# mgcv v1.8-25

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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 | |

betar | GAM beta regression family | |

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

columb | Reduced version of Columbus OH crime data | |

concurvity | GAM concurvity measures | |

formXtViX | Form component of GAMM covariance matrix | |

formula.gam | GAM formula | |

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

gam.models | Specifying generalized additive models | |

Tweedie | GAM Tweedie families | |

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

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

bandchol | Choleski decomposition of a band diagonal matrix | |

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

gam.control | Setting GAM fitting defaults | |

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

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

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

Rrank | Find rank of upper triangular matrix | |

bam | Generalized additive models for very large datasets | |

gaulss | Gaussian location-scale model family | |

fs.test | FELSPLINE test function | |

gam.convergence | GAM convergence and performance issues | |

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

gamm | Generalized Additive Mixed Models | |

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

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

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

k.check | Checking smooth basis dimension | |

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

ldTweedie | Log Tweedie density evaluation | |

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 | |

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

mroot | Smallest square root of matrix | |

inSide | Are points inside boundary? | |

single.index | Single index models with mgcv | |

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

ls.size | Size of list elements | |

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

negbin | GAM negative binomial families | |

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

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

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

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

interpret.gam | Interpret a GAM formula | |

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

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

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

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

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

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

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

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

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

spasm.construct | Experimental sparse smoothers | |

family.mgcv | Distribution families in mgcv | |

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

plot.gam | Default GAM plotting | |

residuals.gam | Generalized Additive Model residuals | |

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

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

gamSim | Simulate example data for GAMs | |

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

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

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

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

sdiag | Extract or modify diagonals of a matrix | |

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

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

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

multinom | GAM multinomial logistic regression | |

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

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

rig | Generate inverse Gaussian random deviates | |

cox.ph | Additive Cox Proportional Hazard Model | |

mvn | Multivariate normal additive models | |

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

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

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

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

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

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

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

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

ocat | GAM ordered categorical family | |

rTweedie | Generate Tweedie random deviates | |

random.effects | Random effects in GAMs | |

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

gam2objective | Objective functions for GAM smoothing parameter estimation | |

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

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

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

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

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

gamObject | Fitted gam object | |

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

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

smooth.terms | Smooth terms in GAM | |

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

identifiability | Identifiability constraints | |

mgcv.parallel | Parallel computation in mgcv. | |

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

vis.gam | Visualization of GAM objects | |

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

notExp2 | Alternative to log parameterization for variance components | |

ziP | GAM zero-inflated Poisson regression family | |

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

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

cSplineDes | Evaluate cyclic B spline basis | |

choose.k | Basis dimension choice for smooths | |

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

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

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

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

gam | Generalized additive models with integrated smoothness estimation | |

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

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

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

step.gam | Alternatives to step.gam | |

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

summary.gam | Summary for a GAM fit | |

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

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

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

ldetS | Getting log generalized determinant of penalty matrices | |

missing.data | Missing data in GAMs | |

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

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

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

pcls | Penalized Constrained Least Squares Fitting | |

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

predict.gam | Prediction from fitted GAM model | |

rmvn | Generate multivariate normal deviates | |

s | Defining smooths in GAM formulae | |

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

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

uniquecombs | find the unique rows in a matrix | |

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

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## Last month downloads

## Details

Priority | recommended |

LazyLoad | yes |

ByteCompile | yes |

License | GPL (>= 2) |

NeedsCompilation | yes |

Packaged | 2018-10-26 08:31:24 UTC; sw283 |

Repository | CRAN |

Date/Publication | 2018-10-26 14:50:06 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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