| Approximate hypothesis tests related to GAM fits | anova.gam print.anova.gam |
| Generalized additive models for very large datasets | bam |
| Update a strictly additive bam model for new data. | bam.update |
| Choleski decomposition of a band diagonal matrix | bandchol |
| Censored Box-Cox Gaussian family | bcg |
| GAM beta regression family | betar |
| BLAS thread safety | blas.thread.test |
| Reporting mgcv bugs. | bug.reports.mgcv |
| Deletion and rank one Cholesky factor update | choldrop cholup |
| Basis dimension choice for smooths | choose.k |
| GAM censored logistic distribution family for log-logistic AFT models | clog |
| GAM censored normal family for log-normal AFT and Tobit models | cnorm Tobit |
| Reduced version of Columbus OH crime data | columb columb.polys |
| GAM concurvity measures | concurvity |
| Additive Cox Proportional Hazard Model | cox.ph |
| Additive Cox proportional hazard models with time varying covariates | cox.pht |
| GAM censored Poisson family | cpois |
| Evaluate cyclic B spline basis | cSplineDes |
| Obtaining derivative w.r.t. linear predictor | dDeta |
| Stable evaluation of difference between normal c.d.f.s | dpnorm |
| Stable evaluation of difference between Poisson c.d.f.s | dppois |
| Exclude prediction grid points too far from data | exclude.too.far |
| Extract the data covariance matrix from an lme object | extract.lme.cov extract.lme.cov2 |
| Factor smooth interactions in GAMs | factor.smooth factor.smooth.interaction |
| Distribution families in mgcv | family.mgcv |
| Level 5 fractional factorial designs | FFdes |
| Modify families for use in GAM fitting and checking | fix.family.link fix.family.ls fix.family.qf fix.family.rd fix.family.var |
| Detect linear dependencies of one matrix on another | fixDependence |
| GAM formula | formula.gam |
| Form component of GAMM covariance matrix | formXtViX |
| FELSPLINE test function | fs.boundary fs.test |
| Generalized additive models with integrated smoothness estimation | gam |
| Some diagnostics for a fitted gam model | gam.check |
| Setting GAM fitting defaults | gam.control |
| GAM convergence and performance issues | gam.convergence gam.performance |
| GAM P-IRLS estimation with GCV/UBRE smoothness estimation (deprecated) | gam.fit |
| P-IRLS GAM estimation with GCV, UBRE/AIC or RE/ML derivative calculation | gam.fit3 |
| Post-processing output of gam.fit5 | gam.fit5.post.proc |
| Simple posterior simulation with gam fits | gam.mh posterior.simulation |
| Specifying generalized additive models | gam.models |
| Minimize GCV or UBRE score of a GAM using `outer' iteration | gam.outer |
| Finding stable orthogonal re-parameterization of the square root penalty. | gam.reparam |
| Scale parameter estimation in GAMs | gam.scale |
| Generalized Additive Model Selection | gam.selection |
| Identifiability side conditions for a GAM | gam.side |
| Report gam smoothness estimates as variance components | gam.vcomp print.gam.vcomp |
| Objective functions for GAM smoothing parameter estimation | gam2derivative gam2objective |
| Transform derivatives wrt mu to derivatives wrt linear predictor | gamlss.etamu |
| Calculating derivatives of log-likelihood wrt regression coefficients | gamlss.gH |
| Generalized Additive Mixed Models | gamm |
| Gamma location-scale model family | gammals |
| Fitted gam object | gamObject |
| Simulate example data for GAMs | gamSim |
| Gaussian location-scale model family | gaulss |
| Get named variable or evaluate expression from list or data.frame | get.var |
| Generalized Extreme Value location-scale model family | gevlss |
| Grouped families | gfam grouped families |
| GAM Integrated Nested Laplace Approximation Newton Enhanced | ginla |
| Gumbel location-scale model family | gumbls |
| Identifiability constraints | identifiability |
| Which of a set of points lie within a polygon defined region | in.out |
| Extract the diagonal of the influence/hat matrix for a GAM | influence.gam |
| Starting values for multiple smoothing parameter estimation | initial.sp |
| Are points inside boundary? | inSide |
| Interpret a GAM formula | interpret.gam |
| Just Another Gibbs Additive Modeller: JAGS support for mgcv. | jagam sim2jam |
| Checking smooth basis dimension | k.check |
| Getting log generalized determinant of penalty matrices | ldetS |
| Log Tweedie density evaluation | ldTweedie |
| Linear functionals of a smooth in GAMs | function.predictors linear.functional.terms signal.regression |
| AIC and Log likelihood for a fitted GAM | AIC.gam logLik.gam |
| Basic linear programming | feasible lp |
| Size of list elements | ls.size |
| Stable Multiple Smoothing Parameter Estimation by GCV or UBRE | magic |
| Auxilliary information from magic fit | magic.post.proc |
| Sparse 'chol' function | mchol |
| Frequently Asked Questions for package mgcv | mgcv.FAQ |
| Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL | mgcv-package mgcv mgcv.package |
| Parallel computation in mgcv. | mgcv.parallel |
| Obtain square roots of penalty matrices | mini.roots |
| Missing data in GAMs | missing.data |
| Extract model matrix from GAM fit | model.matrix.gam |
| Monotonicity constraints for a cubic regression spline | mono.con |
| Smallest square root of matrix | mroot |
| GAM multinomial logistic regression | multinom |
| Multivariate normal additive models | mvn |
| Neighbourhood Cross Validation | NCV |
| GAM negative binomial families | nb negbin |
| Obtain a name for a new variable that is not already in use | new.name |
| Functions for better-than-log positive parameterization | notExp notLog |
| Alternative to log parameterization for variance components | notExp2 notLog2 |
| The basis of the space of un-penalized functions for a TPRS | null.space.dimension |
| GAM ordered categorical family | ocat ordered.categorical |
| The one standard error rule for smoother models | one.se.rule |
| Penalized Constrained Least Squares Fitting | pcls |
| Overflow proof pdMat class for multiples of the identity matrix | coef.pdIdnot corMatrix.pdIdnot Dim.pdIdnot logDet.pdIdnot pdConstruct.pdIdnot pdFactor.pdIdnot pdIdnot pdMatrix.pdIdnot solve.pdIdnot summary.pdIdnot |
| Functions implementing a pdMat class for tensor product smooths | coef.pdTens pdConstruct.pdTens pdFactor.pdTens pdMatrix.pdTens pdTens summary.pdTens |
| Extract the effective degrees of freedom associated with each penalty in a gam fit | pen.edf |
| Automatically place a set of knots evenly through covariate values | place.knots |
| Default GAM plotting | plot.gam |
| Plot geographic regions defined as polygons | polys.plot |
| Prediction from fitted Big Additive Model model | predict.bam |
| Prediction from fitted GAM model | predict.gam |
| Prediction methods for smooth terms in a GAM | Predict.matrix Predict.matrix2 |
| Predict matrix method functions | Predict.matrix.cr.smooth Predict.matrix.cs.smooth Predict.matrix.cyclic.smooth Predict.matrix.pspline.smooth Predict.matrix.t2.smooth Predict.matrix.tensor.smooth Predict.matrix.tprs.smooth Predict.matrix.ts.smooth |
| Prediction matrix for soap film smooth | Predict.matrix.sf.film Predict.matrix.sf.wiggly Predict.matrix.soap.film |
| Print a Generalized Additive Model object. | print.gam |
| Evaluate the c.d.f. of a weighted sum of chi-squared deviates | psum.chisq |
| QQ plots for gam model residuals | qq.gam |
| Random effects in GAMs | random.effects |
| Generalized Additive Model residuals | residuals.gam |
| Generate inverse Gaussian random deviates | rig |
| Generate from or evaluate multivariate normal or t densities. | d.mvt dmvn r.mvt rmvn |
| Find rank of upper triangular matrix | Rrank |
| Generate Tweedie random deviates | rTweedie |
| Defining smooths in GAM formulae | s |
| Shape constrained additive smooth models | scasm |
| GAM scaled t family for heavy tailed data | scat t.scaled |
| Extract or modify diagonals of a matrix | sdiag sdiag<- |
| Sinh-arcsinh location scale and shape model family | shash |
| Single index models with mgcv | single.index |
| Re-parametrizing model matrix X | Sl.inirep Sl.initial.repara |
| Applying re-parameterization from log-determinant of penalty matrix to model matrix. | Sl.repara |
| Setting up a list representing a block diagonal penalty matrix | Sl.setup |
| Compute truncated eigen decomposition of a symmetric matrix | slanczos |
| Constructor functions for smooth terms in a GAM | smooth.construct smooth.construct2 user.defined.smooth |
| Adaptive smooths in GAMs | adaptive.smooth smooth.construct.ad.smooth.spec smooth.construct.scad.smooth.spec |
| Penalized B-splines in GAMs | b.spline d.spline Predict.matrix.Bspline.smooth smooth.construct.bs.smooth.spec smooth.construct.sc.smooth.spec |
| Penalized Cubic regression splines in GAMs | cubic.regression.spline cyclic.cubic.spline smooth.construct.cc.smooth.spec smooth.construct.cr.smooth.spec smooth.construct.cs.smooth.spec |
| Low rank Duchon 1977 splines | Duchon.spline Predict.matrix.duchon.spline smooth.construct.ds.smooth.spec |
| Factor smooth interactions in GAMs | Predict.matrix.fs.interaction smooth.construct.fs.smooth.spec |
| Low rank Gaussian process smooths | gp.smooth Predict.matrix.gp.smooth smooth.construct.gp.smooth.spec |
| Markov Random Field Smooths | mrf Predict.matrix.mrf.smooth smooth.construct.mrf.smooth.spec |
| P-splines in GAMs | cyclic.p.spline p.spline smooth.construct.cp.smooth.spec smooth.construct.ps.smooth.spec |
| Simple random effects in GAMs | Predict.matrix.random.effect smooth.construct.re.smooth.spec |
| Soap film smoother constructer | smooth.construct.sf.smooth.spec smooth.construct.so.smooth.spec smooth.construct.sw.smooth.spec soap |
| Splines on the sphere | Predict.matrix.sos.smooth smooth.construct.sos.smooth.spec Spherical.Spline |
| Constrained factor smooth interactions in GAMs | Predict.matrix.sz.interaction smooth.construct.sz.smooth.spec |
| Tensor product smoothing constructor | smooth.construct.t2.smooth.spec |
| Tensor product smoothing constructor | smooth.construct.tensor.smooth.spec |
| Penalized thin plate regression splines in GAMs | smooth.construct.tp.smooth.spec smooth.construct.ts.smooth.spec tprs |
| Generic function to provide extra information about smooth specification | smooth.info |
| Smooth terms in GAM | smooth.terms smooths |
| Convert a smooth to a form suitable for estimating as random effect | smooth2random |
| Prediction/Construction wrapper functions for GAM smooth terms | PredictMat smoothCon |
| Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit | sp.vcov |
| Experimental sparse smoothers | spasm.construct spasm.smooth spasm.sp |
| Alternatives to step.gam | step.gam |
| Summary for a GAM fit | print.summary.gam summary.gam |
| Define alternative tensor product smooths in GAM formulae | t2 |
| Define tensor product smooths or tensor product interactions in GAM formulae | te ti |
| Row Kronecker product/ tensor product smooth construction | %.% tensor.prod.model.matrix tensor.prod.penalties |
| Obtaining (orthogonal) basis for null space and range of the penalty matrix | totalPenaltySpace |
| Choleski decomposition of a tri-diagonal matrix | trichol |
| Generates index arrays for upper triangular storage | trind.generator |
| GAM Tweedie families | tw Tweedie |
| Tweedie location scale family | twlss |
| find the unique rows in a matrix | uniquecombs |
| Extract parameter (estimator) covariance matrix from GAM fit | vcov.gam |
| Visualization of GAM objects | persp.gam vis.gam |
| Internal functions for discretized model matrix handling | diagXVXd ijXVXd Xbd XWXd XWyd |
| GAM zero-inflated (hurdle) Poisson regression family | ziP |
| Zero inflated (hurdle) Poisson location-scale model family | zipll ziplss |
