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

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 |