RLadyBug: Analysis of Infectious Diseases using Stochastic Epidemic Models

Analysis of small scale infectious disease data using stochastic Susceptible-Exposed-Infectious-Recovered (SEIR) models. The R package wraps functionality of the Java program LadyBug, i.e. a Java virtual machine has to be installed on your computer.

AuthorMichael Hoehle and Ulrike Feldmann with contributions by Sebastian Meyer
Date of publication2014-05-18 20:55:08
MaintainerMichael Hoehle <hoehle@math.su.se>
Licensefile LICENSE
Version0.7-2
http://www.math.su.se./~hoehle/software/RLadyBug

View on R-Forge

Functions

abakaliki Man page
abakaliki.opts Man page
algo Man page
algo<- Man page
algo<-,LBOptionsMCMC-method Man page
algo,LBOptionsMCMC-method Man page
csfv Man page
csfvML Man page
csfvML.opts Man page
csfv.opts Man page
csfvTDprior Man page
csfvTDprior.opts Man page
data2events Man page
data2events,LBExperiment-method Man page
hksars Man page
hksars.opts.ml Man page
ignoreData Man page
ignoreData<- Man page
ignoreData<-,LBOptions-method Man page
ignoreData,LBOptions-method Man page
infValues Man page
infValues<- Man page
infValues<-,LBInferenceMCMC-method Man page
infValues,LBInferenceMCMC-method Man page
infValues<-,LBInference-method Man page
infValues,LBInference-method Man page
infValues<-,LBInferenceMLK-method Man page
infValues,LBInferenceMLK-method Man page
infValues<-,LBInferenceML-method Man page
infValues,LBInferenceML-method Man page
initBeta Man page
initBeta<- Man page
initBeta<-,LBOptions-method Man page
initBeta,LBOptions-method Man page
initBetaN Man page
initBetaN<- Man page
initBetaN<-,LBOptions-method Man page
initBetaN,LBOptions-method Man page
initDia Man page
initDia<- Man page
initDia<-,LBOptions-method Man page
initDia,LBOptions-method Man page
initialize,LBInferenceMCMC-method Man page
initialize,LBOptions-method Man page
initIncu Man page
initIncu<- Man page
initIncu<-,LBOptions-method Man page
initIncu,LBOptions-method Man page
initInf Man page
initInf<- Man page
initInf<-,LBOptions-method Man page
initInf,LBOptions-method Man page
initsAsDataFrame Man page
initsAsDataFrame,LBOptions-method Man page
ladybugExample Man page
laevens Man page
laevensML Man page
laevensML.opts Man page
laevens.opts Man page
laevens.opts.mcmc Man page
layoutAsDataFrame Man page
layoutAsDataFrame,LBLayout-method Man page
layoutMatrixes Man page
layoutMatrixes,LBLayout-method Man page
LBExperiment-class Man page
LBInference-class Man page
LBInferenceMCMC-class Man page
LBInferenceML-class Man page
LBInferenceMLK-class Man page
LBInits Man page
LBInits<- Man page
LBInits<-,LBOptions-method Man page
LBInits,LBOptions-method Man page
LBLayout-class Man page
LBModel Man page
LBModel<- Man page
LBModel<-,LBOptions-method Man page
LBModel,LBOptions-method Man page
LBOptions Man page
LBOptions<- Man page
LBOptions-class Man page
LBOptions<-,LBOptionsMCMC-method Man page
LBOptions,LBOptionsMCMC-method Man page
LBOptions<-,LBOptions-method Man page
LBOptions,LBOptions-method Man page
LBOptionsMCMC-class Man page
LBOptionsML-class Man page
oneill Man page
oneill.opts Man page
optionsAsDataFrame Man page
optionsAsDataFrame,LBOptionsMCMC-method Man page
optionsAsDataFrame,LBOptions-method Man page
plot,LBExperiment-method Man page
plot,LBExperiment,missing-method Man page
plot,LBInferenceMCMC,missing-method Man page
R0 Man page
R0,LBInferenceMCMC-method Man page
R0,LBInferenceML-method Man page
randomWalk Man page
randomWalk<- Man page
randomWalk<-,LBOptionsMCMC-method Man page
randomWalk,LBOptionsMCMC-method Man page
readSpecFile Man page
reset.RLadyBug.options Man page
RLadyBug Man page
RLadyBug.options Man page
RLadyBug-package Man page
samplePaths Man page
samplePaths,LBInferenceMCMC-method Man page
seed Man page
seed<- Man page
seed<-,LBOptions-method Man page
seed,LBOptions-method Man page
seir Man page
show,LBExperiment-method Man page
show,LBInferenceMCMC-method Man page
show,LBInference-method Man page
show,LBInferenceMLK-method Man page
show,LBInferenceML-method Man page
show,LBLayout-method Man page
show,LBOptionsMCMC-method Man page
show,LBOptions-method Man page
show,LBOptionsML-method Man page
simulate,LBOptions-method Man page
summary,LBExperiment-method Man page
summary,LBInferenceMCMC-method Man page
summary,LBInference-method Man page
summary,LBInferenceMLK-method Man page
summary,LBInferenceML-method Man page
summary,LBLayout-method Man page
summary,LBOptionsMCMC-method Man page
summary,LBOptions-method Man page
summary,LBOptionsML-method Man page
writeOptionFile Man page
writeOptionFile,LBOptionsMCMC-method Man page
writeOptionFile,LBOptionsML-method Man page

Files

DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS
R
R/AllClass.R R/AllGeneric.R R/Experiment.R R/Inference.R R/InferenceMCMC.R R/InferenceML.R R/InferenceMLK.R R/Layout.R R/Options.R R/OptionsMCMC.R R/OptionsML.R R/RLadyBugOptions.R R/functions.R R/zzz.R
data
data/abakaliki.RData
data/csfv.RData
data/csfvML.RData
data/csfvTDprior.RData
data/hksars.RData
data/laevens.RData
data/laevensML.RData
data/oneill.RData
demo
demo/00Index
demo/article-csda.R demo/simulate.R
inst
inst/CITATION
inst/LadyBug
inst/LadyBug/LICENSE.txt
inst/LadyBug/README.txt
inst/LadyBug/bin
inst/LadyBug/bin/LICENSE.txt
inst/LadyBug/bin/hydra.jar
inst/LadyBug/bin/ladybug.jar
inst/LadyBug/bin/ladybug.sh
inst/LadyBug/bin/simsellke.sh
inst/LadyBug/examples
inst/LadyBug/examples/README.txt
inst/LadyBug/examples/abakaliki
inst/LadyBug/examples/abakaliki/README.txt
inst/LadyBug/examples/abakaliki/abakaliki.data
inst/LadyBug/examples/abakaliki/mcmc.sir
inst/LadyBug/examples/csfv
inst/LadyBug/examples/csfv/README.txt
inst/LadyBug/examples/csfv/csfv-TDprior.data
inst/LadyBug/examples/csfv/csfv-ml.data
inst/LadyBug/examples/csfv/csfv.data
inst/LadyBug/examples/csfv/csfv.txt
inst/LadyBug/examples/csfv/mcmc.sir
inst/LadyBug/examples/csfv/ml.sir
inst/LadyBug/examples/laevens
inst/LadyBug/examples/laevens/laevens-ml.data
inst/LadyBug/examples/laevens/laevens.data
inst/LadyBug/examples/laevens/mcmc.sir
inst/LadyBug/examples/laevens/ml.sir
inst/LadyBug/examples/oneill
inst/LadyBug/examples/oneill/mcmc.sir
inst/LadyBug/examples/oneill/oneill.data
inst/LadyBug/examples/sim
inst/LadyBug/examples/sim/4x2.data
inst/LadyBug/examples/sim/8x16.data
inst/LadyBug/examples/sim/8x8.data
inst/LadyBug/examples/sim/README.txt
inst/LadyBug/examples/sim/mcmc.sir
inst/LadyBug/examples/sim/ml.sir
inst/LadyBug/examples/sim/show.R
inst/LadyBug/examples/sim/sim8x16-1.pdf
inst/LadyBug/examples/sim/sim8x16-2.pdf
inst/LadyBug/examples/sim/sim8x16-3.pdf
inst/LadyBug/examples/sim/sim8x16-4.pdf
inst/LadyBug/examples/sim/sim8x16-5.pdf
inst/LadyBug/examples/sim/sim8x16-6.pdf
inst/LadyBug/examples/sim/sim8x16-7.pdf
inst/LadyBug/examples/sim/sim8x16-8.pdf
man
man/LBExperiment-class.Rd man/LBInference-class.Rd man/LBInferenceMCMC-class.Rd man/LBInferenceML-class.Rd man/LBInferenceMLK-class.Rd man/LBLayout-class.Rd man/LBOptions-class.Rd man/LBOptionsMCMC-class.Rd man/LBOptionsML-class.Rd man/RLadyBug-package.Rd man/RLadyBug.options.Rd man/abakaliki.Rd man/csfv.Rd man/hksars.Rd man/ladybugExample.Rd man/laevens.Rd man/oneill.Rd man/readSpecFile.Rd man/seir.Rd
test
test/LadyBug.R test/runit.ladybug.r test/runit.plot.r test/test_r_unit.r

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.