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

Documentation for package ‘gratia’ version 0.4.1

Help Pages

-- A --

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_residuals	Add residuals from a model to a data frame
add_residuals.gam	Add residuals from a GAM to a data frame
appraise	Model diagnostic plots
appraise.gam	Model diagnostic plots
appraise.lm	Model diagnostic plots

-- B --

basis	Basis expansions for smooths
bird_move	Simulated bird migration data
by_level	Tests for by variable smooths
by_variable	Tests for by variable smooths

-- C --

check_user_select_smooths	Select smooths based on user's choices
coef.scam	Extract coefficients from a fitted 'scam' model.
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

-- D --

data_class	Vectorized version of 'data.class'
data_sim	Simulate example data for fitting GAMs
data_slice	Prepare a data slice through covariates
data_slice.default	Prepare a data slice through covariates
data_slice.gam	Prepare a data slice through covariates
data_slice.list	Prepare a data slice through 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
difference_smooths	Differences of factor smooth interactions
difference_smooths.gam	Differences of factor smooth interactions
draw	Generic plotting via 'ggplot2'
draw.derivatives	Plot derivatives of smooths
draw.difference_smooth	Plot differences of smooths
draw.evaluated_1d_smooth	Plot estimated smooths
draw.evaluated_2d_smooth	Plot estimated smooths
draw.evaluated_fs_smooth	Plot estimated smooths
draw.evaluated_parametric_term	Plot estimated smooths
draw.evaluated_re_smooth	Plot estimated smooths
draw.evaluated_smooth	Plot estimated smooths
draw.gam	Plot estimated smooths from a fitted GAM
draw.mgcv_smooth	Plot basis functions
draw.smooth_samples	Plot posterior smooths

-- E --

evaluate_parametric_term	Evaluate a smooth
evaluate_parametric_term.gam	Evaluate a smooth
evaluate_smooth	Evaluate a smooth
evaluate_smooth.gam	Evaluate a smooth
evaluate_smooth.gamm	Evaluate a smooth
evaluate_smooth.list	Evaluate a smooth

-- F --

factor_var_names	Names of any factor variables in model data
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
fderiv	First derivatives of fitted GAM functions
fderiv.gam	First derivatives of fitted GAM functions
fderiv.gamm	First derivatives of fitted GAM functions
fitted_samples	Draw fitted values from the posterior distribution
fitted_samples.gam	Draw fitted values from the posterior distribution
fix_offset	Fix the names of a data frame containing an offset variable.

-- G --

geom_rug	Plot estimated smooths
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
gss_vocab	Data from the General Social Survey (GSS) from the National Opinion Research Center of the University of Chicago

-- 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_factor_var	Vectorised checks for variable types
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_numeric_var	Vectorised checks for variable types
is_offset	Is a model term an offset?

-- L --

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

-- N --

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 --

Plot of fitted against observed response values

-- P --

parametric_terms	Names of any parametrix terms in a GAM
parametric_terms.default	Names of any parametrix terms in a GAM
parametric_terms.gam	Names of any parametrix terms in a GAM
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
predicted_samples	Draw fitted values from the posterior distribution
predicted_samples.gam	Draw fitted values from the posterior distribution

-- Q --

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

-- R --

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

-- 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
smooth_coefs	Indices of the parametric terms for a particular 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_samples	Posterior draws for individual smooths
smooth_samples.gam	Posterior draws for individual smooths

-- T --

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
tidy_basis	A tidy basis representation of a smooth object

-- V --

Returns names of variables from a smooth label

-- W --

which_smooths	Identify a smooth term by it's label
which_smooths.bam	Identify a smooth term by it's label
which_smooths.default	Identify a smooth term by it's label
which_smooths.gam	Identify a smooth term by it's label
which_smooths.gamm	Identify a smooth term by it's label

-- Z --

Madison lakes zooplankton data