Dynamic Models with Regime-Switching


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Documentation for package ‘dynr’ version 0.1.16-2

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dynr-package Dynamic Models with Regime-Switching
$-method The dynrCook Class
$-method The dynrModel Class
$-method The dynrRecipe Class
$<--method The dynrModel Class
autoplot.dynrCook The ggplot of the smoothed state estimates and the most likely regimes
autoplot.dynrTaste The ggplot of the outliers estimates.
coef.dynrCook Extract fitted parameters from a dynrCook Object
coef.dynrModel Extract fitted parameters from a dynrCook Object
coef<- Extract fitted parameters from a dynrCook Object
coef<-.dynrModel Extract fitted parameters from a dynrCook Object
confint.dynrCook Confidence Intervals for Model Parameters
deviance.dynrCook Extract the log likelihood from a dynrCook Object
diag Create a diagonal matrix from a character vector
diag-method Create a diagonal matrix from a character vector
diag.character Create a diagonal matrix from a character vector
dynr Dynamic Models with Regime-Switching
dynr.cook Cook a dynr model to estimate its free parameters
dynr.data Create a list of data for parameter estimation (cooking dynr) using 'dynr.cook'
dynr.flowField A Function to plot the flow or velocity field for a one or two dimensional autonomous ODE system from the phaseR package written by Michael J. Grayling.
dynr.ggplot The ggplot of the smoothed state estimates and the most likely regimes
dynr.ldl LDL Decomposition for Matrices
dynr.mi Multiple Imputation of dynrModel objects
dynr.model Create a dynrModel object for parameter estimation (cooking dynr) using 'dynr.cook'
dynr.plotFreq Plot of the estimated frequencies of the regimes across all individuals and time points based on their smoothed regime probabilities
dynr.taste Detect outliers in state space models.
dynr.taste2 Re-fit state-space model using the estimated outliers.
dynr.trajectory A Function to perform numerical integration of the chosen ODE system, for a user-specified set of initial conditions. Plots the resulting solution(s) in the phase plane. This function from the phaseR package written by Michael J. Grayling.
dynr.version Current Version String
dynrCook-class The dynrCook Class
dynrDebug-class The dynrCook Class
dynrDynamics-class The dynrDynamics Class
dynrDynamicsFormula-class The dynrDynamics Class
dynrDynamicsMatrix-class The dynrDynamics Class
dynrInitial-class The dynrInitial Class
dynrMeasurement-class The dynrMeasurement Class
dynrModel-class The dynrModel Class
dynrNoise-class The dynrNoise Class
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 facial electromyography data
getdx A wrapper function to call functions in the fda package to obtain smoothed estimated derivatives at a specified order
internalModelPrep Do internal model preparation for dynr
LinearOsc Simulated time series data for a deterministic linear damped oscillator model
LogisticSetPointSDE Simulated time series data for a stochastic linear damped oscillator model with logistic time-varying setpoints
logLik.dynrCook Extract the log likelihood from a dynrCook Object
names-method Extract the free parameter names of a dynrCook object
names-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 analysis model with nonlinear relations at the latent level
oscData Another simulated multilevel multi-subject time series of a damped oscillator model
Oscillator Simulated time series data of a damped linear oscillator
Outliers Simulated time series data for detecting outliers.
PFAsim Simulated time series data of a multisubject process factor analysis
plot.dynrCook Plot method for dynrCook objects
plotFormula Plot the formula from a model
plotGCV A function to evaluate the generalized cross-validation (GCV) values associated with derivative estimates via Bsplines at a range of specified smoothing parameter (lambda) values
PPsim Simulated time series data for multiple eco-systems based on a predator-and-prey model
predict.dynrModel 'predict' method for 'dynrModel' objects
prep.formulaDynamics Recipe function for specifying dynamic functions using formulas
prep.initial Recipe function for preparing the initial conditions for the model.
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 process noise covariance structures
prep.regimes Recipe function for creating regime switching (Markov transition) functions
prep.tfun Create a dynrTrans object to handle the transformations and inverse transformations of model paramters
print-method The dynrCook Class
print-method The dynrModel Class
print-method The dynrRecipe Class
printex The printex Method
printex-method The printex Method
RSPPsim Simulated time series data for multiple eco-systems based on a regime-switching predator-and-prey model
show-method The dynrCook Class
show-method The dynrModel Class
show-method The dynrRecipe Class
summary.dynrCook Get the summary of a dynrCook object
theta_plot A function to plot simple slopes and region of significance.
TrueInit_Y14 Simulated multilevel multi-subject time series of a Van der Pol Oscillator
VARsim Simulated time series data for multiple imputation in dynamic modeling.
vcov.dynrCook Extract the Variance-Covariance Matrix of a dynrCook object
vdpData Another simulated multilevel multi-subject time series of a Van der Pol Oscillator