# Dynamic Models with Regime-Switching

## Documentation for package ‘dynr’ version 0.1.16-91

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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.config | Check that dynr in configured properly
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
ExpandRandomAsLVModel | Extend a user-specified model to include random varibles
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 Dynamics 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