mgcv v1.8-24

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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
columb Reduced version of Columbus OH crime data
bug.reports.mgcv Reporting mgcv bugs.
gamlss.etamu Transform derivatives wrt mu to derivatives wrt linear predictor
gam.check Some diagnostics for a fitted gam model
influence.gam Extract the diagonal of the influence/hat matrix for a GAM
initial.sp Starting values for multiple smoothing parameter estimation
gam.convergence GAM convergence and performance issues
choose.k Basis dimension choice for smooths
dDeta Obtaining derivative w.r.t. linear predictor
gevlss Generalized Extreme Value location-scale model family
gam.vcomp Report gam smoothness estimates as variance components
gamSim Simulate example data for GAMs
gam.control Setting GAM fitting defaults
full.score GCV/UBRE score for use within nlm
gam.side Identifiability side conditions for a GAM
gam Generalized additive models with integrated smoothness estimation
identifiability Identifiability constraints
formula.gam GAM formula
formXtViX Form component of GAMM covariance matrix
gam.fit GAM P-IRLS estimation with GCV/UBRE smoothness estimation
exclude.too.far Exclude prediction grid points too far from data
gam.fit5.post.proc Post-processing output of gam.fit5
magic Stable Multiple Smoothing Parameter Estimation by GCV or UBRE
family.mgcv Distribution families in mgcv
concurvity GAM concurvity measures
gam.fit3 P-IRLS GAM estimation with GCV \& UBRE/AIC or RE/ML derivative calculation
k.check Checking smooth basis dimension
ldTweedie Log Tweedie density evaluation
magic.post.proc Auxilliary information from magic fit
gam.models Specifying generalized additive models
fix.family.link Modify families for use in GAM fitting and checking
in.out Which of a set of points lie within a polygon defined region
gam2objective Objective functions for GAM smoothing parameter estimation
gamObject Fitted gam object
gam.scale Scale parameter estimation in GAMs
mono.con Monotonicity constraints for a cubic regression spline
inSide Are points inside boundary?
ldetS Getting log generalized determinant of penalty matrices
gam.selection Generalized Additive Model Selection
fixDependence Detect linear dependencies of one matrix on another
gaulss Gaussian location-scale model family
model.matrix.gam Extract model matrix from GAM fit
missing.data Missing data in GAMs
linear.functional.terms Linear functionals of a smooth in GAMs
mroot Smallest square root of matrix
get.var Get named variable or evaluate expression from list or data.frame
notExp2 Alternative to log parameterization for variance components
gam.outer Minimize GCV or UBRE score of a GAM using `outer' iteration
notExp Functions for better-than-log positive parameterization
rig Generate inverse Gaussian random deviates
one.se.rule The one standard error rule for smoother models
residuals.gam Generalized Additive Model residuals
logLik.gam AIC and Log likelihood for a fitted GAM
pcls Penalized Constrained Least Squares Fitting
ls.size Size of list elements
multinom GAM multinomial logistic regression
mgcv.parallel Parallel computation in mgcv.
polys.plot Plot geographic regions defined as polygons
gam.reparam Finding stable orthogonal re-parameterization of the square root penalty.
smooth.construct Constructor functions for smooth terms in a GAM
plot.gam Default GAM plotting
mini.roots Obtain square roots of penalty matrices
smooth.construct.ad.smooth.spec Adaptive smooths in GAMs
smooth.construct.bs.smooth.spec Penalized B-splines in GAMs
gamlss.gH Calculating derivatives of log-likelihood wrt regression coefficients
smooth.construct.cr.smooth.spec Penalized Cubic regression splines in GAMs
pdTens Functions implementing a pdMat class for tensor product smooths
smooth.construct.ps.smooth.spec P-splines in GAMs
smooth.construct.gp.smooth.spec Low rank Gaussian process smooths
pdIdnot Overflow proof pdMat class for multiples of the identity matrix
smooth.construct.re.smooth.spec Simple random effects in GAMs
print.gam Print a Generalized Additive Model object.
sp.vcov Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit
spasm.construct Experimental sparse smoothers
interpret.gam Interpret a GAM formula
gamm Generalized Additive Mixed Models
vcov.gam Extract parameter (estimator) covariance matrix from GAM fit
qq.gam QQ plots for gam model residuals
uniquecombs find the unique rows in a matrix
jagam Just Another Gibbs Additive Modeller: JAGS support for mgcv.
mvn Multivariate normal additive models
scat GAM scaled t family for heavy tailed data
sdiag Extract or modify diagonals of a matrix
smooth.construct.so.smooth.spec Soap film smoother constructer
mgcv.FAQ Frequently Asked Questions for package mgcv
smooth.construct.sos.smooth.spec Splines on the sphere
null.space.dimension The basis of the space of un-penalized functions for a TPRS
predict.bam Prediction from fitted Big Additive Model model
ocat GAM ordered categorical family
predict.gam Prediction from fitted GAM model
mgcv.package Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL
smooth.construct.mrf.smooth.spec Markov Random Field Smooths
single.index Single index models with mgcv
slanczos Compute truncated eigen decomposition of a symmetric matrix
t2 Define alternative tensor product smooths in GAM formulae
negbin GAM negative binomial families
smooth.construct.t2.smooth.spec Tensor product smoothing constructor
smooth.construct.tensor.smooth.spec Tensor product smoothing constructor
te Define tensor product smooths or tensor product interactions in GAM formulae
vis.gam Visualization of GAM objects
smooth.construct.tp.smooth.spec Penalized thin plate regression splines in GAMs
smoothCon Prediction/Construction wrapper functions for GAM smooth terms
smooth2random Convert a smooth to a form suitable for estimating as random effect
ziP GAM zero-inflated Poisson regression family
new.name Obtain a name for a new variable that is not already in use
tensor.prod.model.matrix Utility functions for constructing tensor product smooths
pen.edf Extract the effective degrees of freedom associated with each penalty in a gam fit
totalPenaltySpace Obtaining (orthogonal) basis for null space and range of the penalty matrix
place.knots Automatically place a set of knots evenly through covariate values
smooth.terms Smooth terms in GAM
ziplss Zero inflated Poisson location-scale model family
rTweedie Generate Tweedie random deviates
rmvn Generate multivariate normal deviates
random.effects Random effects in GAMs
s Defining smooths in GAM formulae
smooth.construct.ds.smooth.spec Low rank Duchon 1977 splines
smooth.construct.fs.smooth.spec Factor smooth interactions in GAMs
step.gam Alternatives to step.gam
trind.generator Generates index arrays for upper triangular storage
summary.gam Summary for a GAM fit
trichol Choleski decomposition of a tri-diagonal matrix
Sl.repara Applying re-parameterization from log-determinant of penalty matrix to model matrix.
Sl.initial.repara Re-parametrizing model matrix X
Rrank Find rank of upper triangular matrix
Tweedie GAM Tweedie families
Predict.matrix.soap.film Prediction matrix for soap film smooth
Predict.matrix.cr.smooth Predict matrix method functions
Sl.setup Setting up a list representing a block diagonal penalty matrix
betar GAM beta regression family
Predict.matrix Prediction methods for smooth terms in a GAM
anova.gam Approximate hypothesis tests related to GAM fits
cox.ph Additive Cox Proportional Hazard Model
cSplineDes Evaluate cyclic B spline basis
bandchol Choleski decomposition of a band diagonal matrix
bam.update Update a strictly additive bam model for new data.
bam Generalized additive models for very large datasets
cox.pht Additive Cox proportional hazard models with time varying covariates
extract.lme.cov Extract the data covariance matrix from an lme object
fs.test FELSPLINE test function
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Priority recommended
LazyLoad yes
ByteCompile yes
License GPL (>= 2)
NeedsCompilation yes
Packaged 2018-06-18 13:08:20 UTC; sw283
Repository CRAN
Date/Publication 2018-06-18 19:07:59 UTC

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