mgcv v1.8-25

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Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

Functions in mgcv

Name Description
betar GAM beta regression family
Predict.matrix Prediction methods for smooth terms in a GAM
columb Reduced version of Columbus OH crime data
concurvity GAM concurvity measures
formXtViX Form component of GAMM covariance matrix
formula.gam GAM formula
gam.fit5.post.proc Post-processing output of gam.fit5
gam.models Specifying generalized additive models
Tweedie GAM Tweedie families
anova.gam Approximate hypothesis tests related to GAM fits
gam.side Identifiability side conditions for a GAM
bandchol Choleski decomposition of a band diagonal matrix
bug.reports.mgcv Reporting mgcv bugs.
gam.control Setting GAM fitting defaults
gam.vcomp Report gam smoothness estimates as variance components
Sl.initial.repara Re-parametrizing model matrix X
bam.update Update a strictly additive bam model for new data.
Rrank Find rank of upper triangular matrix
bam Generalized additive models for very large datasets
gaulss Gaussian location-scale model family
fs.test FELSPLINE test function
gam.convergence GAM convergence and performance issues
gamlss.gH Calculating derivatives of log-likelihood wrt regression coefficients
gamm Generalized Additive Mixed Models
in.out Which of a set of points lie within a polygon defined region
full.score GCV/UBRE score for use within nlm
get.var Get named variable or evaluate expression from list or data.frame
k.check Checking smooth basis dimension
gam.fit GAM P-IRLS estimation with GCV/UBRE smoothness estimation
ldTweedie Log Tweedie density evaluation
gam.fit3 P-IRLS GAM estimation with GCV \& UBRE/AIC or RE/ML derivative calculation
gam.scale Scale parameter estimation in GAMs
gam.selection Generalized Additive Model Selection
mono.con Monotonicity constraints for a cubic regression spline
mroot Smallest square root of matrix
inSide Are points inside boundary?
single.index Single index models with mgcv
slanczos Compute truncated eigen decomposition of a symmetric matrix
ls.size Size of list elements
logLik.gam AIC and Log likelihood for a fitted GAM
negbin GAM negative binomial families
smooth.construct.so.smooth.spec Soap film smoother constructer
Predict.matrix.cr.smooth Predict matrix method functions
Predict.matrix.soap.film Prediction matrix for soap film smooth
new.name Obtain a name for a new variable that is not already in use
interpret.gam Interpret a GAM formula
jagam Just Another Gibbs Additive Modeller: JAGS support for mgcv.
magic Stable Multiple Smoothing Parameter Estimation by GCV or UBRE
pen.edf Extract the effective degrees of freedom associated with each penalty in a gam fit
smooth.construct.sos.smooth.spec Splines on the sphere
magic.post.proc Auxilliary information from magic fit
extract.lme.cov Extract the data covariance matrix from an lme object
pdIdnot Overflow proof pdMat class for multiples of the identity matrix
sp.vcov Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit
pdTens Functions implementing a pdMat class for tensor product smooths
spasm.construct Experimental sparse smoothers
family.mgcv Distribution families in mgcv
place.knots Automatically place a set of knots evenly through covariate values
plot.gam Default GAM plotting
residuals.gam Generalized Additive Model residuals
gamlss.etamu Transform derivatives wrt mu to derivatives wrt linear predictor
trind.generator Generates index arrays for upper triangular storage
gamSim Simulate example data for GAMs
trichol Choleski decomposition of a tri-diagonal matrix
polys.plot Plot geographic regions defined as polygons
mgcv.FAQ Frequently Asked Questions for package mgcv
scat GAM scaled t family for heavy tailed data
sdiag Extract or modify diagonals of a matrix
mgcv.package Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL
smooth.construct.t2.smooth.spec Tensor product smoothing constructor
smooth.construct.tensor.smooth.spec Tensor product smoothing constructor
multinom GAM multinomial logistic regression
t2 Define alternative tensor product smooths in GAM formulae
te Define tensor product smooths or tensor product interactions in GAM formulae
rig Generate inverse Gaussian random deviates
cox.ph Additive Cox Proportional Hazard Model
mvn Multivariate normal additive models
smooth.construct.ds.smooth.spec Low rank Duchon 1977 splines
cox.pht Additive Cox proportional hazard models with time varying covariates
smooth.construct.fs.smooth.spec Factor smooth interactions in GAMs
fix.family.link Modify families for use in GAM fitting and checking
null.space.dimension The basis of the space of un-penalized functions for a TPRS
fixDependence Detect linear dependencies of one matrix on another
ziplss Zero inflated Poisson location-scale model family
gam.outer Minimize GCV or UBRE score of a GAM using `outer' iteration
ocat GAM ordered categorical family
rTweedie Generate Tweedie random deviates
random.effects Random effects in GAMs
gam.reparam Finding stable orthogonal re-parameterization of the square root penalty.
gam2objective Objective functions for GAM smoothing parameter estimation
smooth2random Convert a smooth to a form suitable for estimating as random effect
Sl.repara Applying re-parameterization from log-determinant of penalty matrix to model matrix.
smooth.construct.bs.smooth.spec Penalized B-splines in GAMs
smooth.construct.cr.smooth.spec Penalized Cubic regression splines in GAMs
smoothCon Prediction/Construction wrapper functions for GAM smooth terms
gamObject Fitted gam object
Sl.setup Setting up a list representing a block diagonal penalty matrix
smooth.construct.tp.smooth.spec Penalized thin plate regression splines in GAMs
smooth.terms Smooth terms in GAM
gevlss Generalized Extreme Value location-scale model family
identifiability Identifiability constraints
mgcv.parallel Parallel computation in mgcv.
mini.roots Obtain square roots of penalty matrices
vis.gam Visualization of GAM objects
notExp Functions for better-than-log positive parameterization
notExp2 Alternative to log parameterization for variance components
ziP GAM zero-inflated Poisson regression family
print.gam Print a Generalized Additive Model object.
qq.gam QQ plots for gam model residuals
cSplineDes Evaluate cyclic B spline basis
choose.k Basis dimension choice for smooths
dDeta Obtaining derivative w.r.t. linear predictor
smooth.construct Constructor functions for smooth terms in a GAM
smooth.construct.ad.smooth.spec Adaptive smooths in GAMs
exclude.too.far Exclude prediction grid points too far from data
gam Generalized additive models with integrated smoothness estimation
smooth.construct.gp.smooth.spec Low rank Gaussian process smooths
smooth.construct.mrf.smooth.spec Markov Random Field Smooths
gam.check Some diagnostics for a fitted gam model
step.gam Alternatives to step.gam
influence.gam Extract the diagonal of the influence/hat matrix for a GAM
summary.gam Summary for a GAM fit
totalPenaltySpace Obtaining (orthogonal) basis for null space and range of the penalty matrix
tensor.prod.model.matrix Utility functions for constructing tensor product smooths
initial.sp Starting values for multiple smoothing parameter estimation
ldetS Getting log generalized determinant of penalty matrices
missing.data Missing data in GAMs
model.matrix.gam Extract model matrix from GAM fit
linear.functional.terms Linear functionals of a smooth in GAMs
one.se.rule The one standard error rule for smoother models
pcls Penalized Constrained Least Squares Fitting
predict.bam Prediction from fitted Big Additive Model model
predict.gam Prediction from fitted GAM model
rmvn Generate multivariate normal deviates
s Defining smooths in GAM formulae
smooth.construct.ps.smooth.spec P-splines in GAMs
smooth.construct.re.smooth.spec Simple random effects in GAMs
uniquecombs find the unique rows in a matrix
vcov.gam Extract parameter (estimator) covariance matrix from GAM fit
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Priority recommended
LazyLoad yes
ByteCompile yes
License GPL (>= 2)
NeedsCompilation yes
Packaged 2018-10-26 08:31:24 UTC; sw283
Repository CRAN
Date/Publication 2018-10-26 14:50:06 UTC

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