dynr: Dynamic Modeling in R
Version 0.1.10-10

Intensive longitudinal data have become increasingly prevalent in various scientific disciplines. Many such data sets are noisy, multivariate, and multi-subject in nature. The change functions may also be continuous, or continuous but interspersed with periods of discontinuities (i.e., showing regime switches). The package \pkg{dynr} (Dynamic Modeling in R) is an R package that implements a set of computationally efficient algorithms for handling a broad class of linear and nonlinear discrete- and continuous-time models with regime-switching properties under the constraint of linear Gaussian measurement functions. The discrete-time models can generally take on the form of a state- space or difference equation model. The continuous-time models are generally expressed as a set of ordinary or stochastic differential equations. All estimation and computations are performed in C, but users are provided with the option to specify the model of interest via a set of simple and easy-to-learn model specification functions in R. Model fitting can be performed using single- subject time series data or multiple-subject longitudinal data.

AuthorLu Ou [aut], Michael D. Hunter [aut, cre], Sy-Miin Chow [aut]
Date of publication2017-05-21 08:04:30 UTC
MaintainerMichael D. Hunter <mhunter.ou@gmail.com>
LicenseApache License (== 2.0)
Version0.1.10-10
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("dynr")

Getting started

Package overview

Popular man pages

dynr.ggplot: The ggplot of the smoothed state estimates and the most...
dynr-package: Dynamic Modeling in R
dynrRegimes-class: The dynrRegimes Class
NonlinearDFAsim: Simulated multi-subject time series based on a dynamic factor...
plot.dynrCook: Plot method for dynrCook objects
prep.matrixDynamics: Recipe function for creating Linear Dynamcis using matrices
prep.regimes: Recipe function for creating regime switching (Markov...
See all...

All man pages Function index File listing

Man pages

coef.dynrCook: Extract fitted parameters from a dynrCook Object
confint.dynrCook: Confidence Intervals for Model Parameters
diag-character-method: Create a diagonal matrix from a character vector
dynr.cook: Cook a dynr model to estimate its free parameters
dynrCook-class: The dynrCook Class
dynr.data: Create a list of data for parameter estimation (cooking dynr)...
dynrDynamics-class: The dynrDynamics Class
dynr.ggplot: The ggplot of the smoothed state estimates and the most...
dynrInitial-class: The dynrInitial Class
dynr.ldl: LDL Decomposition for Matrices
dynrMeasurement-class: The dynrMeasurement Class
dynr.mi: Multiple Imputation of dynrModel objects
dynr.model: Create a dynrModel object for parameter estimation (cooking...
dynrModel-class: The dynrModel Class
dynrNoise-class: The dynrNoise Class
dynr-package: Dynamic Modeling in R
dynr.plotFreq: Plot of the estimated frequencies of the regimes across all...
dynrRecipe-class: The dynrRecipe Class
dynrRegimes-class: The dynrRegimes Class
dynrTrans-class: The dynrTrans Class
EMG: Single-subject time series of facial electromyography data
EMGsim: Simulated single-subject time series to capture features of...
internalModelPrep: Do internal model preparation for dynr
logLik.dynrCook: Extract the log likelihood from a dynrCook Object
names-dynrCook-method: Extract the free parameter names of a dynrCook object
names-dynrModel-method: Extract the free parameter names of a dynrModel object
nobs.dynrCook: Extract the number of observations for a dynrCook object
nobs.dynrModel: Extract the number of observations for a dynrModel object
NonlinearDFAsim: Simulated multi-subject time series based on a dynamic factor...
Oscillator: Simulated time series data a damped linear oscillator
plot.dynrCook: Plot method for dynrCook objects
plotFormula: Plot the formula from a model
PPsim: Simulated time series data for multiple eco-systems based on...
prep.formulaDynamics: Recipe function for specifying dynamic functions using...
prep.initial: Recipe function for preparing the initial conditions for the...
prep.loadings: Recipe function to quickly create factor loadings
prep.matrixDynamics: Recipe function for creating Linear Dynamcis using matrices
prep.measurement: Prepare the measurement recipe
prep.noise: Recipe function for specifying the measurement error and...
prep.regimes: Recipe function for creating regime switching (Markov...
prep.tfun: Create a dynrTrans object to handle the transformations and...
printex: The printex Method
RSPPsim: Simulated time series data for multiple eco-systems based on...
summary.dynrCook: Get the summary of a dynrCook object
vcov.dynrCook: Extract the Variance-Covariance Matrix of a dynrCook object

Functions

$,dynrCook-method Man page
$,dynrModel-method Man page
$,dynrRecipe-method Man page
$<-,dynrModel-method Man page
C2funcaddress Source code
CompileCode Source code
DollarNames.dynrCook Source code
DollarNames.dynrModel Source code
EMG Man page
EMGsim Man page
LaTeXnames Source code
Mode Source code
NonlinearDFAsim Man page
Oscillator Man page
PPsim Man page
PopBackFormula Source code
PopBackMatrix Source code
PopBackModel Source code
RSPPsim Man page
addFormulas Source code
addLLFormulas Source code
autojacob Source code
autoplot.dynrCook Man page Source code
blasMM Source code
blasMV Source code
checkAndProcessTimeArgument Source code
coProcessValuesParams Source code
coef.dynrCook Man page Source code
coef.dynrModel Man page Source code
coef.summary.dynrCook Source code
coef<- Man page
coef<-.dynrModel Man page
combineModelDataInformation Source code
confint.dynrCook Man page Source code
createGslMatrix Source code
createGslVector Source code
destroyGslMatrix Source code
destroyGslVector Source code
deviance.dynrCook Man page Source code
diag Man page
diag,character-method Man page
diag.character Man page
displayDynrCook Source code
dynr Man page
dynr-package Man page
dynr.cook Man page Source code
dynr.data Man page Source code
dynr.ggplot Man page Source code
dynr.ldl Man page Source code
dynr.mi Man page Source code
dynr.model Man page Source code
dynr.plotFreq Man page Source code
dynrCook-class Man page
dynrDebug-class Man page
dynrDynamics-class Man page
dynrDynamicsFormula-class Man page
dynrDynamicsMatrix-class Man page
dynrInitial-class Man page
dynrMeasurement-class Man page
dynrModel-class Man page
dynrNoise-class Man page
dynrRecipe-class Man page
dynrRegimes-class Man page
dynrTrans-class Man page
endProcessing Source code
endProcessing2 Source code
exchangeNamesAndNumbers Source code
exchangeNamesInFormula Source code
exchangeformulaNamesAndNumbers Source code
extractParams Source code
extractValues Source code
extractWhichParams Source code
findRegime Source code
formula2string Source code
formula2tex Source code
gslVector2Column Source code
gslVectorCopy Source code
gslcovariate.front Source code
implode Source code
internalModelPrep Man page Source code
is.null.pointer Source code
is.positive.definite Source code
is.positive.definite2 Source code
isSymbolNumberFunction Source code
logLik.dynrCook Man page Source code
makeldlchar Source code
mat2vec Source code
matrix2formula Source code
multiplot Source code
names,dynrCook-method Man page
names,dynrModel-method Man page
nobs.dynrCook Man page Source code
nobs.dynrModel Man page Source code
parseFormula Source code
parseNested Source code
plot.dynrCook Man page Source code
plotFormula Man page Source code
plotdf Source code
preProcessModel Source code
preProcessNames Source code
preProcessParams Source code
preProcessValues Source code
prep.formulaDynamics Man page Source code
prep.initial Man page Source code
prep.loadings Man page Source code
prep.matrixDynamics Man page Source code
prep.measurement Man page Source code
prep.noise Man page Source code
prep.regimes Man page Source code
prep.tfun Man page Source code
print,dynrCook-method Man page
print,dynrModel-method Man page
print,dynrRecipe-method Man page
print.summary.dynrCook Source code
printRecipeOrModel Source code
printex Man page
printex,dynrCook-method Man page
printex,dynrDynamicsFormula-method Man page
printex,dynrDynamicsMatrix-method Man page
printex,dynrInitial-method Man page
printex,dynrMeasurement-method Man page
printex,dynrModel-method Man page
printex,dynrNoise-method Man page
printex,dynrRegimes-method Man page
processFormula Source code
processModelOptionsArgument Source code
replaceDiagZero Source code
replaceNamesbyNumbers Source code
reverseldl Source code
sechol Source code
setGslMatrixElements Source code
setGslVectorElements Source code
show,dynrCook-method Man page
show,dynrModel-method Man page
show,dynrRecipe-method Man page
summary.dynrCook Man page
summaryResults Source code
trans2CFunction Source code
transldl Source code
vcov.dynrCook Man page Source code
vec2mat Source code
vecRegime Source code
xtableMatrix Source code

Files

inst
inst/REFERENCES.bib
inst/models
inst/models/passing
inst/models/passing/LinearSDEWithChecks.R
inst/models/slow
inst/models/slow/RSlinearODE.R
inst/models/slow/data
inst/models/slow/data/Model2T1000n20batch2ODETrueStates.txt
inst/models/slow/data/Model2T1000n20batch2ODEsimData.txt
inst/models/slow/data/New2CovT500n10batch1ODEsimData.txt
inst/models/slow/data/Model2T1000n20batch2ODETrueRegimes.txt
inst/models/slow/data/Model2T1000n20batch1ODETrueStates.txt
inst/models/slow/data/Model2T1000n20batch1ODEsimData.txt
inst/models/slow/data/Model2T1000n20batch1ODETrueRegimes.txt
inst/models/slow/RSlinearODE.c
inst/models/slow/RSODEmodel.c
inst/models/slow/MCTest.R
inst/models/slow/RSODEmodel2.c
inst/doc
inst/doc/InstallationForUsers.Rnw
inst/doc/InstallationForUsers.pdf
src
src/stop.c
src/adaodesolver.h
src/nlopt.h
src/adaodesolver.c
src/slsqp.h
src/print_function.c
src/debug_onmac.sh
src/ekf.h
src/neldermead.h
src/mainR.c
src/nldrmd.c
src/redblack.c
src/sbplx.c
src/data_structure.h
src/runnlopt_onair.sh
src/ekf.c
src/redblack.h
src/runnlopt_onmac.sh
src/nlopt-util.h
src/estimation.h
src/model.h
src/mainR.h
src/nlopt-internal.h
src/Makevars.in
src/general.c
src/brekfis.c
src/model.c
src/estimation.c
src/print_function.h
src/runmainC_onair.sh
src/debug_onair.sh
src/math_function.c
src/brekfis.h
src/qsort_r.c
src/numeric_derivatives.c
src/Makevars.win
src/options.c
src/wrappernegloglike.h
src/optimize.c
src/slsqp.c
src/math_function.h
src/wrappernegloglike.c
src/glue.c
src/runnlopt_onairwin.sh
src/numeric_derivatives.h
NAMESPACE
demo
demo/RSNonlinearDiscrete.R
demo/LinearSDE.R
demo/initialExo.R
demo/RSNonlinearODE.R
demo/NonlinearODE.R
demo/RSLinearDiscrete.R
demo/RSLinearDiscreteYang.R
demo/00Index
NEWS
data
data/EMGsim.txt.gz
data/RSPPsim.txt.gz
data/NonlinearDFAsim.txt.gz
data/PPsim.txt.gz
data/datalist
data/EMG.txt.gz
data/Oscillator.txt.gz
R
R/dynrModel.R
R/dynrCook.R
R/dynrVersion.R
R/dynrModelInternal.R
R/dataDoc.R
R/dynrData.R
R/dynrVersion.R.in
R/dynrPlot.R
R/dynrFuncAddress.R
R/dynrRecipe.R
R/dynrMi.R
vignettes
vignettes/InstallationForUsers.Rnw
MD5
build
build/vignette.rds
build/partial.rdb
DESCRIPTION
configure
man
man/dynrMeasurement-class.Rd
man/dynr.mi.Rd
man/EMGsim.Rd
man/plotFormula.Rd
man/vcov.dynrCook.Rd
man/dynrRegimes-class.Rd
man/prep.initial.Rd
man/plot.dynrCook.Rd
man/confint.dynrCook.Rd
man/prep.matrixDynamics.Rd
man/printex.Rd
man/internalModelPrep.Rd
man/names-dynrModel-method.Rd
man/nobs.dynrModel.Rd
man/dynr.ggplot.Rd
man/prep.regimes.Rd
man/diag-character-method.Rd
man/prep.tfun.Rd
man/prep.noise.Rd
man/coef.dynrCook.Rd
man/dynrRecipe-class.Rd
man/EMG.Rd
man/names-dynrCook-method.Rd
man/dynr.ldl.Rd
man/prep.formulaDynamics.Rd
man/PPsim.Rd
man/summary.dynrCook.Rd
man/dynrInitial-class.Rd
man/nobs.dynrCook.Rd
man/dynr.plotFreq.Rd
man/RSPPsim.Rd
man/dynrCook-class.Rd
man/NonlinearDFAsim.Rd
man/prep.measurement.Rd
man/dynrDynamics-class.Rd
man/dynrNoise-class.Rd
man/dynrModel-class.Rd
man/dynr-package.Rd
man/dynr.cook.Rd
man/logLik.dynrCook.Rd
man/Oscillator.Rd
man/dynr.data.Rd
man/dynr.model.Rd
man/dynrTrans-class.Rd
man/prep.loadings.Rd
configure.win
cleanup
tools
tools/buildNum.sh
tools/prep
tools/configureAutoConf.in
tools/testModels.R
tools/roxygenize
dynr documentation built on May 23, 2017, 9:06 a.m.

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