# mgcv v1.8-23

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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. Includes a gam()
function, a wide variety of smoothers, JAGS support and
distributions beyond the exponential family.

## Functions in mgcv

Name | Description | |

Rrank | Find rank of upper triangular matrix | |

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

Tweedie | GAM Tweedie families | |

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

cox.ph | Additive Cox Proportional Hazard Model | |

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

betar | GAM beta regression family | |

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

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

bandchol | Choleski decomposition of a band diagonal matrix | |

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

columb | Reduced version of Columbus OH crime data | |

concurvity | GAM concurvity measures | |

fs.test | FELSPLINE test function | |

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

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

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

bam | Generalized additive models for very large datasets | |

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

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

family.mgcv | Distribution families in mgcv | |

gam | Generalized additive models with integrated smoothness estimation | |

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

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

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

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

identifiability | Identifiability constraints | |

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

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

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

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

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

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

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.scale | Scale parameter estimation in GAMs | |

gam.selection | Generalized Additive Model Selection | |

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

gam.control | Setting GAM fitting defaults | |

gam.convergence | GAM convergence and performance issues | |

gam2objective | Objective functions for GAM smoothing parameter estimation | |

gamObject | Fitted gam object | |

interpret.gam | Interpret a GAM formula | |

ls.size | Size of list elements | |

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

mroot | Smallest square root of matrix | |

missing.data | Missing data in GAMs | |

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

plot.gam | Default GAM plotting | |

predict.gam | Prediction from fitted GAM model | |

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

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

multinom | GAM multinomial logistic regression | |

pcls | Penalized Constrained Least Squares Fitting | |

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

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

gam.models | Specifying generalized additive models | |

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

rTweedie | Generate Tweedie random deviates | |

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

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

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

inSide | Are points inside boundary? | |

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

mgcv.parallel | Parallel computation in mgcv. | |

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

gamm | Generalized Additive Mixed Models | |

mvn | Multivariate normal additive models | |

negbin | GAM negative binomial families | |

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

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

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

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

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

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

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

notExp2 | Alternative to log parameterization for variance components | |

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

random.effects | Random effects in GAMs | |

residuals.gam | Generalized Additive Model residuals | |

sdiag | Extract or modify diagonals of a matrix | |

single.index | Single index models with mgcv | |

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

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

spasm.construct | Experimental sparse smoothers | |

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

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

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

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

ldTweedie | Log Tweedie density evaluation | |

ldetS | Getting log generalized determinant of penalty matrices | |

step.gam | Alternatives to step.gam | |

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

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

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

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

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

rig | Generate inverse Gaussian random deviates | |

rmvn | Generate multivariate normal deviates | |

s | Defining smooths in GAM formulae | |

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

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

summary.gam | Summary for a GAM fit | |

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

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

uniquecombs | find the unique rows in a matrix | |

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

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

vis.gam | Visualization of GAM objects | |

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

smooth.terms | Smooth terms in GAM | |

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

ziP | GAM zero-inflated Poisson regression family | |

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

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

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

cSplineDes | Evaluate cyclic B spline basis | |

choose.k | Basis dimension choice for smooths | |

formXtViX | Form component of GAMM covariance matrix | |

formula.gam | GAM formula | |

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

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

gamSim | Simulate example data for GAMs | |

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

gaulss | Gaussian location-scale model family | |

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

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

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

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

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

ocat | GAM ordered categorical family | |

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

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

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 | |

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

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## Last month downloads

## Details

Priority | recommended |

LazyLoad | yes |

ByteCompile | yes |

License | GPL (>= 2) |

NeedsCompilation | yes |

Packaged | 2018-01-08 15:15:43 UTC; sw283 |

Repository | CRAN |

Date/Publication | 2018-01-15 00:23:36 UTC |

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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