Mixed GAM Computation Vehicle with Automatic Smoothness Estimation


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Documentation for package ‘mgcv’ version 1.8-22

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

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

-- A --

adaptive.smooth Adaptive smooths in GAMs
AIC.gam Log likelihood for a fitted GAM, for AIC
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
betar GAM beta regression family
bug.reports.mgcv Reporting mgcv bugs.

-- 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
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
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 --

dDeta Obtaining derivative w.r.t. linear predictor
Dim.pdIdnot Overflow proof pdMat class for multiples of the identity matrix
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.interaction Factor smooth interactions in GAMs
family.mgcv Distribution families in mgcv
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
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.fit5.post.proc Post-processing output of gam.fit5
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
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
gp.smooth Low rank Gaussian process smooths

-- I --

identifiability Identifiability constraints
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.

-- 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 Log likelihood for a fitted GAM, for AIC
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
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML 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 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
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
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 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.sw Prediction matrix for soap film smooth
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.summary.gam Summary for a GAM fit

-- Q --

qq.gam QQ plots for gam model residuals

-- R --

random.effects Random effects in GAMs
residuals.gam Generalized Additive Model residuals
rig Generate inverse Gaussian random deviates
rmvn Generate multivariate normal deviates
Rrank Find rank of upper triangular matrix
rTweedie Generate Tweedie random deviates

-- S --

s Defining smooths in GAM formulae
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
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.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.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.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.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
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 Utility functions for constructing tensor product smooths
tensor.prod.penalties Utility functions for constructing tensor product smooths
ti Define tensor product smooths or tensor product interactions in GAM formulae
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

-- 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

-- Z --

ziP GAM zero-inflated Poisson regression family
ziplss Zero inflated Poisson location-scale model family