237 lines
12 KiB
Plaintext
237 lines
12 KiB
Plaintext
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FFdes Level 5 fractional factorial designs
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NCV Neighbourhood Cross Validation
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Predict.matrix Prediction methods for smooth terms in a GAM
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Predict.matrix.cr.smooth
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Predict matrix method functions
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Predict.matrix.soap.film
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Prediction matrix for soap film smooth
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Rrank Find rank of upper triangular matrix
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Sl.inirep Re-parametrizing model matrix X
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Sl.repara Applying re-parameterization from
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log-determinant of penalty matrix to model
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matrix.
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Sl.setup Setting up a list representing a block diagonal
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penalty matrix
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Tweedie GAM Tweedie families
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XWXd Internal functions for discretized model matrix
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handling
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anova.gam Approximate hypothesis tests related to GAM
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fits
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bam Generalized additive models for very large
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datasets
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bam.update Update a strictly additive bam model for new
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data.
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bandchol Choleski decomposition of a band diagonal
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matrix
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betar GAM beta regression family
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blas.thread.test BLAS thread safety
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bug.reports.mgcv Reporting mgcv bugs.
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cSplineDes Evaluate cyclic B spline basis
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choldrop Deletion and rank one Cholesky factor update
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choose.k Basis dimension choice for smooths
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cnorm GAM censored normal family for log-normal AFT
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and Tobit models
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columb Reduced version of Columbus OH crime data
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concurvity GAM concurvity measures
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cox.ph Additive Cox Proportional Hazard Model
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cox.pht Additive Cox proportional hazard models with
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time varying covariates
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dDeta Obtaining derivative w.r.t. linear predictor
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dpnorm Stable evaluation of difference between normal
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c.d.f.s
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exclude.too.far Exclude prediction grid points too far from
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data
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extract.lme.cov Extract the data covariance matrix from an lme
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object
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factor.smooth Factor smooth interactions in GAMs
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family.mgcv Distribution families in mgcv
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fix.family.link Modify families for use in GAM fitting and
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checking
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fixDependence Detect linear dependencies of one matrix on
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another
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formXtViX Form component of GAMM covariance matrix
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formula.gam GAM formula
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fs.test FELSPLINE test function
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full.score GCV/UBRE score for use within nlm
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gam Generalized additive models with integrated
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smoothness estimation
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gam.check Some diagnostics for a fitted gam model
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gam.control Setting GAM fitting defaults
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gam.convergence GAM convergence and performance issues
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gam.fit GAM P-IRLS estimation with GCV/UBRE smoothness
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estimation
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gam.fit3 P-IRLS GAM estimation with GCV, UBRE/AIC or
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RE/ML derivative calculation
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gam.fit5.post.proc Post-processing output of gam.fit5
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gam.mh Simple posterior simulation with gam fits
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gam.models Specifying generalized additive models
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gam.outer Minimize GCV or UBRE score of a GAM using
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'outer' iteration
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gam.reparam Finding stable orthogonal re-parameterization
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of the square root penalty.
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gam.scale Scale parameter estimation in GAMs
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gam.selection Generalized Additive Model Selection
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gam.side Identifiability side conditions for a GAM
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gam.vcomp Report gam smoothness estimates as variance
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components
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gam2objective Objective functions for GAM smoothing parameter
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estimation
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gamObject Fitted gam object
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gamSim Simulate example data for GAMs
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gamlss.etamu Transform derivatives wrt mu to derivatives wrt
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linear predictor
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gamlss.gH Calculating derivatives of log-likelihood wrt
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regression coefficients
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gamm Generalized Additive Mixed Models
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gammals Gamma location-scale model family
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gaulss Gaussian location-scale model family
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get.var Get named variable or evaluate expression from
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list or data.frame
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gevlss Generalized Extreme Value location-scale model
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family
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gfam Grouped families
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ginla GAM Integrated Nested Laplace Approximation
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Newton Enhanced
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gumbls Gumbel location-scale model family
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identifiability Identifiability constraints
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in.out Which of a set of points lie within a polygon
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defined region
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inSide Are points inside boundary?
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influence.gam Extract the diagonal of the influence/hat
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matrix for a GAM
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initial.sp Starting values for multiple smoothing
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parameter estimation
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interpret.gam Interpret a GAM formula
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jagam Just Another Gibbs Additive Modeller: JAGS
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support for mgcv.
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k.check Checking smooth basis dimension
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ldTweedie Log Tweedie density evaluation
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ldetS Getting log generalized determinant of penalty
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matrices
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linear.functional.terms
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Linear functionals of a smooth in GAMs
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logLik.gam AIC and Log likelihood for a fitted GAM
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ls.size Size of list elements
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magic Stable Multiple Smoothing Parameter Estimation
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by GCV or UBRE
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magic.post.proc Auxilliary information from magic fit
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mgcv.FAQ Frequently Asked Questions for package mgcv
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mgcv.package Mixed GAM Computation Vehicle with
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GCV/AIC/REML/NCV smoothness estimation and
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GAMMs by REML/PQL
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mgcv.parallel Parallel computation in mgcv.
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mini.roots Obtain square roots of penalty matrices
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missing.data Missing data in GAMs
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model.matrix.gam Extract model matrix from GAM fit
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mono.con Monotonicity constraints for a cubic regression
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spline
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mroot Smallest square root of matrix
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multinom GAM multinomial logistic regression
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mvn Multivariate normal additive models
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negbin GAM negative binomial families
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new.name Obtain a name for a new variable that is not
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already in use
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notExp Functions for better-than-log positive
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parameterization
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notExp2 Alternative to log parameterization for
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variance components
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null.space.dimension The basis of the space of un-penalized
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functions for a TPRS
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ocat GAM ordered categorical family
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one.se.rule The one standard error rule for smoother models
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pcls Penalized Constrained Least Squares Fitting
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pdIdnot Overflow proof pdMat class for multiples of the
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identity matrix
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pdTens Functions implementing a pdMat class for tensor
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product smooths
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pen.edf Extract the effective degrees of freedom
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associated with each penalty in a gam fit
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place.knots Automatically place a set of knots evenly
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through covariate values
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plot.gam Default GAM plotting
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polys.plot Plot geographic regions defined as polygons
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predict.bam Prediction from fitted Big Additive Model model
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predict.gam Prediction from fitted GAM model
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print.gam Print a Generalized Additive Model object.
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psum.chisq Evaluate the c.d.f. of a weighted sum of
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chi-squared deviates
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qq.gam QQ plots for gam model residuals
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rTweedie Generate Tweedie random deviates
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random.effects Random effects in GAMs
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residuals.gam Generalized Additive Model residuals
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rig Generate inverse Gaussian random deviates
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rmvn Generate from or evaluate multivariate normal
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or t densities.
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s Defining smooths in GAM formulae
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scat GAM scaled t family for heavy tailed data
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sdiag Extract or modify diagonals of a matrix
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shash Sinh-arcsinh location scale and shape model
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family
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single.index Single index models with mgcv
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slanczos Compute truncated eigen decomposition of a
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symmetric matrix
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smooth.construct Constructor functions for smooth terms in a GAM
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smooth.construct.ad.smooth.spec
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Adaptive smooths in GAMs
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smooth.construct.bs.smooth.spec
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Penalized B-splines in GAMs
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smooth.construct.cr.smooth.spec
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Penalized Cubic regression splines in GAMs
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smooth.construct.ds.smooth.spec
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Low rank Duchon 1977 splines
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smooth.construct.fs.smooth.spec
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Factor smooth interactions in GAMs
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smooth.construct.gp.smooth.spec
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Low rank Gaussian process smooths
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smooth.construct.mrf.smooth.spec
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Markov Random Field Smooths
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smooth.construct.ps.smooth.spec
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P-splines in GAMs
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smooth.construct.re.smooth.spec
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Simple random effects in GAMs
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smooth.construct.so.smooth.spec
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Soap film smoother constructer
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smooth.construct.sos.smooth.spec
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Splines on the sphere
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smooth.construct.sz.smooth.spec
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Constrained factor smooth interactions in GAMs
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smooth.construct.t2.smooth.spec
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Tensor product smoothing constructor
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smooth.construct.tensor.smooth.spec
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Tensor product smoothing constructor
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smooth.construct.tp.smooth.spec
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Penalized thin plate regression splines in GAMs
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smooth.info Generic function to provide extra information
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about smooth specification
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smooth.terms Smooth terms in GAM
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smooth2random Convert a smooth to a form suitable for
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estimating as random effect
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smoothCon Prediction/Construction wrapper functions for
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GAM smooth terms
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sp.vcov Extract smoothing parameter estimator
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covariance matrix from (RE)ML GAM fit
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spasm.construct Experimental sparse smoothers
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step.gam Alternatives to step.gam
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summary.gam Summary for a GAM fit
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t2 Define alternative tensor product smooths in
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GAM formulae
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te Define tensor product smooths or tensor product
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interactions in GAM formulae
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tensor.prod.model.matrix
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Row Kronecker product/ tensor product smooth
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construction
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totalPenaltySpace Obtaining (orthogonal) basis for null space and
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range of the penalty matrix
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trichol Choleski decomposition of a tri-diagonal matrix
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trind.generator Generates index arrays for upper triangular
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storage
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twlss Tweedie location scale family
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uniquecombs find the unique rows in a matrix
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vcov.gam Extract parameter (estimator) covariance matrix
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from GAM fit
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vis.gam Visualization of GAM objects
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ziP GAM zero-inflated (hurdle) Poisson regression
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family
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ziplss Zero inflated (hurdle) Poisson location-scale
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model family
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