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mgcv (version 1.8-28)

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

62,907

Version

1.8-28

License

GPL (>= 2)

Maintainer

Last Published

March 21st, 2019

Functions in mgcv (1.8-28)

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

Deletion and rank one Cholesky factor update

bug.reports.mgcv

Reporting mgcv bugs.

Additive Cox proportional hazard models with time varying covariates

Approximate hypothesis tests related to GAM fits

Additive Cox Proportional Hazard Model

Reduced version of Columbus OH crime data

GAM concurvity measures

Evaluate cyclic B spline basis

Generalized additive models for very large datasets

Update a strictly additive bam model for new data.

Simulate example data for GAMs

extract.lme.cov

Extract the data covariance matrix from an lme object

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

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

Some diagnostics for a fitted gam model

Generalized additive models with integrated smoothness estimation

Transform derivatives wrt mu to derivatives wrt linear predictor

Distribution families in mgcv

Basis dimension choice for smooths

Are points inside boundary?

fix.family.link

Modify families for use in GAM fitting and checking

Detect linear dependencies of one matrix on another

gam.fit5.post.proc

Post-processing output of gam.fit5

Choleski decomposition of a band diagonal matrix

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

FELSPLINE test function

Form component of GAMM covariance matrix

Generalized Extreme Value location-scale model family

GCV/UBRE score for use within nlm

GAM Integrated Nested Laplace Approximation Newton Enhanced

Obtaining derivative w.r.t. linear predictor

exclude.too.far

Exclude prediction grid points too far from data

Smallest square root of matrix

Scale parameter estimation in GAMs

Setting GAM fitting defaults

Generalized Additive Model Selection

gam.convergence

GAM convergence and performance issues

Identifiability side conditions for a GAM

Log Tweedie density evaluation

Size of list elements

Specifying generalized additive models

Obtain square roots of penalty matrices

Report gam smoothness estimates as variance components

Stable Multiple Smoothing Parameter Estimation by GCV or UBRE

Getting log generalized determinant of penalty matrices

GAM multinomial logistic regression

GAM P-IRLS estimation with GCV/UBRE smoothness estimation

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

Alternative to log parameterization for variance components

null.space.dimension

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

Gaussian location-scale model family

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

Missing data in GAMs

Penalized Constrained Least Squares Fitting

Overflow proof pdMat class for multiples of the identity matrix

Objective functions for GAM smoothing parameter estimation

Fitted gam object

Extract or modify diagonals of a matrix

identifiability

Identifiability constraints

Single index models with mgcv

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

GAM ordered categorical family

linear.functional.terms

Linear functionals of a smooth in GAMs

Calculating derivatives of log-likelihood wrt regression coefficients

Functions implementing a pdMat class for tensor product smooths

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

Just Another Gibbs Additive Modeller: JAGS support for mgcv.

Checking smooth basis dimension

The one standard error rule for smoother models

Automatically place a set of knots evenly through covariate values

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

Parallel computation in mgcv.

Generalized Additive Mixed Models

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

AIC and Log likelihood for a fitted GAM

Functions for better-than-log positive parameterization

Default GAM plotting

Plot geographic regions defined as polygons

Generate inverse Gaussian random deviates

smooth.construct.ad.smooth.spec

Adaptive smooths in GAMs

Starting values for multiple smoothing parameter estimation

smooth.construct.bs.smooth.spec

Penalized B-splines in GAMs

Prediction/Construction wrapper functions for GAM smooth terms

Interpret a GAM formula

magic.post.proc

Auxilliary information from magic fit

Smooth terms in GAM

Generate multivariate normal deviates

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

model.matrix.gam

Extract model matrix from GAM fit

Frequently Asked Questions for package mgcv

smooth.construct.cr.smooth.spec

Penalized Cubic regression splines in GAMs

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

Summary for a GAM fit

trind.generator

Generates index arrays for upper triangular storage

Monotonicity constraints for a cubic regression spline

Define alternative tensor product smooths in GAM formulae

Tweedie location scale family

smooth.construct.ds.smooth.spec

Low rank Duchon 1977 splines

Prediction from fitted GAM model

Multivariate normal additive models

Print a Generalized Additive Model object.

Compute truncated eigen decomposition of a symmetric matrix

totalPenaltySpace

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

smooth.construct

Constructor functions for smooth terms in a GAM

smooth.construct.re.smooth.spec

Simple random effects in GAMs

Choleski decomposition of a tri-diagonal matrix

smooth.construct.so.smooth.spec

Soap film smoother constructer

GAM negative binomial families

Prediction from fitted Big Additive Model model

Defining smooths in GAM formulae

QQ plots for gam model residuals

Generate Tweedie random deviates

GAM scaled t family for heavy tailed data

Zero inflated Poisson location-scale model family

smooth.construct.mrf.smooth.spec

Markov Random Field Smooths

Random effects in GAMs

smooth.construct.sos.smooth.spec

Splines on the sphere

smooth.construct.ps.smooth.spec

P-splines in GAMs

Generalized Additive Model residuals

Visualization of GAM objects

smooth.construct.t2.smooth.spec

Tensor product smoothing constructor

spasm.construct

Experimental sparse smoothers

GAM zero-inflated Poisson regression family

Alternatives to step.gam

find the unique rows in a matrix

smooth.construct.fs.smooth.spec

Factor smooth interactions in GAMs

Extract parameter (estimator) covariance matrix from GAM fit

smooth.construct.gp.smooth.spec

Low rank Gaussian process smooths

smooth.construct.tensor.smooth.spec

Tensor product smoothing constructor

smooth.construct.tp.smooth.spec

Penalized thin plate regression splines in GAMs

Define tensor product smooths or tensor product interactions in GAM formulae

tensor.prod.model.matrix

Utility functions for constructing tensor product smooths

Prediction methods for smooth terms in a GAM

Predict.matrix.cr.smooth

Predict matrix method functions

Predict.matrix.soap.film

Prediction matrix for soap film smooth

Find rank of upper triangular matrix

Setting up a list representing a block diagonal penalty matrix

GAM Tweedie families

GAM beta regression family

Level 5 fractional factorial designs

Sl.initial.repara

Re-parametrizing model matrix X