# mgcv v1.8-31

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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. | |

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

Predict.matrix | Prediction methods for smooth terms in a GAM | |

Rrank | Find rank of upper triangular matrix | |

Sl.inirep | Re-parametrizing model matrix X | |

Predict.matrix.soap.film | Prediction matrix for soap film smooth | |

Predict.matrix.cr.smooth | Predict matrix method functions | |

Tweedie | GAM Tweedie families | |

betar | GAM beta regression family | |

FFdes | Level 5 fractional factorial designs | |

choldrop | Deletion and rank one Cholesky factor update | |

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

XWXd | Internal functions for discretized model matrix handling | |

cox.ph | Additive Cox Proportional Hazard Model | |

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

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

columb | Reduced version of Columbus OH crime data | |

concurvity | GAM concurvity measures | |

cSplineDes | Evaluate cyclic B spline basis | |

choose.k | Basis dimension choice for smooths | |

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

blas.thread.test | BLAS thread safety | |

bandchol | Choleski decomposition of a band diagonal matrix | |

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

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

formXtViX | Form component of GAMM covariance matrix | |

gam.control | Setting GAM fitting defaults | |

gam | Generalized additive models with integrated smoothness estimation | |

formula.gam | GAM formula | |

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

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

fs.test | FELSPLINE test function | |

gam.fit | GAM P-IRLS estimation with GCV/UBRE smoothness estimation | |

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

gam.fit3 | P-IRLS GAM estimation with GCV \& UBRE/AIC or RE/ML derivative calculation | |

gam.models | Specifying generalized additive models | |

family.mgcv | Distribution families in mgcv | |

gam.scale | Scale parameter estimation in GAMs | |

gam.convergence | GAM convergence and performance issues | |

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

gamSim | Simulate example data for GAMs | |

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

gammals | Gamma location-scale model family | |

bam | Generalized additive models for very large datasets | |

gaulss | Gaussian location-scale model family | |

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

interpret.gam | Interpret a GAM formula | |

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

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

gam.selection | Generalized Additive Model Selection | |

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

ldTweedie | Log Tweedie density evaluation | |

k.check | Checking smooth basis dimension | |

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

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

ls.size | Size of list elements | |

ginla | GAM Integrated Nested Laplace Approximation Newton Enhanced | |

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

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

identifiability | Identifiability constraints | |

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

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

inSide | Are points inside boundary? | |

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

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

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

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

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

mvn | Multivariate normal additive models | |

multinom | GAM multinomial logistic regression | |

mgcv.parallel | Parallel computation in mgcv. | |

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

ocat | GAM ordered categorical family | |

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

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

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

missing.data | Missing data in GAMs | |

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

random.effects | Random effects in GAMs | |

rTweedie | Generate Tweedie random deviates | |

pen.edf | Extract the effective degrees of freedom associated with each penalty in a gam fit | |

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

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

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

pdTens | Functions implementing a pdMat class for tensor product smooths | |

notExp2 | Alternative to log parameterization for variance components | |

sdiag | Extract or modify diagonals of a matrix | |

mroot | Smallest square root of matrix | |

predict.gam | Prediction from fitted GAM model | |

plot.gam | Default GAM plotting | |

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

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

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

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

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

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

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

single.index | Single index models with mgcv | |

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

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

rmvn | Generate multivariate normal deviates | |

gam2objective | Objective functions for GAM smoothing parameter estimation | |

ziP | GAM zero-inflated Poisson regression family | |

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

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

rig | Generate inverse Gaussian random deviates | |

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

pcls | Penalized Constrained Least Squares Fitting | |

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

residuals.gam | Generalized Additive Model residuals | |

gamObject | Fitted gam object | |

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

s | Defining smooths in GAM formulae | |

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

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

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

smooth.terms | Smooth terms in GAM | |

gamm | Generalized Additive Mixed Models | |

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

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

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

ldetS | Getting log generalized determinant of penalty matrices | |

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

negbin | GAM negative binomial families | |

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

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

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

vis.gam | Visualization of GAM objects | |

uniquecombs | find the unique rows in a matrix | |

summary.gam | Summary for a GAM fit | |

twlss | Tweedie location scale family | |

step.gam | Alternatives to step.gam | |

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

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

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

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

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

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

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

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

spasm.construct | Experimental sparse smoothers | |

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

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

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

tensor.prod.model.matrix | Row Kronecker product/ tensor product smooth construction | |

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

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## Last month downloads

## Details

Priority | recommended |

LazyLoad | yes |

ByteCompile | yes |

License | GPL (>= 2) |

NeedsCompilation | yes |

Packaged | 2019-11-08 21:21:15 UTC; sw283 |

Repository | CRAN |

Date/Publication | 2019-11-09 05:30:11 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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