model.code Source code
mtc.model.consistency Source code
mtc.model.data Source code
mtc.model.defined Source code
mtc.model.graph Source code
mtc.model.name.consistency Source code
mtc.model.name.nodesplit Source code
mtc.model.name.regression Source code
mtc.model.name.ume Source code
mtc.model.name.use Source code
mtc.model.nodesplit Source code
mtc.model.regression Source code
mtc.model.run Source code
mtc.model.ume Source code
mtc.model.use Source code
mtc.network Man page Source code
mtc.network.graph Source code
mtc.network.validate Source code
mtc.nodesplit Man page Source code
mtc.nodesplit.comparisons Man page Source code
mtc.nr.comparisons Source code
mtc.rel.mle.binom.cloglog Source code
mtc.rel.mle.binom.log Source code
mtc.rel.mle.binom.logit Source code
mtc.rel.mle.normal.identity Source code
mtc.rel.mle.poisson.log Source code
mtc.result Man page
mtc.run Man page Source code
mtc.sample Source code
mtc.studies.list Source code
mtc.study.design Source code
mtc.study.treatment.matrix Source code
mtc.treatment.pairs Source code
mtc.validate.data.ab Source code
mtc.validate.data.re Source code
nice.value Source code
nodesplit.relative.effect.matrix Source code
nodesplit.rewrite.data.ab Source code
nodesplit.rewrite.data.re Source code
nodesplit.rewrite.studies Source code
non.edges Source code
parkinson Man page
parkinson_diff Man page
parkinson_shared Man page
plot.mtc.anohe Man page Source code
plot.mtc.anohe.summary Man page Source code
plot.mtc.deviance Man page Source code
plot.mtc.model Man page Source code
plot.mtc.network Man page Source code
plot.mtc.nodesplit Man page Source code
plot.mtc.nodesplit.summary Man page Source code
plot.mtc.rank.probability Man page Source code
plot.mtc.result Man page Source code
plotCovariateEffect Man page Source code
powerAdjustIncludedStudies Source code
print.mtc.anohe Man page Source code
print.mtc.anohe.summary Man page Source code
print.mtc.model Man page Source code
print.mtc.network Source code
print.mtc.nodesplit Man page Source code
print.mtc.nodesplit.summary Man page Source code
print.mtc.rank.probability Man page Source code
print.mtc.relative.effect.table Man page Source code
print.mtc.result Man page Source code
print.summary.mtc.result Source code
rank.probability Man page Source code
read.mtc.network Man page Source code
read.template Source code
regressionAdjustMatrix Source code
regressionClassMap Source code
regressionParams Source code
rel.mle.ab Source code
rel.mle.re Source code
relative.effect Man page Source code
relative.effect.table Man page Source code
relative.effect.table.to.matrix Source code
remove.onearm Source code
required.columns.ab.normal.identity Source code
required.columns.ab.poisson.log Source code
required.columns.counts Source code
scale.limit.inits.poisson.log Source code
scale.log.binom.cloglog Source code
scale.log.binom.log Source code
scale.log.binom.logit Source code
scale.log.normal.identity Source code
scale.log.poisson.log Source code
scale.name.binom.cloglog Source code
scale.name.binom.log Source code
scale.name.binom.logit Source code
scale.name.normal.identity Source code
scale.name.poisson.log Source code
smoking Man page
solveLP Source code
spanning.tree.mtc.result Source code
sparse.relative.effect.matrix Source code
standardize.data Source code
standardize.treatments Source code
stopIfNotConsistent Source code
study.baseline.priors.binom.cloglog Source code
study.baseline.priors.binom.log Source code
study.baseline.priors.binom.logit Source code
study.baseline.priors.normal.identity Source code
study.baseline.priors.poisson.log Source code
study.seq.ab Source code
study.seq.re Source code
summary.mtc.anohe Man page Source code
summary.mtc.model Man page Source code
summary.mtc.network Source code
summary.mtc.nodesplit Man page Source code
summary.mtc.result Man page Source code
template.block.sub Source code
text.style Source code
thrombolytic Man page
treatment.id.to.description Source code
treatment.pairs Source code
tree.relative.effect Source code
validate.data.counts Source code
validate.data.normal.identity Source code
validate.data.poisson.log Source code

Files

inst
inst/gemtc.likelihood.poisson.txt
inst/gemtc.fixedeffect.txt
inst/gemtc.randomeffects.txt
inst/gemtc.releffect.likelihood.rm.txt
inst/gemtc.model.use.template.txt
inst/gemtc.armeffect.likelihood.txt
inst/gemtc.releffect.likelihood.r2.txt
inst/gemtc.likelihood.normal.txt
inst/gemtc.likelihood.normal.power.txt
inst/gemtc.likelihood.poisson.power.txt
inst/gemtc.releffect.likelihood.power.rm.txt
inst/gemtc.likelihood.binom.txt
inst/extdata
inst/extdata/luades-smoking.gemtc
inst/extdata/parkinson.ns.rds
inst/extdata/parkinson.gemtc
inst/extdata/luades-smoking.samples.gz
inst/gemtc.releffect.likelihood.power.r2.txt
inst/gemtc.model.template.txt
inst/gemtc.likelihood.binom.power.txt
tests
tests/data
tests/data/studyrow
tests/data/studyrow/tsd2-7.data.txt
tests/data/studyrow/tsd2-2.data.txt
tests/data/studyrow/tsd2-5.data.txt
tests/data/studyrow/tsd2-5.out.txt
tests/data/studyrow/tsd2-3.out.txt
tests/data/studyrow/tsd2-2.out.txt
tests/data/studyrow/tsd2-8.data1.txt
tests/data/studyrow/tsd2-8.out1.txt
tests/data/studyrow/tsd2-8.out2.txt
tests/data/studyrow/tsd2-8.data2.txt
tests/data/studyrow/tsd2-1.data.txt
tests/data/studyrow/tsd2-1.out.txt
tests/data/studyrow/tsd2-7.out.txt
tests/data/studyrow/tsd2-3.data.txt
tests/data/riskratio.data.txt
tests/data/diabetes-surv.summaries.txt
tests/data/welton-diastolic.summaries.txt
tests/data/diabetes-surv.data.txt
tests/data/parkinson-shared.summaries.txt
tests/data/dietfat.re.summaries.txt
tests/data/luades-thrombolytic.summaries.txt
tests/data/smoking-ume.data.txt
tests/data/diabetes-surv.fe.summaries.txt
tests/data/riskratio.summaries.txt
tests/data/welton-cholesterol.summaries.txt
tests/data/welton-cholesterol.gemtc
tests/data/rr-pairwise.csv
tests/data/ns-complex.csv
tests/data/smoking-ume.summaries.txt
tests/data/dietfat.fe.summaries.txt
tests/data/anohe-breaking.gemtc
tests/data/cipriani-efficacy.summaries.txt
tests/data/parkinson-diff.summaries.txt
tests/data/luades-smoking.summaries.txt
tests/data/welton-diastolic.gemtc
tests/data/parkinson.summaries.txt
tests/data/welton-systolic.gemtc
tests/data/welton-systolic.summaries.txt
tests/test.R
tests/testthat
tests/testthat/test-unit-read.mtc.network.R
tests/testthat/test-unit-inits.to.monitors.R
tests/testthat/test-unit-arrayize.R
tests/testthat/test-regress-anohe.R
tests/testthat/test-unit-template.R
tests/testthat/test-validate-welton-diastolic.R
tests/testthat/test-unit-minimum.diameter.spanning.tree.R
tests/testthat/test-unit-mtc.model_duparm.R
tests/testthat/test-unit-ll.binom.logit.R
tests/testthat/test-unit-regression.R
tests/testthat/test-validate-parkinson-diff.R
tests/testthat/test-unit-mtc.model.ume.R
tests/testthat/test-validate-parkinson-shared.R
tests/testthat/test-validate-riskratio.R
tests/testthat/test-unit-mtc.model.use.R
tests/testthat/test-unit-mtc.model_inits.R
tests/testthat/helper-validate.R
tests/testthat/test-unit-mtc.model.graph.R
tests/testthat/test-unit-ll.binom.log.R
tests/testthat/test-validate-welton-systolic.R
tests/testthat/test-validate-dietfat-fe.R
tests/testthat/test-validate-diabetes-surv-fe.R
tests/testthat/helper-regress.R
tests/testthat/test-unit-ll.poisson.log.R
tests/testthat/test-unit-mtc.nr.comparisons.R
tests/testthat/test-unit-ll.R
tests/testthat/test-regress-models.R
tests/testthat/test-unit-mtc.network_data.re.R
tests/testthat/test-validate-diabetes-surv.R
tests/testthat/test-validate-luades-smoking.R
tests/testthat/test-validate-dietfat-re.R
tests/testthat/test-unit-nodesplit.R
tests/testthat/test-unit-has.indirect.evidence.R
tests/testthat/test-validate-smoking-ume.R
tests/testthat/test-validate-luades-thrombolytic.R
tests/testthat/test-unit-decompose.R
tests/testthat/test-unit-mtc.model_data.R
tests/testthat/test-unit-mtc.hy.prior.R
tests/testthat/test-unit-mtc.study.treatment.matrix.R
tests/testthat/test-unit-mtc.model.nodesplit.R
tests/testthat/test-unit-allpairs.R
tests/testthat/test-unit-relative.effect.R
tests/testthat/test-validate-welton-cholesterol.R
tests/testthat/test-validate-cipriani-efficacy.R
tests/testthat/test-validate-parkinson.R
tests/testthat/test-unit-mtc.model_columns.R
tests/testthat/test-unit-mtc.model.consistency.R
tests/testthat/test-unit-relative.effect.table.R
tests/testthat/test-unit-studyrow.R
src
src/Makevars
src/rank.c
NAMESPACE
NEWS
data
data/smoking.rdata
data/depression.rdata
data/dietfat.rdata
data/certolizumab.rdata
data/parkinson-diff.rdata
data/hfPrevention.rdata
data/parkinson-shared.rdata
data/atrialFibrillation.rdata
data/parkinson.rdata
data/thrombolytic.rdata
data/blocker.rdata
R
R/inits.R
R/mtc.model.regression.R
R/mtc.model.nodesplit.R
R/mtc.data.studyrow.R
R/regression.R
R/arrayize.R
R/priors.R
R/anohe.R
R/mtc.model.consistency.R
R/stopIfNotConsistent.R
R/mtc.model.R
R/nodesplit.R
R/data.R
R/solveLP.R
R/template.R
R/code.R
R/mtc.model.use.R
R/ll-helper.counts.R
R/relative.effect.R
R/rank.probability.R
R/ll.call.R
R/likelihoods.R
R/mtc.network.xml.R
R/deviance.R
R/mtc.network.R
R/mtc.run.R
R/ll.binom.log.R
R/ll.poisson.log.R
R/mtc.hy.prior.R
R/ll.binom.logit.R
R/relative.effect.table.R
R/mtc.result.R
R/mtc.model.ume.R
R/blobbogram.R
R/ll.normal.identity.R
R/plotCovariateEffect.R
R/minimum.diameter.spanning.tree.R
R/ll.binom.cloglog.R
R/forest.R
MD5
DESCRIPTION
man
man/rank.probability.Rd
man/figures
man/figures/parkinson.png
man/figures/parkinson.pdf
man/thrombolytic.Rd
man/hfPrevention.Rd
man/mtc.deviance.Rd
man/mtc.run.Rd
man/mtc.nodesplit.Rd
man/mtc.anohe.Rd
man/dietfat.Rd
man/blocker.Rd
man/read.mtc.network.Rd
man/mtc.network.Rd
man/ll.call.Rd
man/mtc.hy.prior.Rd
man/relative.effect.table.Rd
man/depression.Rd
man/certolizumab.Rd
man/gemtc-package.Rd
man/mtc.model.Rd
man/smoking.Rd
man/atrialFibrillation.Rd
man/mtc.data.studyrow.Rd
man/relative.effect.Rd
man/blobbogram.Rd
man/parkinson.Rd
man/plotCovariateEffect.Rd
gemtc documentation built on May 19, 2017, 9:20 a.m.