Function reference • mvgam

All functions

GP(): Specify dynamic Gaussian process trends in mvgam models

RW() AR() CAR() VAR(): Specify autoregressive dynamic processes in mvgam

ZMVN(): Specify correlated residual processes in mvgam

add_residuals(): Calculate randomized quantile residuals for mvgam objects

all_neon_tick_data: NEON Amblyomma and Ixodes tick abundance survey data

augment(<mvgam>): Augment an mvgam object's data

code() stancode(<mvgam_prefit>) stancode(<mvgam>) standata(<mvgam_prefit>): Stan code and data objects for mvgam models

conditional_effects(<mvgam>) plot(<mvgam_conditional_effects>) print(<mvgam_conditional_effects>): Display conditional effects of predictors for mvgam models

dynamic(): Defining dynamic coefficients in mvgam formulae

ensemble(): Combine forecasts from mvgam models into evenly weighted ensembles

eval_mvgam() roll_eval_mvgam() compare_mvgams(): Evaluate forecasts from fitted mvgam objects

fevd(): Calculate latent VAR forecast error variance decompositions

fitted(<mvgam>): Expected values of the posterior predictive distribution for mvgam objects

forecast(<mvgam>): Extract or compute hindcasts and forecasts for a fitted mvgam object

formula(<mvgam>) formula(<mvgam_prefit>): Extract formulae from mvgam objects

get_mvgam_priors(): Extract information on default prior distributions for an mvgam model

drawDotmvgam() eval_smoothDothilbertDotsmooth() eval_smoothDotmodDotsmooth() eval_smoothDotmoiDotsmooth(): Enhance post-processing of mvgam models using gratia functionality

hindcast(): Extract hindcasts for a fitted mvgam object

how_to_cite(): Generate a methods description for mvgam models

variables(<mvgam>): Index mvgam objects

irf(): Calculate latent VAR impulse response functions

jsdgam(): Fit Joint Species Distribution Models in mvgam

lfo_cv(): Approximate leave-future-out cross-validation of fitted mvgam objects

logLik(<mvgam>): Compute pointwise Log-Likelihoods from fitted mvgam objects

loo(<mvgam>) loo_compare(<mvgam>): LOO information criteria for mvgam models

lv_correlations(): Calculate trend correlations based on latent factor loadings for mvgam models

mcmc_plot(<mvgam>): MCMC plots of mvgam parameters, as implemented in bayesplot

model.frame(<mvgam>) model.frame(<mvgam_prefit>): Extract model.frame from a fitted mvgam object

smooth.construct(<moi.smooth.spec>) smooth.construct(<mod.smooth.spec>) Predict.matrix(<moi.smooth>) Predict.matrix(<mod.smooth>): Monotonic splines in mvgam models

mvgam-class: Fitted mvgam object description

mvgam(): Fit a Bayesian Dynamic GAM to Univariate or Multivariate Time Series

nuts_params(<mvgam>) log_posterior(<mvgam>) rhat(<mvgam>) neff_ratio(<mvgam>): Extract diagnostic quantities of mvgam models

as.data.frame(<mvgam>) as.matrix(<mvgam>) as.array(<mvgam>) as_draws(<mvgam>) as_draws_matrix(<mvgam>) as_draws_df(<mvgam>) as_draws_array(<mvgam>) as_draws_list(<mvgam>) as_draws_rvars(<mvgam>): Extract posterior draws from fitted mvgam objects

tweedie() student_t() betar() nb() lognormal() student() bernoulli() beta_binomial() nmix(): Supported mvgam families

mvgam_fevd-class: mvgam_fevd object description

mvgam_forecast-class: mvgam_forecast object description

mvgam_formulae: Details of formula specifications in mvgam models

mvgam_irf-class: mvgam_irf object description

get_coef(<mvgam>) set_coef(<mvgam>) get_vcov(<mvgam>) get_predict(<mvgam>) get_data(<mvgam>) get_data(<mvgam_prefit>) find_predictors(<mvgam>) find_predictors(<mvgam_prefit>): Helper functions for marginaleffects calculations in mvgam models

mvgam_residcor-class: mvgam_residcor object description

mvgam_trends: Supported latent trend models in mvgam

mvgam_use_cases: Example use cases for mvgam

ordinate(): Latent variable ordination plots from jsdgam objects

pairs(<mvgam>): Create a matrix of output plots from a mvgam object

PW(): Specify piecewise linear or logistic trends in mvgam models

plot(<mvgam>): Default plots for mvgam models

plot(<mvgam_fevd>): Plot forecast error variance decompositions from an mvgam_fevd object

plot(<mvgam_irf>): Plot impulse responses from an mvgam_irf object

plot(<mvgam_lfo>): Plot Pareto-k and ELPD values from a mvgam_lfo object

plot(<mvgam_residcor>): Plot residual correlations based on latent factors

plot_mvgam_factors(): Latent factor summaries for a fitted mvgam object

plot_mvgam_fc() plot(<mvgam_forecast>): Plot posterior forecast predictions from mvgam models

plot_mvgam_pterms(): Plot parametric term partial effects for mvgam models

plot_mvgam_randomeffects(): Plot random effect terms from mvgam models

plot_mvgam_resids(): Residual diagnostics for a fitted mvgam object

plot_mvgam_series(): Plot observed time series used for mvgam modelling

plot_mvgam_smooth(): Plot smooth terms from mvgam models

plot_mvgam_trend(): Plot latent trend predictions from mvgam models

plot_mvgam_uncertainty(): Plot forecast uncertainty contributions from mvgam models

portal_data: Portal Project rodent capture survey data

posterior_epred(<mvgam>): Draws from the expected value of the posterior predictive distribution for mvgam objects

posterior_linpred(<mvgam>): Posterior draws of the linear predictor for mvgam objects

posterior_predict(<mvgam>): Draws from the posterior predictive distribution for mvgam objects

pp_check(<mvgam>): Posterior Predictive Checks for mvgam models

ppc(): Plot conditional posterior predictive checks from mvgam models

predict(<mvgam>): Predict from a fitted mvgam model

print(<mvgam>): Print a fitted mvgam object

print(<mvgam_summary>): Print method for mvgam_summary objects

residual_cor(): Extract residual correlations based on latent factors

residuals(<mvgam>): Posterior draws of residuals from mvgam models

score(): Compute probabilistic forecast scores for mvgam models

series_to_mvgam(): Convert timeseries object to format necessary for mvgam models

sim_mvgam(): Simulate a set of time series for modelling in mvgam

stability(): Calculate measures of latent VAR community stability

summary(<mvgam>) summary(<mvgam_prefit>) coef(<mvgam>): Summary for a fitted mvgam models

summary(<mvgam_fevd>): Posterior summary of forecast error variance decompositions

summary(<mvgam_forecast>): Posterior summary of hindcast and forecast objects

summary(<mvgam_irf>): Posterior summary of impulse responses

tidy(<mvgam>): Tidy an mvgam object's parameter posteriors

update(<mvgam>) update(<jsdgam>): Update an existing mvgam model object