RLadyBug: Analysis of Infectious Diseases using Stochastic Epidemic Models
Version 0.7-2

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.

Browse man pages Browse package API and functions Browse package files

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
URL http://www.math.su.se./~hoehle/software/RLadyBug
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RLadyBug", repos="http://R-Forge.R-project.org")

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

Functions

LBExperiment-class Man page
LBInference-class Man page
LBInferenceMCMC-class Man page
LBInferenceML-class Man page
LBInferenceMLK-class Man page
LBInits Man page
LBInits,LBOptions-method Man page
LBInits<- Man page
LBInits<-,LBOptions-method Man page
LBLayout-class Man page
LBModel Man page
LBModel,LBOptions-method Man page
LBModel<- Man page
LBModel<-,LBOptions-method Man page
LBOptions Man page
LBOptions,LBOptions-method Man page
LBOptions,LBOptionsMCMC-method Man page
LBOptions-class Man page
LBOptions<- Man page
LBOptions<-,LBOptions-method Man page
LBOptions<-,LBOptionsMCMC-method Man page
LBOptionsMCMC-class Man page
LBOptionsML-class Man page
R0 Man page
R0,LBInferenceMCMC-method Man page
R0,LBInferenceML-method Man page
RLadyBug Man page
RLadyBug-package Man page
RLadyBug.options Man page Source code
abakaliki Man page
abakaliki.opts Man page
algo Man page
algo,LBOptionsMCMC-method Man page
algo<- Man page
algo<-,LBOptionsMCMC-method Man page
csfv Man page
csfv.opts Man page
csfvML Man page
csfvML.opts Man page
csfvTDprior Man page
csfvTDprior.opts Man page
data2events Man page
data2events,LBExperiment-method Man page
draw.bar Source code
draw.slice Source code
exp2interval Source code
get.RLadyBug.options Source code
hksars Man page
hksars.opts.ml Man page
ignoreData Man page
ignoreData,LBOptions-method Man page
ignoreData<- Man page
ignoreData<-,LBOptions-method Man page
infValues Man page
infValues,LBInference-method Man page
infValues,LBInferenceMCMC-method Man page
infValues,LBInferenceML-method Man page
infValues,LBInferenceMLK-method Man page
infValues<- Man page
infValues<-,LBInference-method Man page
infValues<-,LBInferenceMCMC-method Man page
infValues<-,LBInferenceML-method Man page
infValues<-,LBInferenceMLK-method Man page
initBeta Man page
initBeta,LBOptions-method Man page
initBeta<- Man page
initBeta<-,LBOptions-method Man page
initBetaN Man page
initBetaN,LBOptions-method Man page
initBetaN<- Man page
initBetaN<-,LBOptions-method Man page
initDia Man page
initDia,LBOptions-method Man page
initDia<- Man page
initDia<-,LBOptions-method Man page
initIncu Man page
initIncu,LBOptions-method Man page
initIncu<- Man page
initIncu<-,LBOptions-method Man page
initInf Man page
initInf,LBOptions-method Man page
initInf<- Man page
initInf<-,LBOptions-method Man page
initialize,LBInferenceMCMC-method Man page
initialize,LBOptions-method Man page
initsAsDataFrame Man page
initsAsDataFrame,LBOptions-method Man page
kde2dplot Source code
ladybugExample Man page Source code
laevens Man page
laevens.opts Man page
laevens.opts.mcmc Man page
laevensML Man page
laevensML.opts Man page
layoutAsDataFrame Man page
layoutAsDataFrame,LBLayout-method Man page
layoutMatrixes Man page
layoutMatrixes,LBLayout-method Man page
loc2i Source code
loglik.klink Source code
makeLambda2 Source code
makeNeigh Source code
neighbours Source code
onAttach Source code
onLoad Source code
oneill Man page
oneill.opts Man page
optionsAsDataFrame Man page
optionsAsDataFrame,LBOptions-method Man page
optionsAsDataFrame,LBOptionsMCMC-method Man page
parseOutputMCMC Source code
parseOutputML Source code
plot,LBExperiment,missing-method Man page
plot,LBExperiment-method Man page
plot,LBInferenceMCMC,missing-method Man page
preprocess Source code
preprocess.spacetime Source code
r0 Source code
randomWalk Man page
randomWalk,LBOptionsMCMC-method Man page
randomWalk<- Man page
randomWalk<-,LBOptionsMCMC-method Man page
readSpecFile Man page Source code
reset.RLadyBug.options Man page Source code
samplePaths Man page
samplePaths,LBInferenceMCMC-method Man page
seed Man page
seed,LBOptions-method Man page
seed<- Man page
seed<-,LBOptions-method Man page
seir Man page Source code
seir.klinkenberg Source code
show,LBExperiment-method Man page
show,LBInference-method Man page
show,LBInferenceMCMC-method Man page
show,LBInferenceML-method Man page
show,LBInferenceMLK-method Man page
show,LBLayout-method Man page
show,LBOptions-method Man page
show,LBOptionsMCMC-method Man page
show,LBOptionsML-method Man page
simulate,LBOptions-method Man page
summary,LBExperiment-method Man page
summary,LBInference-method Man page
summary,LBInferenceMCMC-method Man page
summary,LBInferenceML-method Man page
summary,LBInferenceMLK-method Man page
summary,LBLayout-method Man page
summary,LBOptions-method Man page
summary,LBOptionsMCMC-method Man page
summary,LBOptionsML-method Man page
writeDataFile Source code
writeDataFileSim Source code
writeFirstPartOfDataFile Source code
writeLastPartOfDataFile Source code
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
RLadyBug documentation built on May 21, 2017, 2:53 a.m.