# GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL

## Documentation for package ‘mgcv’ version 1.6-2

- DESCRIPTION file.

## Help Pages

A B C D E F G I L M N P R S T U V

## -- --

mgcv-package | GAMs with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL

## -- A --

adaptive.smooth | Adaptive smooths in GAMs
anova.gam | Approximate hypothesis tests related to GAM fits

## -- B --

bam | Generalized additive models for very large datasets
bam.update | Update a strictly additive bam model for new data.

## -- C --

choose.k | Basis dimension choice for smooths
coef.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
coef.pdTens | Functions implementing a pdMat class for tensor product smooths
corMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
cSplineDes | Evaluate cyclic B spline basis
cubic.regression.spline | Penalized Cubic regression splines in GAMs
cyclic.cubic.spline | Penalized Cubic regression splines in GAMs
cyclic.p.spline | P-splines in GAMs

## -- D --

Dim.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix

## -- E --

exclude.too.far | Exclude prediction grid points too far from data
extract.lme.cov | Extract the data covariance matrix from an lme object
extract.lme.cov2 | Extract the data covariance matrix from an lme object

## -- F --

fix.family.link | Modify families for use in GAM fitting
fix.family.ls | Modify families for use in GAM fitting
fix.family.var | Modify families for use in GAM fitting
fixDependence | Detect linear dependencies of one matrix on another
formula.gam | GAM formula
formXtViX | Form component of GAMM covariance matrix
full.score | GCV/UBRE score for use within nlm
function.predictors | Linear functionals of a smooth in GAMs

## -- G --

gam | Generalized additive models with integrated smoothness estimation
gam.check | Some diagnostics for a fitted gam model
gam.control | Setting GAM fitting defaults
gam.convergence | GAM convergence and performance issues
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
gam.models | Specifying generalized additive models
gam.outer | Minimize GCV or UBRE score of a GAM using 'outer' iteration
gam.performance | GAM convergence and performance issues
gam.selection | Generalized Additive Model Selection
gam.side | Identifiability side conditions for a GAM
gam.vcomp | Report gam smoothness estimates as variance components
gam2derivative | Objective functions for GAM smoothing parameter estimation
gam2objective | Objective functions for GAM smoothing parameter estimation
gamm | Generalized Additive Mixed Models
gamObject | Fitted gam object
gamSim | Simulate example data for GAMs
get.var | Get named variable or evaluate expression from list or data.frame

## -- I --

influence.gam | Extract the diagonal of the influence/hat matrix for a GAM
initial.sp | Starting values for multiple smoothing parameter estimation
interpret.gam | Interpret a GAM formula

## -- L --

ldTweedie | Log Tweedie density evaluation
linear.functional.terms | Linear functionals of a smooth in GAMs
logDet.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
logLik.gam | Extract the log likelihood for a fitted GAM
ls.size | Size of list elements

## -- M --

magic | Stable Multiple Smoothing Parameter Estimation by GCV or UBRE, with optional fixed penalty
magic.post.proc | Auxilliary information from magic fit
mgcv | Multiple Smoothing Parameter Estimation by GCV or UBRE
mgcv.control | Setting mgcv defaults
model.matrix.gam | Extract model matrix from GAM fit
mono.con | Monotonicity constraints for a cubic regression spline
mroot | Smallest square root of matrix

## -- N --

negbin | GAM negative binomial family
new.name | Obtain a name for a new variable that is not already in use
notExp | Functions for better-than-log positive parameterization
notExp2 | Alternative to log parameterization for variance components
notLog | Functions for better-than-log positive parameterization
notLog2 | Alternative to log parameterization for variance components
null.space.dimension | The basis of the space of un-penalized functions for a TPRS

## -- P --

p.spline | P-splines in GAMs
pcls | Penalized Constrained Least Squares Fitting
pdConstruct.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
pdConstruct.pdTens | Functions implementing a pdMat class for tensor product smooths
pdFactor.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
pdFactor.pdTens | Functions implementing a pdMat class for tensor product smooths
pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
pdMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
pdMatrix.pdTens | Functions implementing a pdMat class for tensor product smooths
pdTens | Functions implementing a pdMat class for tensor product smooths
persp.gam | Visualization of GAM objects
place.knots | Automatically place a set of knots evenly through covariate values
plot.gam | Default GAM plotting
predict.gam | Prediction from fitted GAM model
Predict.matrix | Prediction methods for smooth terms in a GAM
Predict.matrix.cr.smooth | Predict matrix method functions
Predict.matrix.cs.smooth | Predict matrix method functions
Predict.matrix.cyclic.smooth | Predict matrix method functions
Predict.matrix.pspline.smooth | Predict matrix method functions
Predict.matrix.random.effect | Simple random effects in GAMs
Predict.matrix.tensor.smooth | Predict matrix method functions
Predict.matrix.tprs.smooth | Predict matrix method functions
Predict.matrix.ts.smooth | Predict matrix method functions
Predict.matrix2 | Prediction methods for smooth terms in a GAM
PredictMat | Prediction/Construction wrapper functions for GAM smooth terms
print.anova.gam | Approximate hypothesis tests related to GAM fits
print.gam | Print a Generalized Additive Model object.
print.summary.gam | Summary for a GAM fit

## -- R --

random.effects | Random effects in GAMs
residuals.gam | Generalized Additive Model residuals
rig | Generate inverse Gaussian random deviates

## -- S --

s | Defining smooths in GAM formulae
signal.regression | Linear functionals of a smooth in GAMs
smooth.construct | Constructor functions for smooth terms in a GAM
smooth.construct.ad.smooth.spec | Adaptive smooths in GAMs
smooth.construct.cc.smooth.spec | Penalized Cubic regression splines in GAMs
smooth.construct.cp.smooth.spec | P-splines in GAMs
smooth.construct.cr.smooth.spec | Penalized Cubic regression splines in GAMs
smooth.construct.cs.smooth.spec | Penalized Cubic regression splines in GAMs
smooth.construct.ps.smooth.spec | P-splines in GAMs
smooth.construct.re.smooth.spec | Simple random effects in GAMs
smooth.construct.tensor.smooth.spec | Tensor product smoothing constructor
smooth.construct.tp.smooth.spec | Penalized thin plate regression splines in GAMs
smooth.construct.ts.smooth.spec | Penalized thin plate regression splines in GAMs
smooth.construct2 | Constructor functions for smooth terms in a GAM
smooth.terms | Smooth terms in GAM
smoothCon | Prediction/Construction wrapper functions for GAM smooth terms
solve.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
sp.vcov | Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit
step.gam | Alternatives to step.gam
summary.gam | Summary for a GAM fit
summary.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
summary.pdTens | Functions implementing a pdMat class for tensor product smooths

## -- T --

te | Define tensor product smooths in GAM formulae
tensor.prod.model.matrix | Utility functions for constructing tensor product smooths
tensor.prod.penalties | Utility functions for constructing tensor product smooths
tprs | Penalized thin plate regression splines in GAMs
Tweedie | GAM Tweedie family

## -- U --

uniquecombs | find the unique rows in a matrix
user.defined.smooth | Constructor functions for smooth terms in a GAM

## -- V --

vcov.gam | Extract parameter (estimator) covariance matrix from GAM fit
vis.gam | Visualization of GAM objects