Package index • colvR

Core modelling

Fit, model selection, variance and confidence intervals.

Miss.ZIPLNPCA(): ZI‑PLN-PCA with missing data (variational fit + imputation)

select_model_bic(): Model selection by BIC over candidate latent dimensions

V_theta(): Variance–covariance of theta

IC(): 95% interval for a theta 95% confidence interval for theta

BIC(): BIC from ELBO for a ZIP-PLN latent factor model

Initialisation

Helpers for initial parameters.

Init(): Initialize parameters for a PLN-PCA with missing data

Init_ZIP(): Initialize parameters for the ZIP case (zero-inflated)

Init_ZIP_q0(): Init_ZIP_q0

Optimisation & maths

Lower bounds, gradients, covariance utilities.

Elbo_grad(): ELBO and parameter gradients (ZIP‑PLN variational objective)

Elbo_grad_logS(): Calculate the Elbo with log(S) instead of S and the gradients

covmat(): Wrapper for `lori::covmat`

Additional models & helpers

Complementary wrappers and step-wise routines.

Miss.PLNPCA(): PLN-PCA with missing data (variational fit + imputation)

Miss.ZIPLNPCA.logS(): ZI‑PLN-PCA with missing data using log(S) parametrization

Miss.ZIPLNPCA_Steps(): ZI‑PLN-PCA (missing data) with parameterwise optimization steps

Miss.ZIPLNPCA_VE(): ZI‑PLN-PCA (missing data) — variational E‑step solver

Predictions(): Predictive simulations and intervals

Utilities & simulation

Simulation tools and helpers.

Simul(): Simulate zero-inflated Poisson log-normal PCA data

Data

Datasets bundled with colvR.

fuligule_milouin: Fuligule milouin example dataset