Analysis of Infectious Diseases using Stochastic Epidemic Models

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Documentation for package ‘RLadyBug’ version 0.7-2

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A C D H I L O P R S W

RLadyBug-package Analysis of infectious diseases using stochastic epidemic models

-- A --

abakaliki Smallpox epidemic in Abakaliki, Nigeria
abakaliki.opts Smallpox epidemic in Abakaliki, Nigeria
algo Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
algo-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
algo<- Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
algo<--method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.

-- C --

csfv CSFV Transmission Experiment
csfv.opts CSFV Transmission Experiment
csfvML CSFV Transmission Experiment
csfvML.opts CSFV Transmission Experiment
csfvTDprior CSFV Transmission Experiment
csfvTDprior.opts CSFV Transmission Experiment

-- D --

data2events Class "LBExperiment"
data2events-method Class "LBExperiment"

-- H --

hksars Hong Kong SARS outbreak 2003
hksars.opts.ml Hong Kong SARS outbreak 2003

-- I --

ignoreData Class "LBOptions"
ignoreData-method Class "LBOptions"
ignoreData<- Class "LBOptions"
ignoreData<--method Class "LBOptions"
infValues Class "LBInference" - captures results for SEIR inference
infValues-method Class "LBInference" - captures results for SEIR inference
infValues-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
infValues-method Class "LBInferenceML" - results from ML inference in SEIR models
infValues-method Class "LBInferenceMLK" - results from MLK inference in SEIR models
infValues<- Class "LBInference" - captures results for SEIR inference
infValues<--method Class "LBInference" - captures results for SEIR inference
infValues<--method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
infValues<--method Class "LBInferenceML" - results from ML inference in SEIR models
infValues<--method Class "LBInferenceMLK" - results from MLK inference in SEIR models
initBeta Class "LBOptions"
initBeta-method Class "LBOptions"
initBeta<- Class "LBOptions"
initBeta<--method Class "LBOptions"
initBetaN Class "LBOptions"
initBetaN-method Class "LBOptions"
initBetaN<- Class "LBOptions"
initBetaN<--method Class "LBOptions"
initDia Class "LBOptions"
initDia-method Class "LBOptions"
initDia<- Class "LBOptions"
initDia<--method Class "LBOptions"
initialize-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
initialize-method Class "LBOptions"
initIncu Class "LBOptions"
initIncu-method Class "LBOptions"
initIncu<- Class "LBOptions"
initIncu<--method Class "LBOptions"
initInf Class "LBOptions"
initInf-method Class "LBOptions"
initInf<- Class "LBOptions"
initInf<--method Class "LBOptions"
initsAsDataFrame Class "LBOptions"
initsAsDataFrame-method Class "LBOptions"

-- L --

ladybugExample Access files in the LadyBug directory examples directory
laevens CSFV Experiment by Laevens et. al
laevens.opts CSFV Experiment by Laevens et. al
laevens.opts.mcmc CSFV Experiment by Laevens et. al
laevensML CSFV Experiment by Laevens et. al
laevensML.opts CSFV Experiment by Laevens et. al
layoutAsDataFrame Class "LBLayout" - grid layout structure
layoutAsDataFrame-method Class "LBLayout" - grid layout structure
layoutMatrixes Class "LBLayout" - grid layout structure
layoutMatrixes-method Class "LBLayout" - grid layout structure
LBExperiment-class Class "LBExperiment"
LBInference-class Class "LBInference" - captures results for SEIR inference
LBInferenceMCMC-class Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
LBInferenceML-class Class "LBInferenceML" - results from ML inference in SEIR models
LBInferenceMLK-class Class "LBInferenceMLK" - results from MLK inference in SEIR models
LBInits Class "LBOptions"
LBInits-method Class "LBOptions"
LBInits<- Class "LBOptions"
LBInits<--method Class "LBOptions"
LBLayout-class Class "LBLayout" - grid layout structure
LBModel Class "LBOptions"
LBModel-method Class "LBOptions"
LBModel<- Class "LBOptions"
LBModel<--method Class "LBOptions"
LBOptions Class "LBOptions"
LBOptions-class Class "LBOptions"
LBOptions-method Class "LBOptions"
LBOptions-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
LBOptions<- Class "LBOptions"
LBOptions<--method Class "LBOptions"
LBOptions<--method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
LBOptionsMCMC-class Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
LBOptionsML-class Class "LBOptionsML" - maximum likelihood inference in SEIR models

-- O --

oneill Simulated data of 5 recovery times from O'Neill et. al
oneill.opts Simulated data of 5 recovery times from O'Neill et. al
optionsAsDataFrame Class "LBOptions"
optionsAsDataFrame-method Class "LBOptions"
optionsAsDataFrame-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.

-- P --

plot-method Class "LBExperiment"
plot-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models

-- R --

R0 Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
R0-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
R0-method Class "LBInferenceML" - results from ML inference in SEIR models
randomWalk Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
randomWalk-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
randomWalk<- Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
randomWalk<--method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
readSpecFile Read LadyBug files and create corresponding S4 RLadyBug objects
reset.RLadyBug.options Options of the 'RLadyBug' Package
RLadyBug Analysis of infectious diseases using stochastic epidemic models
RLadyBug.options Options of the 'RLadyBug' Package

-- S --

samplePaths Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
samplePaths-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
seed Class "LBOptions"
seed-method Class "LBOptions"
seed<- Class "LBOptions"
seed<--method Class "LBOptions"
seir Parameter estimation in SEIR-Models based on ML or MCMC
show-method Class "LBExperiment"
show-method Class "LBInference" - captures results for SEIR inference
show-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
show-method Class "LBInferenceML" - results from ML inference in SEIR models
show-method Class "LBInferenceMLK" - results from MLK inference in SEIR models
show-method Class "LBLayout" - grid layout structure
show-method Class "LBOptions"
show-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
show-method Class "LBOptionsML" - maximum likelihood inference in SEIR models
simulate-method Class "LBOptions"
summary-method Class "LBExperiment"
summary-method Class "LBInference" - captures results for SEIR inference
summary-method Class "LBInferenceMCMC" - results from MCMC inference in SEIR models
summary-method Class "LBInferenceML" - results from ML inference in SEIR models
summary-method Class "LBInferenceMLK" - results from MLK inference in SEIR models
summary-method Class "LBLayout" - grid layout structure
summary-method Class "LBOptions"
summary-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
summary-method Class "LBOptionsML" - maximum likelihood inference in SEIR models

-- W --

writeOptionFile Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
writeOptionFile-method Class "LBOptionsMCMC" - Specification of MCMC estimation in SEIR models.
writeOptionFile-method Class "LBOptionsML" - maximum likelihood inference in SEIR models