# mgcv v1.8-24

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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 | |

columb | Reduced version of Columbus OH crime data | |

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

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

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.convergence | GAM convergence and performance issues | |

choose.k | Basis dimension choice for smooths | |

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

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

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

gamSim | Simulate example data for GAMs | |

gam.control | Setting GAM fitting defaults | |

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

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

gam | Generalized additive models with integrated smoothness estimation | |

identifiability | Identifiability constraints | |

formula.gam | GAM formula | |

formXtViX | Form component of GAMM covariance matrix | |

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

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

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

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

family.mgcv | Distribution families in mgcv | |

concurvity | GAM concurvity measures | |

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

k.check | Checking smooth basis dimension | |

ldTweedie | Log Tweedie density evaluation | |

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

gam.models | Specifying generalized additive models | |

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

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

gam2objective | Objective functions for GAM smoothing parameter estimation | |

gamObject | Fitted gam object | |

gam.scale | Scale parameter estimation in GAMs | |

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

inSide | Are points inside boundary? | |

ldetS | Getting log generalized determinant of penalty matrices | |

gam.selection | Generalized Additive Model Selection | |

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

gaulss | Gaussian location-scale model family | |

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

missing.data | Missing data in GAMs | |

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

mroot | Smallest square root of matrix | |

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

notExp2 | Alternative to log parameterization for variance components | |

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

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

rig | Generate inverse Gaussian random deviates | |

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

residuals.gam | Generalized Additive Model residuals | |

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

pcls | Penalized Constrained Least Squares Fitting | |

ls.size | Size of list elements | |

multinom | GAM multinomial logistic regression | |

mgcv.parallel | Parallel computation in mgcv. | |

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

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

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

plot.gam | Default GAM plotting | |

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

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

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

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

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

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

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

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

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

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

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

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

spasm.construct | Experimental sparse smoothers | |

interpret.gam | Interpret a GAM formula | |

gamm | Generalized Additive Mixed Models | |

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

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

uniquecombs | find the unique rows in a matrix | |

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

mvn | Multivariate normal additive models | |

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

sdiag | Extract or modify diagonals of a matrix | |

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

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

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

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

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

ocat | GAM ordered categorical family | |

predict.gam | Prediction from fitted GAM model | |

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

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

single.index | Single index models with mgcv | |

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

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

negbin | GAM negative binomial families | |

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

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

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

vis.gam | Visualization of GAM objects | |

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

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

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

ziP | GAM zero-inflated Poisson regression family | |

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

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

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

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

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

smooth.terms | Smooth terms in GAM | |

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

rTweedie | Generate Tweedie random deviates | |

rmvn | Generate multivariate normal deviates | |

random.effects | Random effects in GAMs | |

s | Defining smooths in GAM formulae | |

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

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

step.gam | Alternatives to step.gam | |

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

summary.gam | Summary for a GAM fit | |

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

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

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

Rrank | Find rank of upper triangular matrix | |

Tweedie | GAM Tweedie families | |

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

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

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

betar | GAM beta regression family | |

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

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

cox.ph | Additive Cox Proportional Hazard Model | |

cSplineDes | Evaluate cyclic B spline basis | |

bandchol | Choleski decomposition of a band diagonal matrix | |

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

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 | |

fs.test | FELSPLINE test function | |

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## Last month downloads

## Details

Priority | recommended |

LazyLoad | yes |

ByteCompile | yes |

License | GPL (>= 2) |

NeedsCompilation | yes |

Packaged | 2018-06-18 13:08:20 UTC; sw283 |

Repository | CRAN |

Date/Publication | 2018-06-18 19:07:59 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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