Commit 3b7bd8ba authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 1.3-20

parent 6c314e65
Package: mgcv
Version: 1.3-19
Version: 1.3-20
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Title: GAMs with GCV smoothness estimation and GAMMs by REML/PQL
......@@ -12,4 +12,4 @@ Imports: graphics, stats
Suggests: nlme (>= 3.1-64), MASS (>= 7.2-2)
LazyLoad: yes
License: GPL version 2 or later
Packaged: Tue Sep 12 14:57:25 2006; simon
Packaged: Mon Oct 16 14:17:30 2006; simon
......@@ -418,7 +418,7 @@ newton <- function(lsp,X,y,S,rS,off,H,offset,family,weights,
## Nstep <- -drop(U%*%(d*(t(U)%*%grad))) # (modified) Newton direction
ms <- max(abs(Nstep))
if (ms>maxNstep) Nstep <- Nstep/ms
if (ms>maxNstep) Nstep <- maxNstep * Nstep/ms
## try the step ...
lsp1 <- lsp + Nstep
......@@ -456,10 +456,10 @@ newton <- function(lsp,X,y,S,rS,off,H,offset,family,weights,
printWarn=FALSE,mustart=mustart,use.svd=use.svd,...)
if (scoreType=="GACV") {
score1 <- b$GACV
score1 <- b1$GACV
} else if (scoreType=="UBRE") {
score1 <- b$UBRE
} else score1 <- b$GCV
score1 <- b1$UBRE
} else score1 <- b1$GCV
if (score1 <= score) { ## accept
b<-gam.fit3(x=X, y=y, sp=lsp1, S=S,rS=rS,off=off, H=H,
......
1.3-20
* Bad bug in `newton' - step halving set up so that step *never*
accepted (it still beat all previous methods in simulations)
* Minor bug in `newton' step limiting of Newton steps reduced step
to max component 1, rather than `maxNstep'.
* Some documentation fixes
1.3-19
* numerous changes to NAMESPACE and gamm related functions to pass
......
......@@ -11,8 +11,8 @@ are usually approximate, unless the models are un-penalized.
}
\usage{
anova.gam(object, ..., dispersion = NULL, test = NULL)
print.anova.gam(x, digits = max(3, getOption("digits") - 3),...)
\method{anova}{gam}(object, ..., dispersion = NULL, test = NULL)
\method{print}{anova.gam}(x, digits = max(3, getOption("digits") - 3),...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
......
......@@ -6,7 +6,7 @@
matrix) of a fitted \code{gam} object.
}
\usage{
influence.gam(model,...)
\method{influence}{gam}(model,...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
......
......@@ -7,7 +7,7 @@
predictor. Optionally produces term plots for parametric model components
as well.}
\usage{
plot.gam(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,scale=-1,
\method{plot}{gam}(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,scale=-1,
n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xlab=NULL,
ylab=NULL,main=NULL,ylim=NULL,xlim=NULL,too.far=0.1,
all.terms=FALSE,shade=FALSE,shade.col="gray80",
......
......@@ -13,8 +13,8 @@ for quantities derived from the model, and for lookup table prediction outside
\code{R} (see example code below).}
\usage{
predict.gam(object,newdata,type="link",se.fit=FALSE,terms=NULL,
block.size=1000,newdata.guaranteed=FALSE,na.action=na.pass,...)
\method{predict}{gam}(object,newdata,type="link",se.fit=FALSE,terms=NULL,
block.size=1000,newdata.guaranteed=FALSE,na.action=na.pass,...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
......
......@@ -11,13 +11,8 @@ well as the minimized GCV or UBRE score, depending on which was used.
\references{
Gu and Wahba (1991) Minimizing GCV/GML scores with multiple smoothing parameters via
the Newton method. SIAM J. Sci. Statist. Comput. 12:383-398
Wood, S.N. (2000) Modelling and Smoothing Parameter Estimation
with Multiple Quadratic Penalties. J.R.Statist.Soc.B 62(2):413-428
Wood, S.N. (2003) Thin plate regression splines. J.R.Statist.Soc.B 65(1):95-114
Wood, S.N. (2006) Generalized Additive Models: An Introduction with R. CRC/
Chapmand and Hall, Boca Raton, Florida.
\url{http://www.maths.bath.ac.uk/~sw283/}
}
......
......@@ -8,7 +8,7 @@
}
\usage{
residuals.gam(object, type = c("deviance", "pearson","scaled.pearson", "working", "response"),...)
\method{residuals}{gam}(object, type = c("deviance", "pearson","scaled.pearson", "working", "response"),...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
......
......@@ -7,9 +7,9 @@
summaries from it.
}
\usage{
summary.gam(object, dispersion=NULL, freq=TRUE, ...)
\method{summary}{gam}(object, dispersion=NULL, freq=TRUE, ...)
print.summary.gam(x,digits = max(3, getOption("digits") - 3),
\method{print}{summary.gam}(x,digits = max(3, getOption("digits") - 3),
signif.stars = getOption("show.signif.stars"),...)
}
%- maybe also `usage' for other objects documented here.
......
......@@ -6,7 +6,8 @@
parameters or frequentist covariance matrix of the parameter estimators
from a fitted \code{gam} object.
}
\usage{vcov.gam(object, freq = TRUE, dispersion = NULL, ...)
\usage{
\method{vcov}{gam}(object, freq = TRUE, dispersion = NULL, ...)
}
%- maybe also `usage' for other objects documented here.
\arguments{
......
......@@ -3,8 +3,9 @@
\alias{persp.gam}
\title{Visualization of GAM objects}
\usage{
vis.gam(x,view=NULL,cond=list(),n.grid=30,too.far=0,col=NA,color="heat",
contour.col=NULL,se=-1,type="link",plot.type="persp",zlim=NULL,nCol=50,...)
vis.gam(x,view=NULL,cond=list(),n.grid=30,too.far=0,col=NA,
color="heat",contour.col=NULL,se=-1,type="link",
plot.type="persp",zlim=NULL,nCol=50,...)
}
\arguments{
......
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