# Linear Dynamical System Reconstruction

## Documentation for package ‘ldsr’ version 0.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calculate_metrics | Reconstruction metrics
call_method | Call a reconstruction method
corr | Pearson's correlation
cvLDS | Cross validate LDS model. This is a wrapper for LDS_reconstruction
cvPCR | Cross validation of PCR reconstruction.
exp_ci | Exponential confidence interval
inv_boxcox | Inverse Box-Cox transform
Kalman_smoother | Implement Kalman smoothing
KGE | Kling-Gupta Efficiency
LDS_BFGS | Learn LDS with L-BFGS-B
LDS_BFGS_with_update | Learn LDS with L-BFGS-B
LDS_EM | Learn LDS model
LDS_EM_restart | Learn LDS model with multiple initial conditions
LDS_GA | Learn a linear dynamical system using Genetic Algorithm.
LDS_reconstruction | Learn LDS model.
LDS_rep | Multiple LDS replicates
make_init | Make initial values for parameters.
make_Z | Make cross-validation folds.
metrics_with_transform | Transform the estimates before calculating metrics
Mstep | Maximizing expected likelihood using analytical solution
negLogLik | Calculates the negative log-likelihood
NPannual | Annual streamflow at Nakhon Phanom
NPpc | Selected principal components
nRMSE | Normalized root-mean-square error
NSE | Nash-Sutcliffe Efficiency
one_lds_cv | One cross-validation run
one_LDS_rep | One LDS replicate
one_pcr_cv | One cross-validation run
PCR_ensemble_selection | Select the best reconstruction
PCR_reconstruction | Principal Component Regression Reconstruction
penalized_likelihood | Penalized likelihood objective function
propagate | State propagation
RE | Reduction of Error
theta | LDS parameters
vec_to_list | Converts theta from a vector (as used in GA) to list (as used in Kalman smoothing)