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mgcv (version 1.8-17)

Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation

Description

GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. 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

134,785

Version

1.8-17

License

GPL (>= 2)

Maintainer

Simon Wood

Last Published

February 8th, 2017

Functions in mgcv (1.8-17)

cox.ph

Additive Cox Proportional Hazard Model
cox.pht

Additive Cox proportional hazard models with time varying covariates
choose.k

Basis dimension choice for smooths
bug.reports.mgcv

Reporting mgcv bugs.
betar

GAM beta regression family
bam.update

Update a strictly additive bam model for new data.
bandchol

Choleski decomposition of a band diagonal matrix
cSplineDes

Evaluate cyclic B spline basis
anova.gam

Approximate hypothesis tests related to GAM fits
bam

Generalized additive models for very large datasets
full.score

GCV/UBRE score for use within nlm
fs.test

FELSPLINE test function
extract.lme.cov

Extract the data covariance matrix from an lme object
fixDependence

Detect linear dependencies of one matrix on another
exclude.too.far

Exclude prediction grid points too far from data
formula.gam

GAM formula
family.mgcv

Distribution families in mgcv
fix.family.link

Modify families for use in GAM fitting and checking
formXtViX

Form component of GAMM covariance matrix
gam.check

Some diagnostics for a fitted gam model
gam.control

Setting GAM fitting defaults
gam

Generalized additive models with integrated smoothness estimation
gam.convergence

GAM convergence and performance issues
gam.models

Specifying generalized additive models
gam.selection

Generalized Additive Model Selection
gam.outer

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

Scale parameter estimation in GAMs
gam.side

Identifiability side conditions for a GAM
gam.fit

GAM P-IRLS estimation with GCV/UBRE smoothness estimation
gam.fit3

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

Calculating derivatives of log-likelihood wrt regression coefficients
gamlss.etamu

Transform derivatives wrt mu to derivatives wrt linear predictor
gam.vcomp

Report gam smoothness estimates as variance components
gamSim

Simulate example data for GAMs
gam2objective

Objective functions for GAM smoothing parameter estimation
gevlss

Generalized Extreme Value location-scale model family
identifiability

Identifiability constraints
gaulss

Gaussian location-scale model family
get.var

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

Fitted gam object
ls.size

Size of list elements
interpret.gam

Interpret a GAM formula
inSide

Are points inside boundary?
influence.gam

Extract the diagonal of the influence/hat matrix for a GAM
logLik.gam

Log likelihood for a fitted GAM, for AIC
in.out

Which of a set of points lie within a polygon defined region
initial.sp

Starting values for multiple smoothing parameter estimation
ldTweedie

Log Tweedie density evaluation
jagam

Just Another Gibbs Additive Modeller: JAGS support for mgcv.
linear.functional.terms

Linear functionals of a smooth in GAMs
mroot

Smallest square root of matrix
mgcv.package

Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL
model.matrix.gam

Extract model matrix from GAM fit
missing.data

Missing data in GAMs
mono.con

Monotonicity constraints for a cubic regression spline
mgcv.FAQ

Frequently Asked Questions for package mgcv
multinom

GAM multinomial logistic regression
mvn

Multivariate normal additive models
mgcv.parallel

Parallel computation in mgcv.
negbin

GAM negative binomial families
pdIdnot

Overflow proof pdMat class for multiples of the identity matrix
notExp2

Alternative to log parameterization for variance components
one.se.rule

The one standard error rule for smoother models
pcls

Penalized Constrained Least Squares Fitting
ocat

GAM ordered categorical family
null.space.dimension

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

Functions implementing a pdMat class for tensor product smooths
pen.edf

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

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

Functions for better-than-log positive parameterization
place.knots

Automatically place a set of knots evenly through covariate values
Predict.matrix

Prediction methods for smooth terms in a GAM
plot.gam

Default GAM plotting
Predict.matrix.soap.film

Prediction matrix for soap film smooth
predict.gam

Prediction from fitted GAM model
Predict.matrix.cr.smooth

Predict matrix method functions
print.gam

Print a Generalized Additive Model object.
qq.gam

QQ plots for gam model residuals
s

Defining smooths in GAM formulae
scat

GAM scaled t family for heavy tailed data
random.effects

Random effects in GAMs
residuals.gam

Generalized Additive Model residuals
slanczos

Compute truncated eigen decomposition of a symmetric matrix
predict.bam

Prediction from fitted Big Additive Model model
smooth.construct.ad.smooth.spec

Adaptive smooths in GAMs
polys.plot

Plot geographic regions defined as polygons
smooth.construct.gp.smooth.spec

Low rank Gaussian process smooths
smooth.construct.ps.smooth.spec

P-splines in GAMs
smooth2random

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

Prediction/Construction wrapper functions for GAM smooth terms
smooth.construct.ds.smooth.spec

Low rank Duchon 1977 splines
smooth.construct.fs.smooth.spec

Factor smooth interactions in GAMs
smooth.construct.t2.smooth.spec

Tensor product smoothing constructor
Rrank

Find rank of upper triangular matrix
rTweedie

Generate Tweedie random deviates
smooth.construct.sos.smooth.spec

Splines on the sphere
sp.vcov

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

Experimental sparse smoothers
rig

Generate inverse Gaussian random deviates
rmvn

Generate multivariate normal deviates
smooth.construct.cr.smooth.spec

Penalized Cubic regression splines in GAMs
smooth.construct.bs.smooth.spec

Penalized B-splines in GAMs
smooth.construct.tp.smooth.spec

Penalized thin plate regression splines in GAMs
vis.gam

Visualization of GAM objects
smooth.construct.tensor.smooth.spec

Tensor product smoothing constructor
vcov.gam

Extract parameter (estimator) covariance matrix from GAM fit
sdiag

Extract or modify diagonals of a matrix
smooth.construct.re.smooth.spec

Simple random effects in GAMs
single.index

Single index models with mgcv
smooth.construct.so.smooth.spec

Soap film smoother constructer
summary.gam

Summary for a GAM fit
t2

Define alternative tensor product smooths in GAM formulae
Tweedie

GAM Tweedie families
ziP

GAM zero-inflated Poisson regression family
ziplss

Zero inflated Poisson location-scale model family
uniquecombs

find the unique rows in a matrix
trichol

Choleski decomposition of a tri-diagonal matrix
trind.generator

Generates index arrays for upper triangular storage
te

Define tensor product smooths or tensor product interactions in GAM formulae
tensor.prod.model.matrix

Utility functions for constructing tensor product smooths
concurvity

GAM concurvity measures
columb

Reduced version of Columbus OH crime data
gamm

Generalized Additive Mixed Models
magic.post.proc

Auxilliary information from magic fit
magic

Stable Multiple Smoothing Parameter Estimation by GCV or UBRE
smooth.construct.mrf.smooth.spec

Markov Random Field Smooths
smooth.construct

Constructor functions for smooth terms in a GAM
step.gam

Alternatives to step.gam
smooth.terms

Smooth terms in GAM