# Score Matching Estimation by Automatic Differentiation

## Documentation for package ‘scorematchingad’ version 0.1.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

scorematchingad-package | scorematchingad: Score Matching Estimation by Automatic Differentiation
ADFun | A Class for CppAD Tapes
Bingham | Score Matching Estimators for the Bingham Distribution
cppad_closed | Score Matching Estimator for Quadratic-Form Score Matching Discrepancies
cppad_search | Iterative Score Matching Estimator Using Conjugate-Gradient Descent
dppi | Improper Log-Density of the PPI Model
evaltape | Evaluate a CppAD Tape Many Times
evaltape_wsum | Evaluate a CppAD Tape Many Times
FB | Estimate the Fisher-Bingham Distribution
microbiome | 16s Microbiome Data for Soil-Transmitted Helminths
ppi | Estimation of Polynomially-Tilted Pairwise Interaction (PPI) Model
ppi_cW | Quickly Generate a Vector of Windham Exponents for the PPI Model
ppi_cW_auto | Quickly Generate a Vector of Windham Exponents for the PPI Model
ppi_fromAstar | PPI Parameter Tools
ppi_mmmm | A PPI Score-Matching Marginal Moment Matching Estimator (dimension=3 only)
ppi_parammats | PPI Parameter Tools
ppi_paramvec | PPI Parameter Tools
ppi_param_tools | PPI Parameter Tools
ppi_robust | Robustly Estimate Parameters of the PPI Distribution
ppi_robust_alrgengamma | Robustly Estimate Parameters of the PPI Distribution
ppi_smvalues | Estimation of Polynomially-Tilted Pairwise Interaction (PPI) Model
ppi_toAstar | PPI Parameter Tools
print,Rcpp_ADFun | Print or show a summary of an Rcpp_ADFun
print-method | Print or show a summary of an Rcpp_ADFun
quadratictape_parts | Evaluate the Hessian and Gradient Offset of a Taped Quadratic Function
Rcpp_ADFun | A Class for CppAD Tapes
Rcpp_ADFun-class | A Class for CppAD Tapes
rppi | Simulate from a PPI Model
rppi_egmodel | Simulate from a PPI Model
rsymmetricmatrix | Quickly Generate a Symmetric Matrix for Testing and Examples
scorematchingad | scorematchingad: Score Matching Estimation by Automatic Differentiation
scorematchingtheory | Introduction to Score Matching
show-method | Print or show a summary of an Rcpp_ADFun
smvalues | Compute Score Matching Discrepancy Value, Gradient, and Hessian
smvalues_wsum | Compute Score Matching Discrepancy Value, Gradient, and Hessian
tape_gradoffset | Tape the Gradient Offset of a Quadratic CppAD Tape
tape_Hessian | Tape the Hessian of a CppAD Tape
tape_Jacobian | Tape the Jacobian of CppAD Tape
tape_logJacdet | Tape the log of Jacobian determinant of a CppAD Tape
tape_smd | Build CppAD Tapes for Score Matching
tape_swap | Switch Dynamic and Independent Values of a Tape
tape_uld | Generate a tape of a custom unnormalised log-density
tape_uld_inbuilt | Generate a tape of a custom unnormalised log-density
testquadratic | Test Whether a CppAD Tape is a Quadratic Function
vMF | Score Matching Estimator for the von-Mises Fisher Distribution
vMF_robust | Robust Fitting of von Mises Fisher
Windham | Windham Robustification of Point Estimators for Exponential Family Distributions
Windham_populationinverse | Inverse Transform for the Population Parameters Under Windham Weights
Windham_populationinverse_alternative | Inverse Transform for the Population Parameters Under Windham Weights