Package: gaussianprocesses 1.0.0.9000

gaussianprocesses: Gaussian Processes from First Principles

Gaussian process regression, classification, and count models with explicit covariance kernels, exact Gaussian inference, Laplace approximations for non-Gaussian likelihoods, sparse approximations, marginal-likelihood optimization, derivatives, posterior sampling, calibration diagnostics, and time-series workflows. The implementation follows the core methodology of Rasmussen and Williams (2006) <doi:10.7551/mitpress/3206.001.0001> and emphasizes numerical stability, transparent assumptions, and reproducible statistical workflows.

Authors:Diogo Ribeiro [aut, cre]

gaussianprocesses_1.0.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gaussianprocesses/json (API)

# Install 'gaussianprocesses' in R:
install.packages('gaussianprocesses', repos = c('https://diogoribeiro7.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://gitlab.com/diogoribeiro7/gaussian-processes-r

Pkgdown/docs site:https://gaussian-processes-r-12efed.gitlab.io

On CRAN:

Conda:

5.02 score 87 exports 0 dependencies

Last updated from:8770c93ab0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK156
source / vignettesOK347
linux-releaseOK195
macos-releaseOK139
macos-oldrelOK133
windows-develOK131
windows-releaseOK172
windows-oldrelOK142
wasm-releaseOK93

Exports:basis_meanbenchmark_exact_gp_scalingbenchmark_sparse_gpbernoulli_likelihoodchangepoint_kernelcoefficient_priorcompare_gp_predictionsconstant_meancoregionalization_kernelcoregionalization_matrixestimate_coefficientsevaluate_kernelevaluate_likelihoodevaluate_meanfit_gpfit_heteroscedastic_gpfit_latent_gpfit_sparse_gpfit_time_series_gpforecast_gpforecast_metricsgaussian_likelihoodgp_calibration_diagnosticsgp_classification_scoresgp_count_scoresgp_diagnosticsgp_holdout_scoresgp_hyperparameter_uncertaintygp_loo_scoresgp_numerical_diagnosticsgp_profile_likelihoodgp_scoresgp_simulation_scenariogp_stack_outputsgp_time_indexinitialize_coregionalizationinitialize_spectral_mixturekernel_diagonalkernel_gradientkernel_input_gradientkernel_linearkernel_matern12kernel_matern32kernel_matern52kernel_parameterskernel_periodickernel_rational_quadratickernel_rbfkernel_white_noiselikelihood_predictivelinear_kernellinear_meanlog_marginal_likelihoodlog_marginal_likelihood_gradientloo_gpmatern12_kernelmatern32_kernelmatern52_kerneloptimize_gpoptimize_latent_gpoptimize_sparse_gpoptimize_time_series_gpperiodic_kernelpoisson_likelihoodpolynomial_meanpredict_gppredict_gradient_gppredict_heteroscedastic_gppredict_latent_gppredict_sparse_gpproduct_kernelrational_quadratic_kernelrbf_kernelrolling_origin_gprun_gp_benchmark_suitesample_gp_posteriorsample_gp_priorscale_kernelselect_dimensionsselect_inducing_pointssimulate_gp_dataspectral_mixture_kernelsum_kerneltime_series_kernelupdate_kernel_parameterswhite_noise_kernelzero_mean

Dependencies:

Gaussian Processes for Time Series
Time is an input, not a special likelihood | Trend, periodicity, and local variation | [k(t,t') | Reproducible example | Interpolation versus extrapolation | Rolling-origin evaluation | Point and probabilistic metrics | Structural breaks | Long series: Kalman filtering and smoothing

Last update: 2026-10-08
Started: 2026-10-01

Derivatives of Covariance Kernels
Why derivatives | [\frac{\partial}{\partial \theta_j} \log p(y \mid X, \theta) | Log parameters | [\frac | Scaled distances | The variance parameter | Stationary kernels | [\frac | \sigma^2 f'(r^2), \frac | RBF | Matérn 1/2 | Matérn 3/2 | Matérn 5/2 | [g = \frac | Rational quadratic | [\frac | \alpha, k, \frac | Periodic kernel | [\frac | Composite kernels | Product. For (K = \prod_i K_i), the product rule gives[\frac | Parameter paths | The marginal-likelihood gradient | Derivation | [\log p(y \mid X, \theta) | [\frac | -C^ | [\frac | [\frac | Computation | Numerical verification | Derivatives with respect to the inputs | Derivative processes | [\operatorname{cov}!\left(\frac{\partial f(x)}{\partial x_d}, f(x')\right) | \frac{\partial k(x, x')}{\partial x_d},\qquad\operatorname{cov}!\left(\frac{\partial f(x)}{\partial x_d},\frac{\partial f(x')}{\partial x'_e}\right) | Smoothness | Radial kernels | [\frac | Periodic and linear kernels | [\frac | [\frac | The posterior gradient | [\mathrm{E}!\left[\frac{\partial f(x_)}{\partial x_{,d}} ,\middle|, y\right] | [\operatorname{Var}!\left[\frac{\partial f(x_)}{\partial x_{,d}} ,\middle|, y\right] | Verification | Derivative observations | The joint model | Example

Last update: 2026-10-06
Started: 2026-10-03

Marginal Likelihood, Prediction, and Uncertainty
Marginal likelihood | [\log p(y\mid X,\theta) | [\log|C| | Hyperparameter estimation | Posterior uncertainty | [\operatorname{Var}[f_*\mid y] | k(x_,x_) | [\operatorname{Var}[y_*\mid y] | Exact leave-one-out diagnostics | [\mu_ | [\sigma_{-i}^2 | Universal kriging

Last update: 2026-10-06
Started: 2026-10-01

Multidimensional Gaussian Processes and ARD
Scaled distance | [r^2(x,x') | Example | Parameter paths | Reproducible two-dimensional simulation | ARD and optimization | Interpretation | Additive models | Components

Last update: 2026-10-06
Started: 2026-10-01

Numerical Stability in Gaussian-Process Computation
Why numerical stability matters | Cholesky rather than explicit inversion | Jitter is not observation noise | Jitter is relative to the covariance scale | The trace term of the likelihood gradient | Near-singular scenario | Posterior variances | Benchmarking stability separately from speed

Last update: 2026-10-05
Started: 2026-10-01

Gaussian-Process Regression from First Principles
Model | Conditioning | Minimal reproducible fit | Posterior prediction | [\operatorname{Var}\left[y_*\mid y\right] | Function draws | Known heteroscedastic observation variance

Last update: 2026-10-05
Started: 2026-10-01

Covariance Kernels and Composition
Covariance as model structure | Squared-exponential kernel | [k(x,x') | Matérn family | Rational quadratic | [k(r) | Periodic structure | Sums and products | Parameter paths

Last update: 2026-10-01
Started: 2026-10-01

Readme and manuals

Help Manual

Help pageTopics
Benchmark exact-GP scalingbenchmark_exact_gp_scaling
Benchmark sparse FITC against exact GP regressionbenchmark_sparse_gp
Changepoint kernelschangepoint_kernel
Coefficients of a Gaussian-process meancoef.gaussianprocesses_latent_model coef.gaussianprocesses_model gp_coefficients vcov.gaussianprocesses_model
Compare two GP posterior predictions numericallycompare_gp_predictions
Create a coregionalization kernel for several outputscoregionalization_kernel
Output covariance matrices of coregionalization kernelscoregionalization_matrix
Evaluate a kernel specificationevaluate_kernel
Evaluate a likelihood and its derivativesevaluate_likelihood
Evaluate a Gaussian-process mean functionevaluate_mean
Fit an exact Gaussian-process regression modelfit_gp
Fit an approximate heteroscedastic Gaussian processfit_heteroscedastic_gp
Fit a latent Gaussian-process modelfit_latent_gp
Fit a sparse Gaussian process (FITC or VFE)fit_sparse_gp
Fit a GP to ordered time-series observationsfit_time_series_gp
Forecast or interpolate from a time-aware GP modelforecast_gp
Uncertainty-aware forecast metricsforecast_metrics
Fitted model objectsgaussianprocesses_heteroscedastic_model gaussianprocesses_latent_model gaussianprocesses_model gaussianprocesses_sparse_model gaussianprocesses_state_space_model
Summarize Gaussian-process uncertainty calibrationgp_calibration_diagnostics
Scores of binary probability forecastsgp_classification_scores
Scores of count forecastsgp_count_scores
Comprehensive diagnostics for an exact Gaussian-process modelgp_diagnostics
Uncertainty of estimated hyperparametersgp_hyperparameter_uncertainty
Likelihoods for Gaussian-process modelsbernoulli_likelihood gaussian_likelihood gp_likelihoods poisson_likelihood
Gaussian-process mean functionsconstant_mean gp_mean_functions zero_mean
Base R methods for fitted Gaussian-process modelsfitted.gaussianprocesses_heteroscedastic_model fitted.gaussianprocesses_latent_model fitted.gaussianprocesses_model fitted.gaussianprocesses_sparse_model fitted.gaussianprocesses_state_space_model gp_model_methods logLik.gaussianprocesses_heteroscedastic_model logLik.gaussianprocesses_latent_model logLik.gaussianprocesses_model logLik.gaussianprocesses_sparse_model logLik.gaussianprocesses_state_space_model nobs.gaussianprocesses_heteroscedastic_model nobs.gaussianprocesses_latent_model nobs.gaussianprocesses_model nobs.gaussianprocesses_sparse_model nobs.gaussianprocesses_state_space_model predict.gaussianprocesses_heteroscedastic_model predict.gaussianprocesses_latent_model predict.gaussianprocesses_model predict.gaussianprocesses_sparse_model predict.gaussianprocesses_state_space_model print.summary.gaussianprocesses_model residuals.gaussianprocesses_heteroscedastic_model residuals.gaussianprocesses_model residuals.gaussianprocesses_sparse_model residuals.gaussianprocesses_state_space_model summary.gaussianprocesses_heteroscedastic_model summary.gaussianprocesses_latent_model summary.gaussianprocesses_model summary.gaussianprocesses_sparse_model summary.gaussianprocesses_state_space_model
Summarize numerical conditioning of a fitted GPgp_numerical_diagnostics
Profile likelihood of one hyperparametergp_profile_likelihood
Proper scoring rules for Gaussian predictionsgp_holdout_scores gp_loo_scores gp_scores
Generate standard GP simulation scenariosgp_simulation_scenario
Stack several outputs into one input matrixgp_stack_outputs
Build an explicit Gaussian-process time indexgp_time_index
Initialize a coregionalization kernel from the datainitialize_coregionalization
Initialise a spectral-mixture kernel from the data's spectruminitialize_spectral_mixture
Evaluate only the diagonal of a kernel matrixkernel_diagonal
Derivatives of a covariance matrix with respect to log hyperparameterskernel_gradient
Derivatives of a covariance matrix with respect to the inputskernel_input_gradient
Linear covariance kernelkernel_linear
Matérn covariance kernelskernel_matern kernel_matern12 kernel_matern32 kernel_matern52
Extract kernel parameterskernel_parameters
Periodic covariance kernelkernel_periodic
Rational-quadratic covariance kernelkernel_rational_quadratic
Squared-exponential covariance kernelkernel_rbf
White-noise covariance kernelkernel_white_noise
Predictive distribution of new responseslikelihood_predictive
Create a linear kernel specificationlinear_kernel
Gaussian-process log marginal likelihoodlog_marginal_likelihood
Gradient of the Gaussian-process log marginal likelihoodlog_marginal_likelihood_gradient
Exact leave-one-out Gaussian-process diagnosticsloo_gp
Create Matérn kernel specificationsmatern12_kernel matern32_kernel matern52_kernel matern_kernel_specs
Treatments of mean-function coefficientscoefficient_prior estimate_coefficients mean_coefficients
Optimize Gaussian-process hyperparametersoptimize_gp
Optimize the hyperparameters of a latent Gaussian-process modeloptimize_latent_gp
Optimize the hyperparameters of a sparse Gaussian processoptimize_sparse_gp
Optimize the hyperparameters of a time-series GPoptimize_time_series_gp
Parametric mean functionsbasis_mean linear_mean parametric_means polynomial_mean
Create a periodic kernel specificationperiodic_kernel
Predict from an exact Gaussian-process regression modelpredict_gp
Predict the gradient of the latent functionpredict_gradient_gp
Predict from an approximate heteroscedastic GPpredict_heteroscedastic_gp
Predict from a latent Gaussian-process modelpredict_latent_gp
Predict from a sparse Gaussian-process modelpredict_sparse_gp
Multiply covariance kernelsproduct_kernel
Create a rational-quadratic kernel specificationrational_quadratic_kernel
Create an RBF kernel specificationrbf_kernel
Rolling-origin evaluation for time-aware Gaussian processesrolling_origin_gp
Run the standard GP benchmark suiterun_gp_benchmark_suite
Draw functions from a Gaussian-process posteriorsample_gp_posterior sample_gp_posterior.default sample_gp_posterior.gaussianprocesses_heteroscedastic_model sample_gp_posterior.gaussianprocesses_latent_model sample_gp_posterior.gaussianprocesses_model sample_gp_posterior.gaussianprocesses_sparse_model sample_gp_posterior.gaussianprocesses_state_space_model
Draw functions from a Gaussian-process priorsample_gp_prior
Scale a covariance kernelscale_kernel
Restrict a kernel to selected input columnsselect_dimensions
Select inducing points deterministicallyselect_inducing_points
Simulate observations from a Gaussian processsimulate_gp_data
Spectral-mixture kernelsspectral_mixture_kernel
Add covariance kernelssum_kernel
Create a trend-periodic-local time-series kerneltime_series_kernel
Update parameters in a kernel specificationupdate_kernel_parameters
Create a white-noise kernel specificationwhite_noise_kernel