Multivariate (Dynamic) Generalized Additive Models

Documentation for package ‘mvgam’ version 1.1.4

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A B C D E F G H I J L M N 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	Extract or compute hindcasts and forecasts for a fitted 'mvgam' object
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 a univariate or multivariate set of 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_trends	Supported latent trend models in '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

-- 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_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	Summary for a fitted 'mvgam' object
print.mvgam_conditional_effects	Display conditional effects of predictors for 'mvgam' models
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 from a fitted jsdgam
residual_cor.jsdgam	Extract residual correlations based on latent factors from a fitted jsdgam
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_prefit	Summary for a fitted 'mvgam' models

-- T --

their	Index 'mvgam' objects
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