FFdes Level 5 fractional factorial designs NCV Neighbourhood Cross Validation 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 Rrank Find rank of upper triangular matrix 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 Tweedie GAM Tweedie families XWXd Internal functions for discretized model matrix handling 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. cSplineDes Evaluate cyclic B spline basis 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 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 fix.family.link Modify families for use in GAM fitting and checking fixDependence Detect linear dependencies of one matrix on another formXtViX Form component of GAMM covariance matrix formula.gam GAM formula 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 gamObject Fitted gam object gamSim Simulate example data for GAMs 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 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 gfam Grouped families 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 inSide Are points inside boundary? influence.gam Extract the diagonal of the influence/hat matrix for a GAM initial.sp Starting values for multiple smoothing parameter estimation interpret.gam Interpret a GAM formula jagam Just Another Gibbs Additive Modeller: JAGS support for mgcv. k.check Checking smooth basis dimension ldTweedie Log Tweedie density evaluation ldetS Getting log generalized determinant of penalty matrices 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/NCV 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 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 rTweedie Generate Tweedie random deviates 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. 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 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 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 ziP GAM zero-inflated (hurdle) Poisson regression family ziplss Zero inflated (hurdle) Poisson location-scale model family