# 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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## Last month downloads

## 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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