anova.gam Approximate hypothesis tests related to GAM
fits
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
blas.thread.test BLAS thread safety
bug.reports.mgcv Reporting mgcv bugs.
choldrop Deletion and rank one Cholesky factor update
choose.k Basis dimension choice for smooths
cnorm GAM censored normal family for log-normal AFT
and Tobit models
columb Reduced version of Columbus OH crime data
concurvity GAM concurvity measures
cox.ph Additive Cox Proportional Hazard Model
cox.pht Additive Cox proportional hazard models with
time varying covariates
cSplineDes Evaluate cyclic B spline basis
dDeta Obtaining derivative w.r.t. linear predictor
dpnorm Stable evaluation of difference between normal
c.d.f.s
exclude.too.far Exclude prediction grid points too far from
data
extract.lme.cov Extract the data covariance matrix from an lme
object
factor.smooth Factor smooth interactions in GAMs
family.mgcv Distribution families in mgcv
FFdes Level 5 fractional factorial designs
fix.family.link 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.test FELSPLINE test function
full.score GCV/UBRE score for use within nlm
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.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.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
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
ginla GAM Integrated Nested Laplace Approximation
Newton Enhanced
gumbls Gumbel location-scale model family
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
jagam Just Another Gibbs Additive Modeller: JAGS
support for mgcv.
k.check Checking smooth basis dimension
ldetS Getting log generalized determinant of penalty
matrices
ldTweedie Log Tweedie density evaluation
linear.functional.terms
Linear functionals of a smooth in GAMs
logLik.gam AIC and Log likelihood for a fitted GAM
ls.size Size of list elements
magic Stable Multiple Smoothing Parameter Estimation
by GCV or UBRE
magic.post.proc Auxilliary information from magic fit
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
mroot Smallest square root of matrix
multinom GAM multinomial logistic regression
mvn Multivariate normal additive models
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
null.space.dimension The basis of the space of un-penalized
functions for a TPRS
ocat GAM ordered categorical family
one.se.rule The one standard error rule for smoother models
pcls Penalized Constrained Least Squares Fitting
pdIdnot Overflow proof pdMat class for multiples of the
identity matrix
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
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.cr.smooth
Predict matrix method functions
Predict.matrix.soap.film
Prediction matrix for soap film smooth
print.gam Print a Generalized Additive Model object.
psum.chisq Evaluate the c.d.f. of a weighted sum of
chi-squared deviates
qq.gam QQ plots for gam model residuals
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 Defining smooths in GAM formulae
scat GAM scaled t family for heavy tailed data
sdiag Extract or modify diagonals of a matrix
shash Sinh-arcsinh location scale and shape model
family
single.index Single index models with mgcv
Sl.inirep 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.cr.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.so.smooth.spec
Soap film smoother constructer
smooth.construct.sos.smooth.spec
Splines on the sphere
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.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
sp.vcov Extract smoothing parameter estimator
covariance matrix from (RE)ML GAM fit
spasm.construct Experimental sparse smoothers
step.gam Alternatives to step.gam
summary.gam Summary for a GAM fit
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
totalPenaltySpace Obtaining (orthogonal) basis for null space and
range of the penalty matrix
trichol Choleski decomposition of a tri-diagonal matrix
trind.generator Generates index arrays for upper triangular
storage
Tweedie GAM Tweedie families
twlss Tweedie location scale family
uniquecombs find the unique rows in a matrix
vcov.gam Extract parameter (estimator) covariance matrix
from GAM fit
vis.gam Visualization of GAM objects
XWXd Internal functions for discretized model matrix
handling
ziP GAM zero-inflated (hurdle) Poisson regression
family
ziplss Zero inflated (hurdle) Poisson location-scale
model family
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