mgcv v1.8-17
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by Simon Wood
Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation
GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Functions in mgcv
| Name | Description | |
| cox.ph | Additive Cox Proportional Hazard Model | |
| cox.pht | Additive Cox proportional hazard models with time varying covariates | |
| choose.k | Basis dimension choice for smooths | |
| bug.reports.mgcv | Reporting mgcv bugs. | |
| betar | GAM beta regression family | |
| bam.update | Update a strictly additive bam model for new data. | |
| bandchol | Choleski decomposition of a band diagonal matrix | |
| cSplineDes | Evaluate cyclic B spline basis | |
| anova.gam | Approximate hypothesis tests related to GAM fits | |
| bam | Generalized additive models for very large datasets | |
| full.score | GCV/UBRE score for use within nlm | |
| fs.test | FELSPLINE test function | |
| extract.lme.cov | Extract the data covariance matrix from an lme object | |
| fixDependence | Detect linear dependencies of one matrix on another | |
| exclude.too.far | Exclude prediction grid points too far from data | |
| formula.gam | GAM formula | |
| family.mgcv | Distribution families in mgcv | |
| fix.family.link | Modify families for use in GAM fitting and checking | |
| formXtViX | Form component of GAMM covariance matrix | |
| gam.check | Some diagnostics for a fitted gam model | |
| gam.control | Setting GAM fitting defaults | |
| gam | Generalized additive models with integrated smoothness estimation | |
| gam.convergence | GAM convergence and performance issues | |
| gam.models | Specifying generalized additive models | |
| gam.selection | Generalized Additive Model Selection | |
| gam.outer | Minimize GCV or UBRE score of a GAM using `outer' iteration | |
| gam.scale | Scale parameter estimation in GAMs | |
| gam.side | Identifiability side conditions for a GAM | |
| 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 | |
| gamlss.gH | Calculating derivatives of log-likelihood wrt regression coefficients | |
| gamlss.etamu | Transform derivatives wrt mu to derivatives wrt linear predictor | |
| gam.vcomp | Report gam smoothness estimates as variance components | |
| gamSim | Simulate example data for GAMs | |
| gam2objective | Objective functions for GAM smoothing parameter estimation | |
| gevlss | Generalized Extreme Value location-scale model family | |
| identifiability | Identifiability constraints | |
| gaulss | Gaussian location-scale model family | |
| get.var | Get named variable or evaluate expression from list or data.frame | |
| gamObject | Fitted gam object | |
| ls.size | Size of list elements | |
| interpret.gam | Interpret a GAM formula | |
| inSide | Are points inside boundary? | |
| influence.gam | Extract the diagonal of the influence/hat matrix for a GAM | |
| logLik.gam | Log likelihood for a fitted GAM, for AIC | |
| in.out | Which of a set of points lie within a polygon defined region | |
| initial.sp | Starting values for multiple smoothing parameter estimation | |
| ldTweedie | Log Tweedie density evaluation | |
| jagam | Just Another Gibbs Additive Modeller: JAGS support for mgcv. | |
| linear.functional.terms | Linear functionals of a smooth in GAMs | |
| mroot | Smallest square root of matrix | |
| mgcv.package | Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL | |
| model.matrix.gam | Extract model matrix from GAM fit | |
| missing.data | Missing data in GAMs | |
| mono.con | Monotonicity constraints for a cubic regression spline | |
| mgcv.FAQ | Frequently Asked Questions for package mgcv | |
| multinom | GAM multinomial logistic regression | |
| mvn | Multivariate normal additive models | |
| mgcv.parallel | Parallel computation in mgcv. | |
| negbin | GAM negative binomial families | |
| pdIdnot | Overflow proof pdMat class for multiples of the identity matrix | |
| notExp2 | Alternative to log parameterization for variance components | |
| one.se.rule | The one standard error rule for smoother models | |
| pcls | Penalized Constrained Least Squares Fitting | |
| ocat | GAM ordered categorical family | |
| null.space.dimension | The basis of the space of un-penalized functions for a TPRS | |
| 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 | |
| new.name | Obtain a name for a new variable that is not already in use | |
| notExp | Functions for better-than-log positive parameterization | |
| place.knots | Automatically place a set of knots evenly through covariate values | |
| Predict.matrix | Prediction methods for smooth terms in a GAM | |
| plot.gam | Default GAM plotting | |
| Predict.matrix.soap.film | Prediction matrix for soap film smooth | |
| predict.gam | Prediction from fitted GAM model | |
| Predict.matrix.cr.smooth | Predict matrix method functions | |
| print.gam | Print a Generalized Additive Model object. | |
| qq.gam | QQ plots for gam model residuals | |
| s | Defining smooths in GAM formulae | |
| scat | GAM scaled t family for heavy tailed data | |
| random.effects | Random effects in GAMs | |
| residuals.gam | Generalized Additive Model residuals | |
| slanczos | Compute truncated eigen decomposition of a symmetric matrix | |
| predict.bam | Prediction from fitted Big Additive Model model | |
| smooth.construct.ad.smooth.spec | Adaptive smooths in GAMs | |
| polys.plot | Plot geographic regions defined as polygons | |
| smooth.construct.gp.smooth.spec | Low rank Gaussian process smooths | |
| smooth.construct.ps.smooth.spec | P-splines in GAMs | |
| smooth2random | Convert a smooth to a form suitable for estimating as random effect | |
| smoothCon | Prediction/Construction wrapper functions for GAM smooth terms | |
| smooth.construct.ds.smooth.spec | Low rank Duchon 1977 splines | |
| smooth.construct.fs.smooth.spec | Factor smooth interactions in GAMs | |
| smooth.construct.t2.smooth.spec | Tensor product smoothing constructor | |
| Rrank | Find rank of upper triangular matrix | |
| rTweedie | Generate Tweedie random deviates | |
| smooth.construct.sos.smooth.spec | Splines on the sphere | |
| sp.vcov | Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit | |
| spasm.construct | Experimental sparse smoothers | |
| rig | Generate inverse Gaussian random deviates | |
| rmvn | Generate multivariate normal deviates | |
| smooth.construct.cr.smooth.spec | Penalized Cubic regression splines in GAMs | |
| smooth.construct.bs.smooth.spec | Penalized B-splines in GAMs | |
| smooth.construct.tp.smooth.spec | Penalized thin plate regression splines in GAMs | |
| vis.gam | Visualization of GAM objects | |
| smooth.construct.tensor.smooth.spec | Tensor product smoothing constructor | |
| vcov.gam | Extract parameter (estimator) covariance matrix from GAM fit | |
| sdiag | Extract or modify diagonals of a matrix | |
| smooth.construct.re.smooth.spec | Simple random effects in GAMs | |
| single.index | Single index models with mgcv | |
| smooth.construct.so.smooth.spec | Soap film smoother constructer | |
| summary.gam | Summary for a GAM fit | |
| t2 | Define alternative tensor product smooths in GAM formulae | |
| Tweedie | GAM Tweedie families | |
| ziP | GAM zero-inflated Poisson regression family | |
| ziplss | Zero inflated Poisson location-scale model family | |
| uniquecombs | find the unique rows in a matrix | |
| trichol | Choleski decomposition of a tri-diagonal matrix | |
| trind.generator | Generates index arrays for upper triangular storage | |
| te | Define tensor product smooths or tensor product interactions in GAM formulae | |
| tensor.prod.model.matrix | Utility functions for constructing tensor product smooths | |
| concurvity | GAM concurvity measures | |
| columb | Reduced version of Columbus OH crime data | |
| gamm | Generalized Additive Mixed Models | |
| magic.post.proc | Auxilliary information from magic fit | |
| magic | Stable Multiple Smoothing Parameter Estimation by GCV or UBRE | |
| smooth.construct.mrf.smooth.spec | Markov Random Field Smooths | |
| smooth.construct | Constructor functions for smooth terms in a GAM | |
| step.gam | Alternatives to step.gam | |
| smooth.terms | Smooth terms in GAM | |
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Details
| Priority | recommended |
| LazyLoad | yes |
| ByteCompile | yes |
| License | GPL (>= 2) |
| NeedsCompilation | yes |
| Packaged | 2017-02-06 11:03:57 UTC; sw283 |
| Repository | CRAN |
| Date/Publication | 2017-02-08 21:30:16 |
| imports | graphics , Matrix , methods , stats |
| suggests | MASS , parallel , splines , survival |
| depends | nlme (>= 3.1-64) , R (>= 2.14.0) |
| Contributors | Simon Wood |
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