A B C D E F G I J K L M N O P Q R S T U V X Z misc
mgcv-package | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL |
adaptive.smooth | Adaptive smooths in GAMs |
AIC.gam | AIC and Log likelihood for a fitted GAM |
anova.gam | Approximate hypothesis tests related to GAM fits |
b.spline | Penalized B-splines in GAMs |
bam | Generalized additive models for very large datasets |
bam.update | Update a strictly additive bam model for new data. |
bandchol | Choleski decomposition of a band diagonal matrix |
betar | GAM beta regression family |
blas.thread.test | BLAS thread safety |
bug.reports.mgcv | Reporting mgcv bugs. |
choldrop | Deletion and rank one Cholesky factor update |
cholup | Deletion and rank one Cholesky factor update |
choose.k | Basis dimension choice for smooths |
cnorm | GAM censored normal family for log-normal AFT and Tobit models |
coef.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
coef.pdTens | Functions implementing a pdMat class for tensor product smooths |
columb | Reduced version of Columbus OH crime data |
columb.polys | Reduced version of Columbus OH crime data |
concurvity | GAM concurvity measures |
corMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
cox.ph | Additive Cox Proportional Hazard Model |
cox.pht | Additive Cox proportional hazard models with time varying covariates |
cSplineDes | Evaluate cyclic B spline basis |
cubic.regression.spline | Penalized Cubic regression splines in GAMs |
cyclic.cubic.spline | Penalized Cubic regression splines in GAMs |
cyclic.p.spline | P-splines in GAMs |
d.mvt | Generate from or evaluate multivariate normal or t densities. |
d.spline | Penalized B-splines in GAMs |
dDeta | Obtaining derivative w.r.t. linear predictor |
diagXVXd | Internal functions for discretized model matrix handling |
Dim.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
dmvn | Generate from or evaluate multivariate normal or t densities. |
dpnorm | Stable evaluation of difference between normal c.d.f.s |
Duchon.spline | Low rank Duchon 1977 splines |
exclude.too.far | Exclude prediction grid points too far from data |
extract.lme.cov | Extract the data covariance matrix from an lme object |
extract.lme.cov2 | Extract the data covariance matrix from an lme object |
factor.smooth | Factor smooth interactions in GAMs |
factor.smooth.interaction | Factor smooth interactions in GAMs |
family.mgcv | Distribution families in mgcv |
FFdes | Level 5 fractional factorial designs |
fix.family.link | Modify families for use in GAM fitting and checking |
fix.family.ls | Modify families for use in GAM fitting and checking |
fix.family.qf | Modify families for use in GAM fitting and checking |
fix.family.rd | Modify families for use in GAM fitting and checking |
fix.family.var | Modify families for use in GAM fitting and checking |
fixDependence | Detect linear dependencies of one matrix on another |
formula.gam | GAM formula |
formXtViX | Form component of GAMM covariance matrix |
fs.boundary | FELSPLINE test function |
fs.test | FELSPLINE test function |
full.score | GCV/UBRE score for use within nlm |
function.predictors | Linear functionals of a smooth in GAMs |
gam | Generalized additive models with integrated smoothness estimation |
gam.check | Some diagnostics for a fitted gam model |
gam.control | Setting GAM fitting defaults |
gam.convergence | GAM convergence and performance issues |
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.fit5.post.proc | Post-processing output of gam.fit5 |
gam.mh | Simple posterior simulation with gam fits |
gam.models | Specifying generalized additive models |
gam.outer | Minimize GCV or UBRE score of a GAM using 'outer' iteration |
gam.performance | GAM convergence and performance issues |
gam.reparam | Finding stable orthogonal re-parameterization of the square root penalty. |
gam.scale | Scale parameter estimation in GAMs |
gam.selection | Generalized Additive Model Selection |
gam.side | Identifiability side conditions for a GAM |
gam.vcomp | Report gam smoothness estimates as variance components |
gam2derivative | Objective functions for GAM smoothing parameter estimation |
gam2objective | Objective functions for GAM smoothing parameter estimation |
gamlss.etamu | Transform derivatives wrt mu to derivatives wrt linear predictor |
gamlss.gH | Calculating derivatives of log-likelihood wrt regression coefficients |
gamm | Generalized Additive Mixed Models |
gammals | Gamma location-scale model family |
gamObject | Fitted gam object |
gamSim | Simulate example data for GAMs |
gaulss | Gaussian location-scale model family |
get.var | Get named variable or evaluate expression from list or data.frame |
gevlss | Generalized Extreme Value location-scale model family |
gfam | Grouped families |
ginla | GAM Integrated Nested Laplace Approximation Newton Enhanced |
gp.smooth | Low rank Gaussian process smooths |
grouped families | Grouped families |
gumbls | Gumbel location-scale model family |
identifiability | Identifiability constraints |
in.out | Which of a set of points lie within a polygon defined region |
influence.gam | Extract the diagonal of the influence/hat matrix for a GAM |
initial.sp | Starting values for multiple smoothing parameter estimation |
inSide | Are points inside boundary? |
interpret.gam | Interpret a GAM formula |
jagam | Just Another Gibbs Additive Modeller: JAGS support for mgcv. |
k.check | Checking smooth basis dimension |
ldetS | Getting log generalized determinant of penalty matrices |
ldTweedie | Log Tweedie density evaluation |
linear.functional.terms | Linear functionals of a smooth in GAMs |
logDet.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
logLik.gam | AIC and Log likelihood for a fitted GAM |
ls.size | Size of list elements |
magic | Stable Multiple Smoothing Parameter Estimation by GCV or UBRE |
magic.post.proc | Auxilliary information from magic fit |
mgcv | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL |
mgcv.FAQ | Frequently Asked Questions for package mgcv |
mgcv.package | Mixed GAM Computation Vehicle with GCV/AIC/REML/NCV smoothness estimation and GAMMs by REML/PQL |
mgcv.parallel | Parallel computation in mgcv. |
mini.roots | Obtain square roots of penalty matrices |
missing.data | Missing data in GAMs |
model.matrix.gam | Extract model matrix from GAM fit |
mono.con | Monotonicity constraints for a cubic regression spline |
mrf | Markov Random Field Smooths |
mroot | Smallest square root of matrix |
multinom | GAM multinomial logistic regression |
mvn | Multivariate normal additive models |
nb | GAM negative binomial families |
NCV | Neighbourhood Cross Validation |
negbin | GAM negative binomial families |
new.name | Obtain a name for a new variable that is not already in use |
notExp | Functions for better-than-log positive parameterization |
notExp2 | Alternative to log parameterization for variance components |
notLog | Functions for better-than-log positive parameterization |
notLog2 | Alternative to log parameterization for variance components |
null.space.dimension | The basis of the space of un-penalized functions for a TPRS |
ocat | GAM ordered categorical family |
one.se.rule | The one standard error rule for smoother models |
ordered.categorical | GAM ordered categorical family |
p.spline | P-splines in GAMs |
pcls | Penalized Constrained Least Squares Fitting |
pdConstruct.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
pdConstruct.pdTens | Functions implementing a pdMat class for tensor product smooths |
pdFactor.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
pdFactor.pdTens | Functions implementing a pdMat class for tensor product smooths |
pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
pdMatrix.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
pdMatrix.pdTens | Functions implementing a pdMat class for tensor product smooths |
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 |
persp.gam | Visualization of GAM objects |
place.knots | Automatically place a set of knots evenly through covariate values |
plot.gam | Default GAM plotting |
polys.plot | Plot geographic regions defined as polygons |
posterior.simulation | Simple posterior simulation with gam fits |
predict.bam | Prediction from fitted Big Additive Model model |
predict.gam | Prediction from fitted GAM model |
Predict.matrix | Prediction methods for smooth terms in a GAM |
Predict.matrix.Bspline.smooth | Penalized B-splines in GAMs |
Predict.matrix.cr.smooth | Predict matrix method functions |
Predict.matrix.cs.smooth | Predict matrix method functions |
Predict.matrix.cyclic.smooth | Predict matrix method functions |
Predict.matrix.duchon.spline | Low rank Duchon 1977 splines |
Predict.matrix.fs.interaction | Factor smooth interactions in GAMs |
Predict.matrix.gp.smooth | Low rank Gaussian process smooths |
Predict.matrix.mrf.smooth | Markov Random Field Smooths |
Predict.matrix.pspline.smooth | Predict matrix method functions |
Predict.matrix.random.effect | Simple random effects in GAMs |
Predict.matrix.sf | Prediction matrix for soap film smooth |
Predict.matrix.soap.film | Prediction matrix for soap film smooth |
Predict.matrix.sos.smooth | Splines on the sphere |
Predict.matrix.sw | Prediction matrix for soap film smooth |
Predict.matrix.sz.interaction | Constrained factor smooth interactions in GAMs |
Predict.matrix.t2.smooth | Predict matrix method functions |
Predict.matrix.tensor.smooth | Predict matrix method functions |
Predict.matrix.tprs.smooth | Predict matrix method functions |
Predict.matrix.ts.smooth | Predict matrix method functions |
Predict.matrix2 | Prediction methods for smooth terms in a GAM |
PredictMat | Prediction/Construction wrapper functions for GAM smooth terms |
print.anova.gam | Approximate hypothesis tests related to GAM fits |
print.gam | Print a Generalized Additive Model object. |
print.summary.gam | Summary for a GAM fit |
psum.chisq | Evaluate the c.d.f. of a weighted sum of chi-squared deviates |
qq.gam | QQ plots for gam model residuals |
r.mvt | Generate from or evaluate multivariate normal or t densities. |
random.effects | Random effects in GAMs |
residuals.gam | Generalized Additive Model residuals |
rig | Generate inverse Gaussian random deviates |
rmvn | Generate from or evaluate multivariate normal or t densities. |
Rrank | Find rank of upper triangular matrix |
rTweedie | Generate Tweedie random deviates |
s | Defining smooths in GAM formulae |
scat | GAM scaled t family for heavy tailed data |
sdiag | Extract or modify diagonals of a matrix |
sdiag<- | Extract or modify diagonals of a matrix |
shash | Sinh-arcsinh location scale and shape model family |
signal.regression | Linear functionals of a smooth in GAMs |
sim2jam | Just Another Gibbs Additive Modeller: JAGS support for mgcv. |
single.index | Single index models with mgcv |
Sl.inirep | Re-parametrizing model matrix X |
Sl.initial.repara | Re-parametrizing model matrix X |
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 |
slanczos | Compute truncated eigen decomposition of a symmetric matrix |
smooth.construct | Constructor functions for smooth terms in a GAM |
smooth.construct.ad.smooth.spec | Adaptive smooths in GAMs |
smooth.construct.bs.smooth.spec | Penalized B-splines in GAMs |
smooth.construct.cc.smooth.spec | Penalized Cubic regression splines in GAMs |
smooth.construct.cp.smooth.spec | P-splines in GAMs |
smooth.construct.cr.smooth.spec | Penalized Cubic regression splines in GAMs |
smooth.construct.cs.smooth.spec | Penalized Cubic regression splines in GAMs |
smooth.construct.ds.smooth.spec | Low rank Duchon 1977 splines |
smooth.construct.fs.smooth.spec | Factor smooth interactions in GAMs |
smooth.construct.gp.smooth.spec | Low rank Gaussian process smooths |
smooth.construct.mrf.smooth.spec | Markov Random Field Smooths |
smooth.construct.ps.smooth.spec | P-splines in GAMs |
smooth.construct.re.smooth.spec | Simple random effects in GAMs |
smooth.construct.sf.smooth.spec | Soap film smoother constructer |
smooth.construct.so.smooth.spec | Soap film smoother constructer |
smooth.construct.sos.smooth.spec | Splines on the sphere |
smooth.construct.sw.smooth.spec | Soap film smoother constructer |
smooth.construct.sz.smooth.spec | Constrained factor smooth interactions in GAMs |
smooth.construct.t2.smooth.spec | Tensor product smoothing constructor |
smooth.construct.tensor.smooth.spec | Tensor product smoothing constructor |
smooth.construct.tp.smooth.spec | Penalized thin plate regression splines in GAMs |
smooth.construct.ts.smooth.spec | Penalized thin plate regression splines in GAMs |
smooth.construct2 | Constructor functions for smooth terms in a GAM |
smooth.info | Generic function to provide extra information about smooth specification |
smooth.terms | Smooth terms in GAM |
smooth2random | Convert a smooth to a form suitable for estimating as random effect |
smoothCon | Prediction/Construction wrapper functions for GAM smooth terms |
smooths | Smooth terms in GAM |
soap | Soap film smoother constructer |
solve.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
sp.vcov | Extract smoothing parameter estimator covariance matrix from (RE)ML GAM fit |
spasm.construct | Experimental sparse smoothers |
spasm.smooth | Experimental sparse smoothers |
spasm.sp | Experimental sparse smoothers |
Spherical.Spline | Splines on the sphere |
step.gam | Alternatives to step.gam |
summary.gam | Summary for a GAM fit |
summary.pdIdnot | Overflow proof pdMat class for multiples of the identity matrix |
summary.pdTens | Functions implementing a pdMat class for tensor product smooths |
t.scaled | GAM scaled t family for heavy tailed data |
t2 | Define alternative tensor product smooths in GAM formulae |
te | Define tensor product smooths or tensor product interactions in GAM formulae |
tensor.prod.model.matrix | Row Kronecker product/ tensor product smooth construction |
tensor.prod.penalties | Row Kronecker product/ tensor product smooth construction |
ti | Define tensor product smooths or tensor product interactions in GAM formulae |
Tobit | GAM censored normal family for log-normal AFT and Tobit models |
totalPenaltySpace | Obtaining (orthogonal) basis for null space and range of the penalty matrix |
tprs | Penalized thin plate regression splines in GAMs |
trichol | Choleski decomposition of a tri-diagonal matrix |
trind.generator | Generates index arrays for upper triangular storage |
tw | GAM Tweedie families |
Tweedie | GAM Tweedie families |
twlss | Tweedie location scale family |
uniquecombs | find the unique rows in a matrix |
user.defined.smooth | Constructor functions for smooth terms in a GAM |
vcov.gam | Extract parameter (estimator) covariance matrix from GAM fit |
vis.gam | Visualization of GAM objects |
Xbd | Internal functions for discretized model matrix handling |
XWXd | Internal functions for discretized model matrix handling |
XWyd | Internal functions for discretized model matrix handling |
ziP | GAM zero-inflated (hurdle) Poisson regression family |
zipll | Zero inflated (hurdle) Poisson location-scale model family |
ziplss | Zero inflated (hurdle) Poisson location-scale model family |
%.% | Row Kronecker product/ tensor product smooth construction |