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mgcv (version 1.9-3)

Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Description

Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.

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Version

Install

install.packages('mgcv')

Monthly Downloads

57,632

Version

1.9-3

License

GPL (>= 2)

Maintainer

Simon Wood

Last Published

April 4th, 2025

Functions in mgcv (1.9-3)

Applying re-parameterization from log-determinant of penalty matrix to model matrix.

Setting up a list representing a block diagonal penalty matrix

Find rank of upper triangular matrix

blas.thread.test

BLAS thread safety

GAM beta regression family

Re-parametrizing model matrix X

Approximate hypothesis tests related to GAM fits

Obtaining derivative w.r.t. linear predictor

Predict.matrix.soap.film

Prediction matrix for soap film smooth

Stable evaluation of difference between normal c.d.f.s

fix.family.link

Modify families for use in GAM fitting and checking

Neighbourhood Cross Validation

Update a strictly additive bam model for new data.

Detect linear dependencies of one matrix on another

Prediction methods for smooth terms in a GAM

gam.fit5.post.proc

Post-processing output of gam.fit5

Level 5 fractional factorial designs

GAM Tweedie families

Evaluate cyclic B spline basis

Internal functions for discretized model matrix handling

Simple posterior simulation with gam fits

Deletion and rank one Cholesky factor update

exclude.too.far

Exclude prediction grid points too far from data

extract.lme.cov

Extract the data covariance matrix from an lme object

Setting GAM fitting defaults

Basis dimension choice for smooths

GAM censored logistic distribution family for log-logistic AFT models

Choleski decomposition of a band diagonal matrix

Additive Cox proportional hazard models with time varying covariates

GAM censored Poisson family

bug.reports.mgcv

Reporting mgcv bugs.

GAM censored normal family for log-normal AFT and Tobit models

Reduced version of Columbus OH crime data

Generalized additive models with integrated smoothness estimation

Generalized Additive Model Selection

Factor smooth interactions in GAMs

Identifiability side conditions for a GAM

Generalized additive models for very large datasets

GAM concurvity measures

Starting values for multiple smoothing parameter estimation

Form component of GAMM covariance matrix

gam.convergence

GAM convergence and performance issues

Additive Cox Proportional Hazard Model

Finding stable orthogonal re-parameterization of the square root penalty.

Some diagnostics for a fitted gam model

Scale parameter estimation in GAMs

Interpret a GAM formula

Gaussian location-scale model family

identifiability

Identifiability constraints

Specifying generalized additive models

Which of a set of points lie within a polygon defined region

Get named variable or evaluate expression from list or data.frame

Are points inside boundary?

Extract the diagonal of the influence/hat matrix for a GAM

FELSPLINE test function

Minimize GCV or UBRE score of a GAM using `outer' iteration

Fitted gam object

Sparse chol function

GCV/UBRE score for use within nlm

Obtain square roots of penalty matrices

Simulate example data for GAMs

Just Another Gibbs Additive Modeller: JAGS support for mgcv.

Checking smooth basis dimension

Basic linear programming

Frequently Asked Questions for package mgcv

Missing data in GAMs

GAM Integrated Nested Laplace Approximation Newton Enhanced

Distribution families in mgcv

Size of list elements

Alternative to log parameterization for variance components

GAM P-IRLS estimation with GCV/UBRE smoothness estimation

Report gam smoothness estimates as variance components

Gumbel location-scale model family

Objective functions for GAM smoothing parameter estimation

P-IRLS GAM estimation with GCV, UBRE/AIC or RE/ML derivative calculation

Transform derivatives wrt mu to derivatives wrt linear predictor

Stable Multiple Smoothing Parameter Estimation by GCV or UBRE

null.space.dimension

The basis of the space of un-penalized functions for a TPRS

Penalized Constrained Least Squares Fitting

Plot geographic regions defined as polygons

model.matrix.gam

Extract model matrix from GAM fit

Calculating derivatives of log-likelihood wrt regression coefficients

Generalized Extreme Value location-scale model family

Monotonicity constraints for a cubic regression spline

Generalized Additive Mixed Models

magic.post.proc

Auxilliary information from magic fit

Grouped families

Multivariate normal additive models

GAM negative binomial families

Gamma location-scale model family

Log Tweedie density evaluation

Functions implementing a pdMat class for tensor product smooths

Extract the effective degrees of freedom associated with each penalty in a gam fit

smooth.construct.ad.smooth.spec

Adaptive smooths in GAMs

Automatically place a set of knots evenly through covariate values

smooth.construct.bs.smooth.spec

Penalized B-splines in GAMs

Overflow proof pdMat class for multiples of the identity matrix

Default GAM plotting

linear.functional.terms

Linear functionals of a smooth in GAMs

AIC and Log likelihood for a fitted GAM

Getting log generalized determinant of penalty matrices

Prediction from fitted Big Additive Model model

Generalized Additive Model residuals

Generate Tweedie random deviates

Generate inverse Gaussian random deviates

Random effects in GAMs

Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL

smooth.construct.cr.smooth.spec

Penalized Cubic regression splines in GAMs

smooth.construct.t2.smooth.spec

Tensor product smoothing constructor

Parallel computation in mgcv.

Obtain a name for a new variable that is not already in use

Functions for better-than-log positive parameterization

Smallest square root of matrix

GAM multinomial logistic regression

Generate from or evaluate multivariate normal or t densities.

smooth.construct.mrf.smooth.spec

Markov Random Field Smooths

Defining smooths in GAM formulae

smooth.construct.ds.smooth.spec

Low rank Duchon 1977 splines

GAM ordered categorical family

smooth.construct.tensor.smooth.spec

Tensor product smoothing constructor

smooth.construct.re.smooth.spec

Simple random effects in GAMs

smooth.construct.so.smooth.spec

Soap film smoother constructer

Convert a smooth to a form suitable for estimating as random effect

Smooth terms in GAM

Visualization of GAM objects

Prediction from fitted GAM model

Sinh-arcsinh location scale and shape model family

Prediction/Construction wrapper functions for GAM smooth terms

Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit

smooth.construct.ps.smooth.spec

P-splines in GAMs

Print a Generalized Additive Model object.

Single index models with mgcv

GAM zero-inflated (hurdle) Poisson regression family

The one standard error rule for smoother models

smooth.construct.tp.smooth.spec

Penalized thin plate regression splines in GAMs

Evaluate the c.d.f. of a weighted sum of chi-squared deviates

GAM scaled t family for heavy tailed data

QQ plots for gam model residuals

Generic function to provide extra information about smooth specification

spasm.construct

Experimental sparse smoothers

trind.generator

Generates index arrays for upper triangular storage

Tweedie location scale family

Extract or modify diagonals of a matrix

Compute truncated eigen decomposition of a symmetric matrix

smooth.construct

Constructor functions for smooth terms in a GAM

smooth.construct.sos.smooth.spec

Splines on the sphere

smooth.construct.fs.smooth.spec

Factor smooth interactions in GAMs

Alternatives to step.gam

smooth.construct.gp.smooth.spec

Low rank Gaussian process smooths

smooth.construct.sz.smooth.spec

Constrained factor smooth interactions in GAMs

find the unique rows in a matrix

Summary for a GAM fit

Extract parameter (estimator) covariance matrix from GAM fit

Zero inflated (hurdle) Poisson location-scale model family

Define tensor product smooths or tensor product interactions in GAM formulae

tensor.prod.model.matrix

Row Kronecker product/ tensor product smooth construction

Define alternative tensor product smooths in GAM formulae

totalPenaltySpace

Obtaining (orthogonal) basis for null space and range of the penalty matrix

Choleski decomposition of a tri-diagonal matrix

Predict.matrix.cr.smooth

Predict matrix method functions