# mgcv v1.8-28

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## Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.

## Functions in mgcv

Name | Description | |

Sl.repara | Applying re-parameterization from log-determinant of penalty matrix to model matrix. | |

choldrop | Deletion and rank one Cholesky factor update | |

bug.reports.mgcv | Reporting mgcv bugs. | |

cox.pht | Additive Cox proportional hazard models with time varying covariates | |

anova.gam | Approximate hypothesis tests related to GAM fits | |

cox.ph | Additive Cox Proportional Hazard Model | |

columb | Reduced version of Columbus OH crime data | |

concurvity | GAM concurvity measures | |

cSplineDes | Evaluate cyclic B spline basis | |

bam | Generalized additive models for very large datasets | |

bam.update | Update a strictly additive bam model for new data. | |

gamSim | Simulate example data for GAMs | |

extract.lme.cov | Extract the data covariance matrix from an lme object | |

gam.reparam | Finding stable orthogonal re-parameterization of the square root penalty. | |

gam.outer | Minimize GCV or UBRE score of a GAM using `outer' iteration | |

gam.check | Some diagnostics for a fitted gam model | |

gam | Generalized additive models with integrated smoothness estimation | |

gamlss.etamu | Transform derivatives wrt mu to derivatives wrt linear predictor | |

family.mgcv | Distribution families in mgcv | |

choose.k | Basis dimension choice for smooths | |

inSide | Are points inside boundary? | |

fix.family.link | Modify families for use in GAM fitting and checking | |

fixDependence | Detect linear dependencies of one matrix on another | |

gam.fit5.post.proc | Post-processing output of gam.fit5 | |

bandchol | Choleski decomposition of a band diagonal matrix | |

influence.gam | Extract the diagonal of the influence/hat matrix for a GAM | |

fs.test | FELSPLINE test function | |

formXtViX | Form component of GAMM covariance matrix | |

gevlss | Generalized Extreme Value location-scale model family | |

full.score | GCV/UBRE score for use within nlm | |

ginla | GAM Integrated Nested Laplace Approximation Newton Enhanced | |

dDeta | Obtaining derivative w.r.t. linear predictor | |

formula.gam | GAM formula | |

exclude.too.far | Exclude prediction grid points too far from data | |

mroot | Smallest square root of matrix | |

gam.scale | Scale parameter estimation in GAMs | |

gam.control | Setting GAM fitting defaults | |

gam.selection | Generalized Additive Model Selection | |

gam.convergence | GAM convergence and performance issues | |

gam.side | Identifiability side conditions for a GAM | |

ldTweedie | Log Tweedie density evaluation | |

ls.size | Size of list elements | |

gam.models | Specifying generalized additive models | |

mini.roots | Obtain square roots of penalty matrices | |

gam.vcomp | Report gam smoothness estimates as variance components | |

magic | Stable Multiple Smoothing Parameter Estimation by GCV or UBRE | |

ldetS | Getting log generalized determinant of penalty matrices | |

multinom | GAM multinomial logistic regression | |

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 | |

notExp2 | Alternative to log parameterization for variance components | |

null.space.dimension | The basis of the space of un-penalized functions for a TPRS | |

gaulss | Gaussian location-scale model family | |

get.var | Get named variable or evaluate expression from list or data.frame | |

missing.data | Missing data in GAMs | |

pcls | Penalized Constrained Least Squares Fitting | |

pdIdnot | Overflow proof pdMat class for multiples of the identity matrix | |

gam2objective | Objective functions for GAM smoothing parameter estimation | |

gamObject | Fitted gam object | |

sdiag | Extract or modify diagonals of a matrix | |

identifiability | Identifiability constraints | |

single.index | Single index models with mgcv | |

in.out | Which of a set of points lie within a polygon defined region | |

ocat | GAM ordered categorical family | |

linear.functional.terms | Linear functionals of a smooth in GAMs | |

gamlss.gH | Calculating derivatives of log-likelihood wrt regression coefficients | |

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 | |

jagam | Just Another Gibbs Additive Modeller: JAGS support for mgcv. | |

k.check | Checking smooth basis dimension | |

one.se.rule | The one standard error rule for smoother models | |

place.knots | Automatically place a set of knots evenly through covariate values | |

mgcv.package | Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation and GAMMs by REML/PQL | |

mgcv.parallel | Parallel computation in mgcv. | |

gamm | Generalized Additive Mixed Models | |

new.name | Obtain a name for a new variable that is not already in use | |

logLik.gam | AIC and Log likelihood for a fitted GAM | |

notExp | Functions for better-than-log positive parameterization | |

plot.gam | Default GAM plotting | |

polys.plot | Plot geographic regions defined as polygons | |

rig | Generate inverse Gaussian random deviates | |

smooth.construct.ad.smooth.spec | Adaptive smooths in GAMs | |

initial.sp | Starting values for multiple smoothing parameter estimation | |

smooth.construct.bs.smooth.spec | Penalized B-splines in GAMs | |

smoothCon | Prediction/Construction wrapper functions for GAM smooth terms | |

interpret.gam | Interpret a GAM formula | |

magic.post.proc | Auxilliary information from magic fit | |

smooth.terms | Smooth terms in GAM | |

rmvn | Generate multivariate normal deviates | |

smooth2random | Convert a smooth to a form suitable for estimating as random effect | |

model.matrix.gam | Extract model matrix from GAM fit | |

mgcv.FAQ | Frequently Asked Questions for package mgcv | |

smooth.construct.cr.smooth.spec | Penalized Cubic regression splines in GAMs | |

sp.vcov | Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit | |

summary.gam | Summary for a GAM fit | |

trind.generator | Generates index arrays for upper triangular storage | |

mono.con | Monotonicity constraints for a cubic regression spline | |

t2 | Define alternative tensor product smooths in GAM formulae | |

twlss | Tweedie location scale family | |

smooth.construct.ds.smooth.spec | Low rank Duchon 1977 splines | |

predict.gam | Prediction from fitted GAM model | |

mvn | Multivariate normal additive models | |

print.gam | Print a Generalized Additive Model object. | |

slanczos | Compute truncated eigen decomposition of a symmetric matrix | |

totalPenaltySpace | Obtaining (orthogonal) basis for null space and range of the penalty matrix | |

smooth.construct | Constructor functions for smooth terms in a GAM | |

smooth.construct.re.smooth.spec | Simple random effects in GAMs | |

trichol | Choleski decomposition of a tri-diagonal matrix | |

smooth.construct.so.smooth.spec | Soap film smoother constructer | |

negbin | GAM negative binomial families | |

predict.bam | Prediction from fitted Big Additive Model model | |

s | Defining smooths in GAM formulae | |

qq.gam | QQ plots for gam model residuals | |

rTweedie | Generate Tweedie random deviates | |

scat | GAM scaled t family for heavy tailed data | |

ziplss | Zero inflated Poisson location-scale model family | |

smooth.construct.mrf.smooth.spec | Markov Random Field Smooths | |

random.effects | Random effects in GAMs | |

smooth.construct.sos.smooth.spec | Splines on the sphere | |

smooth.construct.ps.smooth.spec | P-splines in GAMs | |

residuals.gam | Generalized Additive Model residuals | |

vis.gam | Visualization of GAM objects | |

smooth.construct.t2.smooth.spec | Tensor product smoothing constructor | |

spasm.construct | Experimental sparse smoothers | |

ziP | GAM zero-inflated Poisson regression family | |

step.gam | Alternatives to step.gam | |

uniquecombs | find the unique rows in a matrix | |

smooth.construct.fs.smooth.spec | Factor smooth interactions in GAMs | |

vcov.gam | Extract parameter (estimator) covariance matrix from GAM fit | |

smooth.construct.gp.smooth.spec | Low rank Gaussian process smooths | |

smooth.construct.tensor.smooth.spec | Tensor product smoothing constructor | |

smooth.construct.tp.smooth.spec | Penalized thin plate regression splines in GAMs | |

te | Define tensor product smooths or tensor product interactions in GAM formulae | |

tensor.prod.model.matrix | Utility functions for constructing tensor product smooths | |

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.setup | Setting up a list representing a block diagonal penalty matrix | |

Tweedie | GAM Tweedie families | |

betar | GAM beta regression family | |

FFdes | Level 5 fractional factorial designs | |

Sl.initial.repara | Re-parametrizing model matrix X | |

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## Last month downloads

## Details

Priority | recommended |

LazyLoad | yes |

ByteCompile | yes |

License | GPL (>= 2) |

NeedsCompilation | yes |

Packaged | 2019-03-21 08:56:32 UTC; sw283 |

Repository | CRAN |

Date/Publication | 2019-03-21 11:40:07 UTC |

imports | graphics , Matrix , methods , splines , stats , utils |

suggests | MASS , parallel , survival |

depends | nlme (>= 3.1-64) , R (>= 2.14.0) |

Contributors | Simon Wood |

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