R: Multivariate (Dynamic) Generalized Additive Models

# Multivariate (Dynamic) Generalized Additive Models

## Documentation for package ‘mvgam’ version 1.1.594

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

## Help Pages

A B C D E F G H I J L M N O P R S T U V Z misc

## -- A --

add_residuals | Calculate randomized quantile residuals for 'mvgam' objects
add_residuals.mvgam | Calculate randomized quantile residuals for 'mvgam' objects
all_neon_tick_data | NEON Amblyomma and Ixodes tick abundance survey data
and | Index 'mvgam' objects
AR | Specify autoregressive dynamic processes in 'mvgam'
as.array.mvgam | Extract posterior draws from fitted 'mvgam' objects
as.data.frame.mvgam | Extract posterior draws from fitted 'mvgam' objects
as.matrix.mvgam | Extract posterior draws from fitted 'mvgam' objects
as_draws.mvgam | Extract posterior draws from fitted 'mvgam' objects
as_draws_array.mvgam | Extract posterior draws from fitted 'mvgam' objects
as_draws_df.mvgam | Extract posterior draws from fitted 'mvgam' objects
as_draws_list.mvgam | Extract posterior draws from fitted 'mvgam' objects
as_draws_matrix.mvgam | Extract posterior draws from fitted 'mvgam' objects
as_draws_rvars.mvgam | Extract posterior draws from fitted 'mvgam' objects
augment.mvgam | Augment an 'mvgam' object's data

## -- B --

bernoulli | Supported 'mvgam' families
betar | Supported 'mvgam' families
beta_binomial | Supported 'mvgam' families

## -- C --

CAR | Specify autoregressive dynamic processes in 'mvgam'
code | Stan code and data objects for 'mvgam' models
coef.mvgam | Summary for a fitted 'mvgam' models
coefficient | Index 'mvgam' objects
compare_mvgams | Evaluate forecasts from fitted 'mvgam' objects
conditional_effects.mvgam | Display conditional effects of predictors for 'mvgam' models

## -- D --

draw.mvgam | Enhance post-processing of 'mvgam' models using 'gratia' functionality
drawDotmvgam | Enhance post-processing of 'mvgam' models using 'gratia' functionality
dynamic | Defining dynamic coefficients in 'mvgam' formulae

## -- E --

ensemble | Combine forecasts from 'mvgam' models into evenly weighted ensembles
ensemble.mvgam_forecast | Combine forecasts from 'mvgam' models into evenly weighted ensembles
evaluate_mvgams | Evaluate forecasts from fitted 'mvgam' objects
eval_mvgam | Evaluate forecasts from fitted 'mvgam' objects
eval_smooth.hilbert.smooth | Enhance post-processing of 'mvgam' models using 'gratia' functionality
eval_smooth.mod.smooth | Enhance post-processing of 'mvgam' models using 'gratia' functionality
eval_smooth.moi.smooth | Enhance post-processing of 'mvgam' models using 'gratia' functionality
eval_smoothDothilbertDotsmooth | Enhance post-processing of 'mvgam' models using 'gratia' functionality
eval_smoothDotmodDotsmooth | Enhance post-processing of 'mvgam' models using 'gratia' functionality
eval_smoothDotmoiDotsmooth | Enhance post-processing of 'mvgam' models using 'gratia' functionality

## -- F --

fevd | Calculate latent VAR forecast error variance decompositions
fevd.mvgam | Calculate latent VAR forecast error variance decompositions
find_predictors.mvgam | Helper functions for 'marginaleffects' calculations in 'mvgam' models
find_predictors.mvgam_prefit | Helper functions for 'marginaleffects' calculations in 'mvgam' models
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 | Extract formulae from 'mvgam' objects
formula.mvgam_prefit | Extract formulae from 'mvgam' objects

## -- G --

get_coef.mvgam | Helper functions for 'marginaleffects' calculations in 'mvgam' models
get_data.mvgam | Helper functions for 'marginaleffects' calculations in 'mvgam' models
get_data.mvgam_prefit | Helper functions for 'marginaleffects' calculations in 'mvgam' models
get_mvgam_priors | Extract information on default prior distributions for an 'mvgam' model
get_predict.mvgam | Helper functions for 'marginaleffects' calculations in 'mvgam' models
get_vcov.mvgam | Helper functions for 'marginaleffects' calculations in 'mvgam' models
GP | Specify dynamic Gaussian process trends in 'mvgam' models
gratia_mvgam_enhancements | Enhance post-processing of 'mvgam' models using 'gratia' functionality

## -- H --

hindcast | Extract hindcasts for a fitted 'mvgam' object
hindcast.mvgam | Extract hindcasts for a fitted 'mvgam' object
how_to_cite | Generate a methods description for 'mvgam' models
how_to_cite.mvgam | Generate a methods description for 'mvgam' models

## -- I --

Index | Index 'mvgam' objects
index-mvgam | Index 'mvgam' objects
irf | Calculate latent VAR impulse response functions
irf.mvgam | Calculate latent VAR impulse response functions

## -- J --

jsdgam | Fit Joint Species Distribution Models in 'mvgam'

## -- L --

lfo_cv | Approximate leave-future-out cross-validation of fitted 'mvgam' objects
lfo_cv.mvgam | Approximate leave-future-out cross-validation of fitted 'mvgam' objects
logLik.mvgam | Compute pointwise Log-Likelihoods from fitted 'mvgam' objects
lognormal | Supported 'mvgam' families
log_posterior.mvgam | Extract diagnostic quantities of 'mvgam' models
loo.mvgam | LOO information criteria for 'mvgam' models
loo_compare.mvgam | LOO information criteria for 'mvgam' models
lv_correlations | Calculate trend correlations based on latent factor loadings for 'mvgam' models

## -- M --

mcmc_plot.mvgam | MCMC plots of 'mvgam' parameters, as implemented in 'bayesplot'
model.frame.mvgam | Extract model.frame from a fitted 'mvgam' object
model.frame.mvgam_prefit | Extract model.frame from a fitted 'mvgam' object
monotonic | Monotonic splines in 'mvgam' models
mvgam | Fit a Bayesian Dynamic GAM to Univariate or Multivariate Time Series
mvgam-class | Fitted 'mvgam' object description
mvgam_diagnostics | Extract diagnostic quantities of 'mvgam' models
mvgam_draws | Extract posterior draws from fitted 'mvgam' objects
mvgam_families | 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
mvgam_marginaleffects | 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'

## -- N --

names | Index 'mvgam' objects
nb | Supported 'mvgam' families
neff_ratio | Extract diagnostic quantities of 'mvgam' models
neff_ratio.mvgam | Extract diagnostic quantities of 'mvgam' models
nmix | Supported 'mvgam' families
nuts_params | Extract diagnostic quantities of 'mvgam' models
nuts_params.mvgam | Extract diagnostic quantities of 'mvgam' models

## -- O --

ordinate | Latent variable ordination plots from jsdgam objects
ordinate.jsdgam | Latent variable ordination plots from jsdgam objects

## -- P --

pairs.mvgam | Create a matrix of output plots from a 'mvgam' object
plot.mvgam | Default plots for 'mvgam' models
plot.mvgam_conditional_effects | Display conditional effects of predictors for 'mvgam' models
plot.mvgam_fevd | Plot forecast error variance decompositions from an 'mvgam_fevd' object
plot.mvgam_forecast | Plot posterior forecast predictions from 'mvgam' models
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 posterior forecast predictions from 'mvgam' models
plot_mvgam_forecasts | 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
ppc | Plot conditional posterior predictive checks from 'mvgam' models
ppc.mvgam | Plot conditional posterior predictive checks from 'mvgam' models
pp_check | Posterior Predictive Checks for 'mvgam' models
pp_check.mvgam | Posterior Predictive Checks for 'mvgam' models
Predict.matrix.mod.smooth | Monotonic splines in 'mvgam' models
Predict.matrix.moi.smooth | Monotonic splines in 'mvgam' models
predict.mvgam | Predict from a fitted 'mvgam' model
print.mvgam | Print a fitted 'mvgam' object
print.mvgam_conditional_effects | Display conditional effects of predictors for 'mvgam' models
print.mvgam_summary | Print method for mvgam_summary objects
PW | Specify piecewise linear or logistic trends in 'mvgam' models

## -- R --

residuals.mvgam | Posterior draws of residuals from 'mvgam' models
residual_cor | Extract residual correlations based on latent factors
residual_cor.jsdgam | Extract residual correlations based on latent factors
residual_cor.mvgam | Extract residual correlations based on latent factors
rhat | Extract diagnostic quantities of 'mvgam' models
rhat.mvgam | Extract diagnostic quantities of 'mvgam' models
roll_eval_mvgam | Evaluate forecasts from fitted 'mvgam' objects
RW | Specify autoregressive dynamic processes in 'mvgam'

## -- S --

score | Compute probabilistic forecast scores for 'mvgam' models
score.mvgam_forecast | Compute probabilistic forecast scores for 'mvgam' models
series_to_mvgam | Convert timeseries object to format necessary for 'mvgam' models
set_coef.mvgam | Helper functions for 'marginaleffects' calculations in 'mvgam' models
sim_mvgam | Simulate a set of time series for modelling in 'mvgam'
smooth.construct.mod.smooth.spec | Monotonic splines in 'mvgam' models
smooth.construct.moi.smooth.spec | Monotonic splines in 'mvgam' models
stability | Calculate measures of latent VAR community stability
stability.mvgam | Calculate measures of latent VAR community stability
stancode.mvgam | Stan code and data objects for 'mvgam' models
stancode.mvgam_prefit | Stan code and data objects for 'mvgam' models
standata.mvgam_prefit | Stan code and data objects for 'mvgam' models
student | Supported 'mvgam' families
student_t | Supported 'mvgam' families
summary.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
summary.mvgam_prefit | Summary for a fitted 'mvgam' models

## -- T --

their | Index 'mvgam' objects
tidy.mvgam | Tidy an 'mvgam' object's parameter posteriors
tweedie | Supported 'mvgam' families

## -- U --

update.jsdgam | Update an existing 'mvgam' model object
update.mvgam | Update an existing 'mvgam' model object

## -- V --

VAR | Specify autoregressive dynamic processes in 'mvgam'
variables | Index 'mvgam' objects
variables.mvgam | Index 'mvgam' objects

## -- Z --

ZMVN | Specify correlated residual processes in 'mvgam'

## -- misc --

`mgcv` | Index 'mvgam' objects