# Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

## Documentation for package ‘mgcv’ version 1.9-4

- DESCRIPTION file

## Help Pages

A B C D E F G I J K L M N O P Q R S T U V X Z misc

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

## -- A --

adaptive.smooth | Adaptive smooths in GAMs
AIC.gam | AIC and Log likelihood for a fitted GAM
anova.gam | Approximate hypothesis tests related to GAM fits

## -- B --

b.spline | Penalized B-splines in GAMs
bam | Generalized additive models for very large datasets
bam.update | Update a strictly additive bam model for new data.
bandchol | Choleski decomposition of a band diagonal matrix
bcg | Censored Box-Cox Gaussian family
betar | GAM beta regression family
blas.thread.test | BLAS thread safety
bug.reports.mgcv | Reporting mgcv bugs.

## -- C --

choldrop | Deletion and rank one Cholesky factor update
cholup | Deletion and rank one Cholesky factor update
choose.k | Basis dimension choice for smooths
clog | GAM censored logistic distribution family for log-logistic AFT models
cnorm | GAM censored normal family for log-normal AFT and Tobit models
coef.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
coef.pdTens | Functions implementing a pdMat class for tensor product smooths
columb | Reduced version of Columbus OH crime data
columb.polys | Reduced version of Columbus OH crime data
concurvity | GAM concurvity measures
corMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
cox.ph | Additive Cox Proportional Hazard Model
cox.pht | Additive Cox proportional hazard models with time varying covariates
cpois | GAM censored Poisson family
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 --

d.mvt | Generate from or evaluate multivariate normal or t densities.
d.spline | Penalized B-splines in GAMs
dDeta | Obtaining derivative w.r.t. linear predictor
diagXVXd | Internal functions for discretized model matrix handling
Dim.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix
dmvn | Generate from or evaluate multivariate normal or t densities.
dpnorm | Stable evaluation of difference between normal c.d.f.s
dppois | Stable evaluation of difference between Poisson c.d.f.s
Duchon.spline | Low rank Duchon 1977 splines

## -- 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 --

factor.smooth | Factor smooth interactions in GAMs
factor.smooth.interaction | Factor smooth interactions in GAMs
family.mgcv | Distribution families in mgcv
feasible | Basic linear programming
FFdes | Level 5 fractional factorial designs
fix.family.link | Modify families for use in GAM fitting and checking
fix.family.ls | Modify families for use in GAM fitting and checking
fix.family.qf | Modify families for use in GAM fitting and checking
fix.family.rd | Modify families for use in GAM fitting and checking
fix.family.var | Modify families for use in GAM fitting and checking
fixDependence | Detect linear dependencies of one matrix on another
formula.gam | GAM formula
formXtViX | Form component of GAMM covariance matrix
fs.boundary | FELSPLINE test function
fs.test | FELSPLINE test function
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 (deprecated)
gam.fit3 | P-IRLS GAM estimation with GCV, UBRE/AIC or RE/ML derivative calculation
gam.fit5.post.proc | Post-processing output of gam.fit5
gam.mh | Simple posterior simulation with gam fits
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.reparam | Finding stable orthogonal re-parameterization of the square root penalty.
gam.scale | Scale parameter estimation in GAMs
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
gamlss.etamu | Transform derivatives wrt mu to derivatives wrt linear predictor
gamlss.gH | Calculating derivatives of log-likelihood wrt regression coefficients
gamm | Generalized Additive Mixed Models
gammals | Gamma location-scale model family
gamObject | Fitted gam object
gamSim | Simulate example data for GAMs
gaulss | Gaussian location-scale model family
get.var | Get named variable or evaluate expression from list or data.frame
gevlss | Generalized Extreme Value location-scale model family
gfam | Grouped families
ginla | GAM Integrated Nested Laplace Approximation Newton Enhanced
gp.smooth | Low rank Gaussian process smooths
grouped families | Grouped families
gumbls | Gumbel location-scale model family

## -- I --

identifiability | Identifiability constraints
ijXVXd | Internal functions for discretized model matrix handling
in.out | Which of a set of points lie within a polygon defined region
influence.gam | Extract the diagonal of the influence/hat matrix for a GAM
initial.sp | Starting values for multiple smoothing parameter estimation
inSide | Are points inside boundary?
interpret.gam | Interpret a GAM formula

## -- J --

jagam | Just Another Gibbs Additive Modeller: JAGS support for mgcv.

## -- K --

k.check | Checking smooth basis dimension

## -- L --

ldetS | Getting log generalized determinant of penalty matrices
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 | AIC and Log likelihood for a fitted GAM
lp | Basic linear programming
ls.size | Size of list elements

## -- M --

magic | Stable Multiple Smoothing Parameter Estimation by GCV or UBRE
magic.post.proc | Auxilliary information from magic fit
mchol | Sparse 'chol' function
mgcv | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL
mgcv.FAQ | Frequently Asked Questions for package mgcv
mgcv.package | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL
mgcv.parallel | Parallel computation in mgcv.
mini.roots | Obtain square roots of penalty matrices
missing.data | Missing data in GAMs
model.matrix.gam | Extract model matrix from GAM fit
mono.con | Monotonicity constraints for a cubic regression spline
mrf | Markov Random Field Smooths
mroot | Smallest square root of matrix
multinom | GAM multinomial logistic regression
mvn | Multivariate normal additive models

## -- N --

nb | GAM negative binomial families
NCV | Neighbourhood Cross Validation
negbin | GAM negative binomial families
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

## -- O --

ocat | GAM ordered categorical family
one.se.rule | The one standard error rule for smoother models
ordered.categorical | GAM ordered categorical family

## -- 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
pen.edf | Extract the effective degrees of freedom associated with each penalty in a gam fit
persp.gam | Visualization of GAM objects
place.knots | Automatically place a set of knots evenly through covariate values
plot.gam | Default GAM plotting
polys.plot | Plot geographic regions defined as polygons
posterior.simulation | Simple posterior simulation with gam fits
predict.bam | Prediction from fitted Big Additive Model model
predict.gam | Prediction from fitted GAM model
Predict.matrix | Prediction methods for smooth terms in a GAM
Predict.matrix.Bspline.smooth | Penalized B-splines in GAMs
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.duchon.spline | Low rank Duchon 1977 splines
Predict.matrix.fs.interaction | Factor smooth interactions in GAMs
Predict.matrix.gp.smooth | Low rank Gaussian process smooths
Predict.matrix.mrf.smooth | Markov Random Field Smooths
Predict.matrix.pspline.smooth | Predict matrix method functions
Predict.matrix.random.effect | Simple random effects in GAMs
Predict.matrix.sf.film | Prediction matrix for soap film smooth
Predict.matrix.sf.wiggly | Prediction matrix for soap film smooth
Predict.matrix.soap.film | Prediction matrix for soap film smooth
Predict.matrix.sos.smooth | Splines on the sphere
Predict.matrix.sz.interaction | Constrained factor smooth interactions in GAMs
Predict.matrix.t2.smooth | Predict matrix method functions
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.gam.vcomp | Report gam smoothness estimates as variance components
print.summary.gam | Summary for a GAM fit
psum.chisq | Evaluate the c.d.f. of a weighted sum of chi-squared deviates

## -- Q --

qq.gam | QQ plots for gam model residuals

## -- R --

r.mvt | Generate from or evaluate multivariate normal or t densities.
random.effects | Random effects in GAMs
residuals.gam | Generalized Additive Model residuals
rig | Generate inverse Gaussian random deviates
rmvn | Generate from or evaluate multivariate normal or t densities.
Rrank | Find rank of upper triangular matrix
rTweedie | Generate Tweedie random deviates

## -- S --

s | Defining smooths in GAM formulae
scasm | Shape constrained additive smooth models
scat | GAM scaled t family for heavy tailed data
sdiag | Extract or modify diagonals of a matrix
sdiag<- | Extract or modify diagonals of a matrix
shash | Sinh-arcsinh location scale and shape model family
signal.regression | Linear functionals of a smooth in GAMs
sim2jam | Just Another Gibbs Additive Modeller: JAGS support for mgcv.
single.index | Single index models with mgcv
Sl.inirep | Re-parametrizing model matrix X
Sl.initial.repara | Re-parametrizing model matrix X
Sl.repara | Applying re-parameterization from log-determinant of penalty matrix to model matrix.
Sl.setup | Setting up a list representing a block diagonal penalty matrix
slanczos | Compute truncated eigen decomposition of a symmetric matrix
smooth.construct | Constructor functions for smooth terms in a GAM
smooth.construct.ad.smooth.spec | Adaptive smooths in GAMs
smooth.construct.bs.smooth.spec | Penalized B-splines 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.ds.smooth.spec | Low rank Duchon 1977 splines
smooth.construct.fs.smooth.spec | Factor smooth interactions in GAMs
smooth.construct.gp.smooth.spec | Low rank Gaussian process smooths
smooth.construct.mrf.smooth.spec | Markov Random Field Smooths
smooth.construct.ps.smooth.spec | P-splines in GAMs
smooth.construct.re.smooth.spec | Simple random effects in GAMs
smooth.construct.sc.smooth.spec | Penalized B-splines in GAMs
smooth.construct.scad.smooth.spec | Adaptive smooths in GAMs
smooth.construct.sf.smooth.spec | Soap film smoother constructer
smooth.construct.so.smooth.spec | Soap film smoother constructer
smooth.construct.sos.smooth.spec | Splines on the sphere
smooth.construct.sw.smooth.spec | Soap film smoother constructer
smooth.construct.sz.smooth.spec | Constrained factor smooth interactions in GAMs
smooth.construct.t2.smooth.spec | Tensor product smoothing constructor
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.info | Generic function to provide extra information about smooth specification
smooth.terms | Smooth terms in GAM
smooth2random | Convert a smooth to a form suitable for estimating as random effect
smoothCon | Prediction/Construction wrapper functions for GAM smooth terms
smooths | Smooth terms in GAM
soap | Soap film smoother constructer
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
spasm.construct | Experimental sparse smoothers
spasm.smooth | Experimental sparse smoothers
spasm.sp | Experimental sparse smoothers
Spherical.Spline | Splines on the sphere
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 --

t.scaled | GAM scaled t family for heavy tailed data
t2 | Define alternative tensor product smooths in GAM formulae
te | Define tensor product smooths or tensor product interactions in GAM formulae
tensor.prod.model.matrix | Row Kronecker product/ tensor product smooth construction
tensor.prod.penalties | Row Kronecker product/ tensor product smooth construction
ti | Define tensor product smooths or tensor product interactions in GAM formulae
Tobit | GAM censored normal family for log-normal AFT and Tobit models
totalPenaltySpace | Obtaining (orthogonal) basis for null space and range of the penalty matrix
tprs | Penalized thin plate regression splines in GAMs
trichol | Choleski decomposition of a tri-diagonal matrix
trind.generator | Generates index arrays for upper triangular storage
tw | GAM Tweedie families
Tweedie | GAM Tweedie families
twlss | Tweedie location scale 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

## -- X --

Xbd | Internal functions for discretized model matrix handling
XWXd | Internal functions for discretized model matrix handling
XWyd | Internal functions for discretized model matrix handling

## -- Z --

ziP | GAM zero-inflated (hurdle) Poisson regression family
zipll | Zero inflated (hurdle) Poisson location-scale model family
ziplss | Zero inflated (hurdle) Poisson location-scale model family

## -- misc --

%.% | Row Kronecker product/ tensor product smooth construction