Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

Documentation for package ‘gratia’ version 0.9.2

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

-- A --

add_confint	Add a confidence interval to an existing object
add_confint.default	Add a confidence interval to an existing object
add_confint.parametric_effects	Add a confidence interval to an existing object
add_confint.smooth_estimates	Add a confidence interval to an existing object
add_constant	Add a constant to estimated values
add_constant.evaluated_parametric_term	Add a constant to estimated values
add_constant.mgcv_smooth	Add a constant to estimated values
add_constant.parametric_effects	Add a constant to estimated values
add_constant.smooth_estimates	Add a constant to estimated values
add_constant.smooth_samples	Add a constant to estimated values
add_constant.tbl_df	Add a constant to estimated values
add_fitted	Add fitted values from a model to a data frame
add_fitted.gam	Add fitted values from a GAM to a data frame
add_fitted_samples	Add posterior draws from a model to a data object
add_partial_residuals	Add partial residuals
add_partial_residuals.gam	Add partial residuals
add_posterior_samples	Add posterior draws from a model to a data object
add_predicted_samples	Add posterior draws from a model to a data object
add_residuals	Add residuals from a model to a data frame
add_residuals.gam	Add residuals from a GAM to a data frame
add_sizer	Add indicators of significant change after SiZeR
add_sizer.derivatives	Add indicators of significant change after SiZeR
add_sizer.smooth_estimates	Add indicators of significant change after SiZeR
add_smooth_samples	Add posterior draws from a model to a data object
appraise	Model diagnostic plots
appraise.gam	Model diagnostic plots
appraise.lm	Model diagnostic plots

-- B --

basis	Basis expansions for smooths
basis.default	Basis expansions for smooths
basis.gam	Basis expansions for smooths
basis.gamm	Basis expansions for smooths
basis.list	Basis expansions for smooths
basis.scam	Basis expansions for smooths
basis_size	Extract basis dimension of a smooth
basis_size.gam	Extract basis dimension of a smooth
basis_size.gamm	Extract basis dimension of a smooth
basis_size.mgcv.smooth	Extract basis dimension of a smooth
bird_move	Simulated bird migration data
boundary	Extract the boundary of a soap film smooth
boundary.gam	Extract the boundary of a soap film smooth
boundary.soap.film	Extract the boundary of a soap film smooth
by_level	Tests for by variable smooths
by_variable	Tests for by variable smooths

-- C --

check_is_mgcv_smooth	Check if objects are smooths or are a particular type of smooth
check_user_select_smooths	Select smooths based on user's choices
coef.scam	Extract coefficients from a fitted 'scam' model.
compare_smooths	Compare smooths across models
concrvity	Concurvity of an estimated GAM
confint.fderiv	Point-wise and simultaneous confidence intervals for derivatives of smooths
confint.gam	Point-wise and simultaneous confidence intervals for smooths
confint.gamm	Point-wise and simultaneous confidence intervals for smooths
confint.list	Point-wise and simultaneous confidence intervals for smooths

-- D --

data_combos	All combinations of factor levels plus typical values of continuous variables
data_combos.gam	All combinations of factor levels plus typical values of continuous variables
data_sim	Simulate example data for fitting GAMs
data_slice	Prepare a data slice through model covariates
data_slice.data.frame	Prepare a data slice through model covariates
data_slice.default	Prepare a data slice through model covariates
data_slice.gam	Prepare a data slice through model covariates
data_slice.gamm	Prepare a data slice through model covariates
data_slice.list	Prepare a data slice through model covariates
data_slice.scam	Prepare a data slice through model covariates
derivatives	Derivatives of estimated smooths via finite differences
derivatives.default	Derivatives of estimated smooths via finite differences
derivatives.gam	Derivatives of estimated smooths via finite differences
derivatives.gamm	Derivatives of estimated smooths via finite differences
derivative_samples	Posterior expectations of derivatives from an estimated model
derivative_samples.default	Posterior expectations of derivatives from an estimated model
derivative_samples.gam	Posterior expectations of derivatives from an estimated model
derivative_samples.gamm	Posterior expectations of derivatives from an estimated model
difference_smooths	Differences of factor smooth interactions
difference_smooths.gam	Differences of factor smooth interactions
draw	Generic plotting via 'ggplot2'
draw.basis	Plot basis functions
draw.compare_smooths	Plot comparisons of smooths
draw.derivatives	Plot derivatives of smooths
draw.difference_smooth	Plot differences of smooths
draw.evaluated_parametric_term	Plot estimated parametric effects
draw.gam	Plot estimated smooths from a fitted GAM
draw.gamlss	Plot smooths of a GAMLSS model estimated by 'GJRM::gamlss'
draw.mgcv_smooth	Plot basis functions
draw.overall_concurvity	Plot concurvity measures
draw.pairwise_concurvity	Plot concurvity measures
draw.parametric_effects	Plot estimated effects for model parametric terms
draw.partial_derivatives	Plot derivatives of smooths
draw.penalty_df	Display penalty matrices of smooths using 'ggplot'
draw.rootogram	Draw a rootogram
draw.smooth_estimates	Plot the result of a call to 'smooth_estimates()'
draw.smooth_samples	Plot posterior smooths

-- E --

edf	Effective degrees of freedom for smooths and GAMs
edf.gam	Effective degrees of freedom for smooths and GAMs
evaluate_parametric_term	Evaluate parametric model terms
evaluate_parametric_term.gam	Evaluate parametric model terms
evaluate_smooth	Evaluate a smooth
eval_smooth	S3 methods to evaluate individual smooths
eval_smooth.fs.interaction	S3 methods to evaluate individual smooths
eval_smooth.mgcv.smooth	S3 methods to evaluate individual smooths
eval_smooth.mrf.smooth	S3 methods to evaluate individual smooths
eval_smooth.random.effect	S3 methods to evaluate individual smooths
eval_smooth.scam_smooth	S3 methods to evaluate individual smooths
eval_smooth.soap.film	S3 methods to evaluate individual smooths
eval_smooth.sz.interaction	S3 methods to evaluate individual smooths
eval_smooth.t2.smooth	S3 methods to evaluate individual smooths
eval_smooth.tensor.smooth	S3 methods to evaluate individual smooths
evenly	Create a sequence of evenly-spaced values
extract_link	Extract link and inverse link functions from models
extract_link.family	Extract link and inverse link functions from models
extract_link.general.family	Extract link and inverse link functions from models

-- F --

factor_combos	All combinations of factor levels
factor_combos.gam	All combinations of factor levels
family.bam	Extract family objects from models
family.gam	Extract family objects from models
family.gamm	Extract family objects from models
family.list	Extract family objects from models
family_name	Name of family used to fit model
family_type	Extracts the type of family in a consistent way
family_type.default	Extracts the type of family in a consistent way
family_type.family	Extracts the type of family in a consistent way
fitted_samples	Draw fitted values from the posterior distribution
fitted_samples.gam	Draw fitted values from the posterior distribution
fitted_values	Generate fitted values from a estimated GAM
fitted_values.gam	Generate fitted values from a estimated GAM
fitted_values.gamm	Generate fitted values from a estimated GAM
fitted_values.scam	Generate fitted values from a estimated GAM
fixed_effects	Extract fixed effects estimates from a fitted GAM
fixed_effects.default	Extract fixed effects estimates from a fitted GAM
fixef	Extract fixed effects estimates
fixef.gam	Extract fixed effects estimates from a fitted GAM
fixef.gamm	Extract fixed effects estimates from a fitted GAM
fixef.glm	Extract fixed effects estimates from a fitted GAM
fixef.lm	Extract fixed effects estimates from a fitted GAM
fix_offset	Fix the names of a data frame containing an offset variable.

-- G --

gaussian_draws	Posterior samples using a simple Metropolis Hastings sampler
gaussian_draws.gam	Posterior samples using a simple Metropolis Hastings sampler
gaussian_draws.scam	Posterior samples using a simple Metropolis Hastings sampler
generate_draws	Low-level Functions to generate draws from the posterior distribution of model coefficients
generate_draws.gam	Low-level Functions to generate draws from the posterior distribution of model coefficients
get_by_smooth	Extract an factor-by smooth by name
get_smooth	Extract an mgcv smooth by name
get_smooths_by_id	Extract an mgcv smooth given its position in the model object
get_smooths_by_id.gam	Extract an mgcv smooth given its position in the model object
get_smooths_by_id.gamm	Extract an mgcv smooth given its position in the model object
get_smooths_by_id.gamm4	Extract an mgcv smooth given its position in the model object
get_smooths_by_id.list	Extract an mgcv smooth given its position in the model object
get_smooths_by_id.scam	Extract an mgcv smooth given its position in the model object
gss_vocab	Data from the General Social Survey (GSS) from the National Opinion Research Center of the University of Chicago
gw_f0	Gu and Wabha test functions
gw_f1	Gu and Wabha test functions
gw_f2	Gu and Wabha test functions
gw_f3	Gu and Wabha test functions
gw_functions	Gu and Wabha test functions

-- H --

has_theta

Are additional parameters available for a GAM?

-- I --

inv_link	Extract link and inverse link functions from models
inv_link.bam	Extract link and inverse link functions from models
inv_link.family	Extract link and inverse link functions from models
inv_link.gam	Extract link and inverse link functions from models
inv_link.gamm	Extract link and inverse link functions from models
inv_link.glm	Extract link and inverse link functions from models
inv_link.list	Extract link and inverse link functions from models
is_by_smooth	Tests for by variable smooths
is_continuous_by_smooth	Tests for by variable smooths
is_factor_by_smooth	Tests for by variable smooths
is_factor_term	Is a model term a factor (categorical)?
is_factor_term.bam	Is a model term a factor (categorical)?
is_factor_term.gam	Is a model term a factor (categorical)?
is_factor_term.gamm	Is a model term a factor (categorical)?
is_factor_term.list	Is a model term a factor (categorical)?
is_factor_term.terms	Is a model term a factor (categorical)?
is_mgcv_smooth	Check if objects are smooths or are a particular type of smooth
is_mrf_smooth	Check if objects are smooths or are a particular type of smooth
is_offset	Is a model term an offset?

-- L --

level	Return the reference or specific level of a factor
link	Extract link and inverse link functions from models
link.bam	Extract link and inverse link functions from models
link.family	Extract link and inverse link functions from models
link.gam	Extract link and inverse link functions from models
link.gamm	Extract link and inverse link functions from models
link.glm	Extract link and inverse link functions from models
link.list	Extract link and inverse link functions from models
load_mgcv	Load mgcv quietly
lp_matrix	Return the linear prediction matrix of a fitted GAM
lp_matrix.gam	Return the linear prediction matrix of a fitted GAM

-- M --

mh_draws	Posterior samples using a Gaussian approximation to the posterior distribution
mh_draws.gam	Posterior samples using a Gaussian approximation to the posterior distribution
model_concurvity	Concurvity of an estimated GAM
model_concurvity.gam	Concurvity of an estimated GAM
model_constant	Extract the model constant term
model_edf	Effective degrees of freedom for smooths and GAMs
model_vars	List the variables involved in a model fitted with a formula
model_vars.bam	List the variables involved in a model fitted with a formula
model_vars.default	List the variables involved in a model fitted with a formula
model_vars.gam	List the variables involved in a model fitted with a formula
model_vars.gamm	List the variables involved in a model fitted with a formula
model_vars.gamm4	List the variables involved in a model fitted with a formula
model_vars.list	List the variables involved in a model fitted with a formula

-- N --

nb_theta	Negative binomial parameter theta
nb_theta.gam	Negative binomial parameter theta
null_deviance	Extract the null deviance of a fitted model
null_deviance.default	Extract the null deviance of a fitted model
n_smooths	How many smooths in a fitted model
n_smooths.bam	How many smooths in a fitted model
n_smooths.default	How many smooths in a fitted model
n_smooths.gam	How many smooths in a fitted model
n_smooths.gamm	How many smooths in a fitted model

-- O --

observed_fitted_plot	Plot of fitted against observed response values
overview	Provides an overview of a model and the terms in that model
overview.gam	Provides an overview of a model and the terms in that model

-- P --

parametric_effects	Estimated values for parametric model terms
parametric_effects.gam	Estimated values for parametric model terms
parametric_terms	Names of any parametric terms in a GAM
parametric_terms.default	Names of any parametric terms in a GAM
parametric_terms.gam	Names of any parametric terms in a GAM
partial_derivatives	Partial derivatives of estimated multivariate smooths via finite differences
partial_derivatives.default	Partial derivatives of estimated multivariate smooths via finite differences
partial_derivatives.gam	Partial derivatives of estimated multivariate smooths via finite differences
partial_derivatives.gamm	Partial derivatives of estimated multivariate smooths via finite differences
partial_residuals	Partial residuals
partial_residuals.gam	Partial residuals
penalty	Extract and tidy penalty matrices
penalty.default	Extract and tidy penalty matrices
penalty.gam	Extract and tidy penalty matrices
penalty.mgcv.smooth	Extract and tidy penalty matrices
penalty.re.smooth.spec	Extract and tidy penalty matrices
penalty.t2.smooth	Extract and tidy penalty matrices
penalty.tensor.smooth	Extract and tidy penalty matrices
posterior_samples	Draw samples from the posterior distribution of an estimated model
posterior_samples.gam	Draw samples from the posterior distribution of an estimated model
post_draws	Low-level Functions to generate draws from the posterior distribution of model coefficients
post_draws.default	Low-level Functions to generate draws from the posterior distribution of model coefficients
predicted_samples	Draw new response values from the conditional distribution of the response
predicted_samples.gam	Draw new response values from the conditional distribution of the response

-- Q --

qq_plot	Quantile-quantile plot of model residuals
qq_plot.default	Quantile-quantile plot of model residuals
qq_plot.gam	Quantile-quantile plot of model residuals
qq_plot.glm	Quantile-quantile plot of model residuals
qq_plot.lm	Quantile-quantile plot of model residuals

-- R --

ref_level	Return the reference or specific level of a factor
ref_sims	Reference simulation data
rep_first_factor_value	Repeat the first level of a factor n times
residuals_hist_plot	Histogram of model residuals
residuals_linpred_plot	Plot of residuals versus linear predictor values
response_derivatives	Derivatives on the response scale from an estimated GAM
response_derivatives.default	Derivatives on the response scale from an estimated GAM
response_derivatives.gam	Derivatives on the response scale from an estimated GAM
response_derivatives.gamm	Derivatives on the response scale from an estimated GAM
rootogram	Rootograms to assess goodness of model fit
rootogram.gam	Rootograms to assess goodness of model fit

-- S --

seq_min_max	Create a sequence of evenly-spaced values
seq_min_max_eps	Create a sequence of evenly-spaced values adjusted to accommodate a small adjustment
shift_values	Shift numeric values in a data frame by an amount 'eps'
simulate.gam	Simulate from the posterior distribution of a GAM
simulate.gamm	Simulate from the posterior distribution of a GAM
simulate.scam	Simulate from the posterior distribution of a GAM
smallAges	Lead-210 age-depth measurements for Small Water
smooths	Names of smooths in a GAM
smooths.default	Names of smooths in a GAM
smooths.gamm	Names of smooths in a GAM
smooth_coefs	Coefficients for a particular smooth
smooth_coefs.bam	Coefficients for a particular smooth
smooth_coefs.gam	Coefficients for a particular smooth
smooth_coefs.gamm	Coefficients for a particular smooth
smooth_coefs.gamm4	Coefficients for a particular smooth
smooth_coefs.list	Coefficients for a particular smooth
smooth_coefs.mgcv.smooth	Coefficients for a particular smooth
smooth_coefs.scam	Coefficients for a particular smooth
smooth_coef_indices	Indices of the parametric terms for a particular smooth
smooth_data	Generate regular data over the covariates of a smooth
smooth_dim	Dimension of a smooth
smooth_dim.gam	Dimension of a smooth
smooth_dim.gamm	Dimension of a smooth
smooth_dim.mgcv.smooth	Dimension of a smooth
smooth_estimates	Evaluate smooths at covariate values
smooth_estimates.gam	Evaluate smooths at covariate values
smooth_label	Extract the label for a smooth used by 'mgcv'
smooth_label.gam	Extract the label for a smooth used by 'mgcv'
smooth_label.mgcv.smooth	Extract the label for a smooth used by 'mgcv'
smooth_samples	Posterior draws for individual smooths
smooth_samples.gam	Posterior draws for individual smooths
smooth_terms	List the variables involved in smooths
smooth_type	Determine the type of smooth and return it n a human readable form
smooth_type.Bspline.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.cp.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.cr.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.cs.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.cv.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.cx.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.cyclic.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.default	Determine the type of smooth and return it n a human readable form
smooth_type.duchon.spline	Determine the type of smooth and return it n a human readable form
smooth_type.fs.interaction	Determine the type of smooth and return it n a human readable form
smooth_type.gp.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.mdcv.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.mdcx.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.micv.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.micx.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.mifo.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.miso.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.mpd.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.mpi.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.mrf.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.pspline.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.random.effect	Determine the type of smooth and return it n a human readable form
smooth_type.sf	Determine the type of smooth and return it n a human readable form
smooth_type.soap.film	Determine the type of smooth and return it n a human readable form
smooth_type.sos.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.sw	Determine the type of smooth and return it n a human readable form
smooth_type.sz.interaction	Determine the type of smooth and return it n a human readable form
smooth_type.t2.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.tensor.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.tprs.smooth	Determine the type of smooth and return it n a human readable form
smooth_type.ts.smooth	Determine the type of smooth and return it n a human readable form
spline_values	Evaluate a spline at provided covariate values
stop_if_not_mgcv_smooth	Check if objects are smooths or are a particular type of smooth

-- T --

term_names	Extract names of all variables needed to fit a GAM or a smooth
term_names.gam	Extract names of all variables needed to fit a GAM or a smooth
term_names.gamm	Extract names of all variables needed to fit a GAM or a smooth
term_names.mgcv.smooth	Extract names of all variables needed to fit a GAM or a smooth
term_variables	Names of variables involved in a specified model term
term_variables.bam	Names of variables involved in a specified model term
term_variables.gam	Names of variables involved in a specified model term
term_variables.terms	Names of variables involved in a specified model term
theta	General extractor for additional parameters in mgcv models
theta.gam	General extractor for additional parameters in mgcv models
tidy_basis	A tidy basis representation of a smooth object
too_far	Exclude values that lie too far from the support of data
too_far_to_na	Set rows of data to 'NA' if the lie too far from a reference set of values
to_na	Sets the elements of vector to 'NA'
transform_fun	Transform estimated values and confidence intervals by applying a function
transform_fun.evaluated_parametric_term	Transform estimated values and confidence intervals by applying a function
transform_fun.mgcv_smooth	Transform estimated values and confidence intervals by applying a function
transform_fun.parametric_effects	Transform estimated values and confidence intervals by applying a function
transform_fun.smooth_estimates	Transform estimated values and confidence intervals by applying a function
transform_fun.smooth_samples	Transform estimated values and confidence intervals by applying a function
transform_fun.tbl_df	Transform estimated values and confidence intervals by applying a function
typical_values	Typical values of model covariates
typical_values.data.frame	Typical values of model covariates
typical_values.gam	Typical values of model covariates

-- U --

user_draws

Handle user-supplied posterior draws

-- V --

variance_comp	Variance components of smooths from smoothness estimates
variance_comp.gam	Variance components of smooths from smoothness estimates
vars_from_label	Returns names of variables from a smooth label

-- W --

which_smooths	Identify a smooth term by its label
which_smooths.bam	Identify a smooth term by its label
which_smooths.default	Identify a smooth term by its label
which_smooths.gam	Identify a smooth term by its label
which_smooths.gamm	Identify a smooth term by its label
worm_plot	Worm plot of model residuals
worm_plot.gam	Worm plot of model residuals
worm_plot.glm	Worm plot of model residuals
worm_plot.lm	Worm plot of model residuals

-- Z --

zooplankton

Madison lakes zooplankton data