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.

Author
Michael Hoehle and Ulrike Feldmann with contributions by Sebastian Meyer
Date of publication
2014-05-18 20:55:08
Maintainer
Michael Hoehle <hoehle@math.su.se>
License
file LICENSE
Version
0.7-2
URLs

View on R-Forge

Man pages

abakaliki
Smallpox epidemic in Abakaliki, Nigeria
csfv
CSFV Transmission Experiment
hksars
Hong Kong SARS outbreak 2003
ladybugExample
Access files in the LadyBug directory examples directory
laevens
CSFV Experiment by Laevens et. al
LBExperiment-class
Class "LBExperiment"
LBInference-class
Class "LBInference" - captures results for SEIR inference
LBInferenceMCMC-class
Class "LBInferenceMCMC" - results from MCMC inference in SEIR...
LBInferenceML-class
Class "LBInferenceML" - results from ML inference in SEIR...
LBInferenceMLK-class
Class "LBInferenceMLK" - results from MLK inference in SEIR...
LBLayout-class
Class "LBLayout" - grid layout structure
LBOptions-class
Class "LBOptions"
LBOptionsMCMC-class
Class "LBOptionsMCMC" - Specification of MCMC estimation in...
LBOptionsML-class
Class "LBOptionsML" - maximum likelihood inference in SEIR...
oneill
Simulated data of 5 recovery times from O'Neill et. al
readSpecFile
Read LadyBug files and create corresponding S4 RLadyBug...
RLadyBug.options
Options of the 'RLadyBug' Package
RLadyBug-package
Analysis of infectious diseases using stochastic epidemic...
seir
Parameter estimation in SEIR-Models based on ML or MCMC

Files in this package

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