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mgcv (version 1.8-31)

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

65,728

Version

1.8-31

License

GPL (>= 2)

Maintainer

Last Published

November 9th, 2019

Functions in mgcv (1.8-31)

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

Setting up a list representing a block diagonal penalty matrix

Prediction methods for smooth terms in a GAM

Find rank of upper triangular matrix

Re-parametrizing model matrix X

Predict.matrix.soap.film

Prediction matrix for soap film smooth

Predict.matrix.cr.smooth

Predict matrix method functions

GAM Tweedie families

GAM beta regression family

Level 5 fractional factorial designs

Deletion and rank one Cholesky factor update

bug.reports.mgcv

Reporting mgcv bugs.

Internal functions for discretized model matrix handling

Additive Cox Proportional Hazard Model

Additive Cox proportional hazard models with time varying covariates

Approximate hypothesis tests related to GAM fits

Reduced version of Columbus OH crime data

GAM concurvity measures

Evaluate cyclic B spline basis

Basis dimension choice for smooths

extract.lme.cov

Extract the data covariance matrix from an lme object

blas.thread.test

BLAS thread safety

Choleski decomposition of a band diagonal matrix

fix.family.link

Modify families for use in GAM fitting and checking

Detect linear dependencies of one matrix on another

Form component of GAMM covariance matrix

Setting GAM fitting defaults

Generalized additive models with integrated smoothness estimation

GCV/UBRE score for use within nlm

Identifiability side conditions for a GAM

FELSPLINE test function

GAM P-IRLS estimation with GCV/UBRE smoothness estimation

gam.fit5.post.proc

Post-processing output of gam.fit5

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

Specifying generalized additive models

Distribution families in mgcv

Scale parameter estimation in GAMs

gam.convergence

GAM convergence and performance issues

Transform derivatives wrt mu to derivatives wrt linear predictor

Simulate example data for GAMs

Some diagnostics for a fitted gam model

Gamma location-scale model family

Generalized additive models for very large datasets

Gaussian location-scale model family

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

Interpret a GAM formula

AIC and Log likelihood for a fitted GAM

Just Another Gibbs Additive Modeller: JAGS support for mgcv.

Generalized Additive Model Selection

Generalized Extreme Value location-scale model family

Log Tweedie density evaluation

Checking smooth basis dimension

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

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

Size of list elements

GAM Integrated Nested Laplace Approximation Newton Enhanced

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

Report gam smoothness estimates as variance components

identifiability

Identifiability constraints

Starting values for multiple smoothing parameter estimation

Frequently Asked Questions for package mgcv

Are points inside boundary?

null.space.dimension

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

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

Monotonicity constraints for a cubic regression spline

Obtain square roots of penalty matrices

Update a strictly additive bam model for new data.

Multivariate normal additive models

GAM multinomial logistic regression

Parallel computation in mgcv.

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

GAM ordered categorical family

Prediction from fitted Big Additive Model model

Functions for better-than-log positive parameterization

Obtaining derivative w.r.t. linear predictor

Missing data in GAMs

Automatically place a set of knots evenly through covariate values

Random effects in GAMs

Generate Tweedie random deviates

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

smooth.construct.gp.smooth.spec

Low rank Gaussian process smooths

Overflow proof pdMat class for multiples of the identity matrix

GAM scaled t family for heavy tailed data

Functions implementing a pdMat class for tensor product smooths

Alternative to log parameterization for variance components

Extract or modify diagonals of a matrix

Smallest square root of matrix

Prediction from fitted GAM model

Default GAM plotting

model.matrix.gam

Extract model matrix from GAM fit

Print a Generalized Additive Model object.

smooth.construct.sos.smooth.spec

Splines on the sphere

Plot geographic regions defined as polygons

Compute truncated eigen decomposition of a symmetric matrix

QQ plots for gam model residuals

smooth.construct.so.smooth.spec

Soap film smoother constructer

Single index models with mgcv

exclude.too.far

Exclude prediction grid points too far from data

Define alternative tensor product smooths in GAM formulae

Generate multivariate normal deviates

Objective functions for GAM smoothing parameter estimation

GAM zero-inflated Poisson regression family

Define tensor product smooths or tensor product interactions in GAM formulae

Zero inflated Poisson location-scale model family

Generate inverse Gaussian random deviates

smooth.construct.cr.smooth.spec

Penalized Cubic regression splines in GAMs

Penalized Constrained Least Squares Fitting

The one standard error rule for smoother models

Generalized Additive Model residuals

Fitted gam object

smooth.construct.bs.smooth.spec

Penalized B-splines in GAMs

Defining smooths in GAM formulae

smooth.construct.tp.smooth.spec

Penalized thin plate regression splines in GAMs

smooth.construct.ps.smooth.spec

P-splines in GAMs

smooth.construct.re.smooth.spec

Simple random effects in GAMs

Smooth terms in GAM

Generalized Additive Mixed Models

magic.post.proc

Auxilliary information from magic fit

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

linear.functional.terms

Linear functionals of a smooth in GAMs

Getting log generalized determinant of penalty matrices

Calculating derivatives of log-likelihood wrt regression coefficients

GAM negative binomial families

Stable Multiple Smoothing Parameter Estimation by GCV or UBRE

smooth.construct.ds.smooth.spec

Low rank Duchon 1977 splines

Extract parameter (estimator) covariance matrix from GAM fit

Visualization of GAM objects

find the unique rows in a matrix

Summary for a GAM fit

Tweedie location scale family

Alternatives to step.gam

smooth.construct.t2.smooth.spec

Tensor product smoothing constructor

smooth.construct.tensor.smooth.spec

Tensor product smoothing constructor

smooth.construct.mrf.smooth.spec

Markov Random Field Smooths

Choleski decomposition of a tri-diagonal matrix

smooth.construct

Constructor functions for smooth terms in a GAM

trind.generator

Generates index arrays for upper triangular storage

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

smooth.construct.fs.smooth.spec

Factor smooth interactions in GAMs

spasm.construct

Experimental sparse smoothers

smooth.construct.ad.smooth.spec

Adaptive smooths in GAMs

Prediction/Construction wrapper functions for GAM smooth terms

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

tensor.prod.model.matrix

Row Kronecker product/ tensor product smooth construction

totalPenaltySpace

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