Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘mgcv’ version 1.9-1
Help Pages
A B C D E F G I J K L M N O P Q R S T U V X Z misc
| mgcv-package | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL |
-- A --
| adaptive.smooth | Adaptive smooths in GAMs |
| AIC.gam | AIC and Log likelihood for a fitted GAM |
| anova.gam | Approximate hypothesis tests related to GAM fits |
-- B --
| b.spline | Penalized B-splines in GAMs |
| 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. |
-- C --
| choldrop | Deletion and rank one Cholesky factor update |
| cholup | 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 |
| coef.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| coef.pdTens | Functions implementing a pdMat class for tensor product smooths |
| columb | Reduced version of Columbus OH crime data |
| columb.polys | Reduced version of Columbus OH crime data |
| concurvity | GAM concurvity measures |
| corMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| cox.ph | Additive Cox Proportional Hazard Model |
| cox.pht | Additive Cox proportional hazard models with time varying covariates |
| cSplineDes | Evaluate cyclic B spline basis |
| cubic.regression.spline | Penalized Cubic regression splines in GAMs |
| cyclic.cubic.spline | Penalized Cubic regression splines in GAMs |
| cyclic.p.spline | P-splines in GAMs |
-- D --
| d.mvt | Generate from or evaluate multivariate normal or t densities. |
| d.spline | Penalized B-splines in GAMs |
| dDeta | Obtaining derivative w.r.t. linear predictor |
| diagXVXd | Internal functions for discretized model matrix handling |
| Dim.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| dmvn | Generate from or evaluate multivariate normal or t densities. |
| dpnorm | Stable evaluation of difference between normal c.d.f.s |
| Duchon.spline | Low rank Duchon 1977 splines |
-- E --
| exclude.too.far | Exclude prediction grid points too far from data |
| extract.lme.cov | Extract the data covariance matrix from an lme object |
| extract.lme.cov2 | Extract the data covariance matrix from an lme object |
-- F --
| factor.smooth | Factor smooth interactions in GAMs |
| factor.smooth.interaction | 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 |
| fix.family.ls | Modify families for use in GAM fitting and checking |
| fix.family.qf | Modify families for use in GAM fitting and checking |
| fix.family.rd | Modify families for use in GAM fitting and checking |
| fix.family.var | 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.boundary | FELSPLINE test function |
| fs.test | FELSPLINE test function |
| full.score | GCV/UBRE score for use within nlm |
| function.predictors | Linear functionals of a smooth in GAMs |
-- G --
| 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.performance | GAM convergence and performance issues |
| 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 |
| gam2derivative | Objective functions for GAM smoothing parameter estimation |
| 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 |
| gfam | Grouped families |
| ginla | GAM Integrated Nested Laplace Approximation Newton Enhanced |
| gp.smooth | Low rank Gaussian process smooths |
| grouped families | Grouped families |
| gumbls | Gumbel location-scale model family |
-- I --
| 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 |
-- J --
| jagam | Just Another Gibbs Additive Modeller: JAGS support for mgcv. |
-- K --
| k.check | Checking smooth basis dimension |
-- L --
| ldetS | Getting log generalized determinant of penalty matrices |
| ldTweedie | Log Tweedie density evaluation |
| linear.functional.terms | Linear functionals of a smooth in GAMs |
| logDet.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| logLik.gam | AIC and Log likelihood for a fitted GAM |
| ls.size | Size of list elements |
-- M --
| magic | Stable Multiple Smoothing Parameter Estimation by GCV or UBRE |
| magic.post.proc | Auxilliary information from magic fit |
| mgcv | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL |
| 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 |
| mrf | Markov Random Field Smooths |
| mroot | Smallest square root of matrix |
| multinom | GAM multinomial logistic regression |
| mvn | Multivariate normal additive models |
-- N --
| nb | GAM negative binomial families |
| NCV | Neighbourhood Cross Validation |
| 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 |
| notLog | Functions for better-than-log positive parameterization |
| notLog2 | Alternative to log parameterization for variance components |
| null.space.dimension | The basis of the space of un-penalized functions for a TPRS |
-- O --
| ocat | GAM ordered categorical family |
| one.se.rule | The one standard error rule for smoother models |
| ordered.categorical | GAM ordered categorical family |
-- P --
| p.spline | P-splines in GAMs |
| pcls | Penalized Constrained Least Squares Fitting |
| pdConstruct.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| pdConstruct.pdTens | Functions implementing a pdMat class for tensor product smooths |
| pdFactor.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| pdFactor.pdTens | Functions implementing a pdMat class for tensor product smooths |
| pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| pdMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| pdMatrix.pdTens | Functions implementing a pdMat class for tensor product smooths |
| 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 |
| persp.gam | Visualization of GAM objects |
| 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 |
| posterior.simulation | Simple posterior simulation with gam fits |
| 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.Bspline.smooth | Penalized B-splines in GAMs |
| Predict.matrix.cr.smooth | Predict matrix method functions |
| Predict.matrix.cs.smooth | Predict matrix method functions |
| Predict.matrix.cyclic.smooth | Predict matrix method functions |
| Predict.matrix.duchon.spline | Low rank Duchon 1977 splines |
| Predict.matrix.fs.interaction | Factor smooth interactions in GAMs |
| Predict.matrix.gp.smooth | Low rank Gaussian process smooths |
| Predict.matrix.mrf.smooth | Markov Random Field Smooths |
| Predict.matrix.pspline.smooth | Predict matrix method functions |
| Predict.matrix.random.effect | Simple random effects in GAMs |
| Predict.matrix.sf | Prediction matrix for soap film smooth |
| Predict.matrix.soap.film | Prediction matrix for soap film smooth |
| Predict.matrix.sos.smooth | Splines on the sphere |
| Predict.matrix.sw | Prediction matrix for soap film smooth |
| Predict.matrix.sz.interaction | Constrained factor smooth interactions in GAMs |
| Predict.matrix.t2.smooth | Predict matrix method functions |
| Predict.matrix.tensor.smooth | Predict matrix method functions |
| Predict.matrix.tprs.smooth | Predict matrix method functions |
| Predict.matrix.ts.smooth | Predict matrix method functions |
| Predict.matrix2 | Prediction methods for smooth terms in a GAM |
| PredictMat | Prediction/Construction wrapper functions for GAM smooth terms |
| print.anova.gam | Approximate hypothesis tests related to GAM fits |
| print.gam | Print a Generalized Additive Model object. |
| print.summary.gam | Summary for a GAM fit |
| psum.chisq | Evaluate the c.d.f. of a weighted sum of chi-squared deviates |
-- Q --
| qq.gam | QQ plots for gam model residuals |
-- R --
| r.mvt | Generate from or evaluate multivariate normal or t densities. |
| 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 --
| s | Defining smooths in GAM formulae |
| scat | GAM scaled t family for heavy tailed data |
| sdiag | Extract or modify diagonals of a matrix |
| sdiag<- | Extract or modify diagonals of a matrix |
| shash | Sinh-arcsinh location scale and shape model family |
| signal.regression | Linear functionals of a smooth in GAMs |
| sim2jam | Just Another Gibbs Additive Modeller: JAGS support for mgcv. |
| single.index | Single index models with mgcv |
| Sl.inirep | Re-parametrizing model matrix X |
| Sl.initial.repara | 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.cc.smooth.spec | Penalized Cubic regression splines in GAMs |
| smooth.construct.cp.smooth.spec | P-splines in GAMs |
| smooth.construct.cr.smooth.spec | Penalized Cubic regression splines in GAMs |
| smooth.construct.cs.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.sf.smooth.spec | Soap film smoother constructer |
| smooth.construct.so.smooth.spec | Soap film smoother constructer |
| smooth.construct.sos.smooth.spec | Splines on the sphere |
| smooth.construct.sw.smooth.spec | Soap film smoother constructer |
| 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.construct.ts.smooth.spec | Penalized thin plate regression splines in GAMs |
| smooth.construct2 | Constructor functions for smooth terms in a GAM |
| 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 |
| smooths | Smooth terms in GAM |
| soap | Soap film smoother constructer |
| solve.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| sp.vcov | Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit |
| spasm.construct | Experimental sparse smoothers |
| spasm.smooth | Experimental sparse smoothers |
| spasm.sp | Experimental sparse smoothers |
| Spherical.Spline | Splines on the sphere |
| step.gam | Alternatives to step.gam |
| summary.gam | Summary for a GAM fit |
| summary.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
| summary.pdTens | Functions implementing a pdMat class for tensor product smooths |
-- T --
| t.scaled | GAM scaled t family for heavy tailed data |
| 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 |
| tensor.prod.penalties | Row Kronecker product/ tensor product smooth construction |
| ti | Define tensor product smooths or tensor product interactions in GAM formulae |
| Tobit | GAM censored normal family for log-normal AFT and Tobit models |
| totalPenaltySpace | Obtaining (orthogonal) basis for null space and range of the penalty matrix |
| tprs | Penalized thin plate regression splines in GAMs |
| trichol | Choleski decomposition of a tri-diagonal matrix |
| trind.generator | Generates index arrays for upper triangular storage |
| tw | GAM Tweedie families |
| Tweedie | GAM Tweedie families |
| twlss | Tweedie location scale family |
-- U --
| uniquecombs | find the unique rows in a matrix |
| user.defined.smooth | Constructor functions for smooth terms in a GAM |
-- V --
| vcov.gam | Extract parameter (estimator) covariance matrix from GAM fit |
| vis.gam | Visualization of GAM objects |
-- X --
| Xbd | Internal functions for discretized model matrix handling |
| XWXd | Internal functions for discretized model matrix handling |
| XWyd | Internal functions for discretized model matrix handling |
-- Z --
| ziP | GAM zero-inflated (hurdle) Poisson regression family |
| zipll | Zero inflated (hurdle) Poisson location-scale model family |
| ziplss | Zero inflated (hurdle) Poisson location-scale model family |
-- misc --
| %.% | Row Kronecker product/ tensor product smooth construction |