mgcv v1.8-17

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by Simon Wood

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

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.

Functions in mgcv

Name Description
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
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Priority recommended
LazyLoad yes
ByteCompile yes
License GPL (>= 2)
NeedsCompilation yes
Packaged 2017-02-06 11:03:57 UTC; sw283
Repository CRAN
Date/Publication 2017-02-08 21:30:16

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