[Robast-commits] r884 - pkg/RobAStBase/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 1 16:11:24 CEST 2016
Author: ruckdeschel
Date: 2016-09-01 16:11:24 +0200 (Thu, 01 Sep 2016)
New Revision: 884
Added:
pkg/RobAStBase/man/biastype-methods.Rd
pkg/RobAStBase/man/internal_GridHelpers.Rd
pkg/RobAStBase/man/normtype-methods.Rd
Modified:
pkg/RobAStBase/man/0RobAStBase-package.Rd
pkg/RobAStBase/man/InfoPlotWrapper.Rd
pkg/RobAStBase/man/comparePlot.Rd
pkg/RobAStBase/man/cutoff.Rd
pkg/RobAStBase/man/ddPlot-methods.Rd
pkg/RobAStBase/man/infoPlot.Rd
pkg/RobAStBase/man/internal_plots.Rd
pkg/RobAStBase/man/internals_ddPlot.Rd
pkg/RobAStBase/man/outlyingPlotIC.Rd
pkg/RobAStBase/man/plot-methods.Rd
Log:
Manuals updated
Modified: pkg/RobAStBase/man/0RobAStBase-package.Rd
===================================================================
--- pkg/RobAStBase/man/0RobAStBase-package.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/0RobAStBase-package.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -11,11 +11,12 @@
\details{
\tabular{ll}{
Package: \tab RobAStBase \cr
-Version: \tab 0.9 \cr
-Date: \tab 2013-09-11 \cr
-Depends: \tab R(>= 2.12.0), methods, distr(>= 2.0), distrEx(>= 2.0),
-distrMod(>= 2.0), RandVar(>= 0.6.3)\cr
-LazyLoad: \tab yes \cr
+Version: \tab 1.0 \cr
+Date: \tab 2015-05-03 \cr
+Depends: \tab R(>= 2.14.0), methods, rrcov, distr(>= 2.5.2), distrEx(>= 2.5), distrMod(>= 2.5.2), RandVar(>= 0.9.2)\cr
+Suggests: \tab ROptEst, RUnit (>= 0.4.26)\cr
+Imports: \tab startupmsg\cr
+ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
URL: \tab http://robast.r-forge.r-project.org/\cr
SVNRevision: \tab 694 \cr
Modified: pkg/RobAStBase/man/InfoPlotWrapper.Rd
===================================================================
--- pkg/RobAStBase/man/InfoPlotWrapper.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/InfoPlotWrapper.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -43,7 +43,7 @@
fam <- GammaFamily()
IC <- optIC(model = fam, risk = asCov())
Y <- distribution(fam)
-data <- r(Y)(1000)
+data <- r(Y)(500)
InfoPlot(IC, data, withCall = FALSE)
}
Copied: pkg/RobAStBase/man/biastype-methods.Rd (from rev 881, branches/robast-1.0/pkg/RobAStBase/man/biastype-methods.Rd)
===================================================================
--- pkg/RobAStBase/man/biastype-methods.Rd (rev 0)
+++ pkg/RobAStBase/man/biastype-methods.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -0,0 +1,18 @@
+\name{biastype-methods}
+\docType{methods}
+\alias{biastype,interpolRisk-method}
+\alias{biastype}
+\title{Methods for Function biastype in Package `RobAStBase'}
+\description{biastype-methods}
+
+\section{Methods}{\describe{
+
+\item{biastype}{\code{signature(object = "interpolrisk")}:
+ returns the slot \code{biastype} of an object of class \code{"interpolrisk"}. }
+}}
+\examples{
+myrisk <- MBRRisk(samplesize=100)
+biastype(myrisk)
+}
+\concept{risk}
+\keyword{classes}
Modified: pkg/RobAStBase/man/comparePlot.Rd
===================================================================
--- pkg/RobAStBase/man/comparePlot.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/comparePlot.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -17,18 +17,21 @@
col = par("col"), lwd = par("lwd"), lty,
col.inner = par("col.main"), cex.inner = 0.8,
bmar = par("mar")[1], tmar = par("mar")[3],
+ with.automatic.grid = TRUE,
with.legend = FALSE, legend = NULL, legend.bg = "white",
legend.location = "bottomright", legend.cex = 0.8,
withMBR = FALSE, MBRB = NA, MBR.fac = 2, col.MBR = par("col"),
lty.MBR = "dashed", lwd.MBR = 0.8,
- scaleX = FALSE, scaleX.fct, scaleX.inv,
+ x.vec = NULL, scaleX = FALSE, scaleX.fct, scaleX.inv,
scaleY = FALSE, scaleY.fct = pnorm, scaleY.inv=qnorm,
scaleN = 9, x.ticks = NULL, y.ticks = NULL,
mfColRow = TRUE, to.draw.arg = NULL,
- cex.pts = 1, col.pts = par("col"),
- pch.pts = 1, jitter.fac = 1, with.lab = FALSE,
+ cex.pts = 1, cex.pts.fun = NULL, col.pts = par("col"),
+ pch.pts = 1, jit.fac = 1, jit.tol = .Machine$double.eps, with.lab = FALSE,
lab.pts = NULL, lab.font = NULL, alpha.trsp = NA,
- which.lbs = NULL, which.Order = NULL, return.Order = FALSE)
+ which.lbs = NULL, which.Order = NULL, return.Order = FALSE,
+ draw.nonlbl = TRUE, cex.nonlbl=0.3, pch.nonlbl=".",
+ withSubst = TRUE)
}
\arguments{
\item{obj1}{ object of class \code{"InfluenceCurve"} }
@@ -61,6 +64,9 @@
to the current setting of \code{cex}; as in
\code{\link[graphics]{par}}}
\item{col.inner}{character or integer code; color for the inner title}
+ \item{with.automatic.grid}{logical; should a grid be plotted alongside
+ with the ticks of the axes, automatically? If \code{TRUE} a respective
+ call to \code{grid} in argument \code{panel.first} is ignored. }
\item{with.legend}{logical; shall a legend be plotted?}
\item{legend}{either \code{NULL} or a list of length (number of plotted panels)
of items which can be used as argument \code{legend} in
@@ -80,6 +86,15 @@
\item{col.MBR}{color for the MBR lines; as usual \code{col}-argument;}
\item{lty.MBR}{line type for the MBR lines; as usual \code{lty}-argument;}
\item{lwd.MBR}{line width for the MBR lines; as usual \code{lwd}-argument;}
+ \item{x.vec}{a numeric vector of grid points to evaluate the influence curve;
+ by default, \code{x.vec} is \code{NULL}; then the grid is
+ produced automatically according to the distribution of the IC.
+ \code{x.vec} can be useful for usage with a rescaling of the
+ x-axis to avoid that the evaluation points be selected too
+ unevenly (i.e. on an equally spaced grid in the original scale,
+ but then, after rescaling non-equally).
+ The grid has to be specified in original scale; i.e.; when used
+ with rescaling, it should be chosen non-equally spaced. }
\item{scaleX}{logical; shall X-axis be rescaled (by default according to the cdf of
the underlying distribution)?}
\item{scaleY}{logical; shall Y-axis be rescaled (by default according to a probit scale)?}
@@ -94,10 +109,14 @@
missing, the quantile function of the underlying observation distribution.}
\item{scaleY.fct}{an isotone, vectorized function mapping for each coordinate the
range of the respective coordinate of the IC
- to [0,1]; defaulting to the cdf of \eqn{{\cal N}(0,1)}{N(0,1)}.}
+ to [0,1]; defaulting to the cdf of \eqn{{\cal N}(0,1)}{N(0,1)};
+ can also be a list of functions with one list element for each
+ of the panels to be plot. }
\item{scaleY.inv}{an isotone, vectorized function mapping for each coordinate
the range [0,1] into the range of the respective coordinate of the IC;
- defaulting to the quantile function of \eqn{{\cal N}(0,1)}{N(0,1)}.}
+ defaulting to the quantile function of \eqn{{\cal N}(0,1)}{N(0,1)};
+ can also be a list of functions with one list element for each
+ of the panels to be plot. }
\item{scaleN}{integer; defaults to 9; on rescaled axes, number of x
and y ticks if drawn automatically;}
\item{x.ticks}{numeric; defaults to NULL; (then ticks are chosen automatically);
@@ -117,7 +136,17 @@
vector \code{"dim<dimnr>"}, \code{dimnr} running through
the number of rows of the trafo matrix.
}
+ \item{withSubst}{logical; if \code{TRUE} (default) pattern substitution for
+ titles and lables is used; otherwise no substitution is used. }
\item{cex.pts}{size of the points of the \code{data} argument plotted}
+ \item{cex.pts.fun}{rescaling function for the size of the points to be plotted;
+ either \code{NULL} (default), then \code{log(1+abs(x))} is used for each of
+ the rescalings, or a function which is then used for each of the
+ rescalings, or a list of functions; if it is a function or a list of
+ functions, if necessary it is recylced to length \code{nIC * dim}
+ where \code{nIC} is the number of pICs and \code{dim} is the number of
+ dimensions of the pICs to be plotted; in the index of this list,
+ \code{nIC} is incremented first; then \code{dim}.}
\item{col.pts}{color of the points of the \code{data} argument plotted}
\item{pch.pts}{symbol of the points of the \code{data} argument plotted}
\item{with.lab}{logical; shall labels be plotted to the observations?}
@@ -132,8 +161,10 @@
while for the remaining ones, the alpha channel in rgb space is set
to the respective coordinate value of \code{alpha.trsp}. The non-NA
entries must be integers in [0,255] (0 invisible, 255 opaque).}
- \item{jitter.fac}{jittering factor used in case of a \code{DiscreteDistribution}
+ \item{jit.fac}{jittering factor used in case of a \code{DiscreteDistribution}
for plotting points of the \code{data} argument in a jittered fashion.}
+ \item{jit.tol}{threshold for jittering: if distance between points is smaller
+ than \code{jit.tol}, points are considered replicates.}
\item{which.lbs}{either an integer vector with the indices of the observations
to be plotted into graph or \code{NULL} --- then no observation is excluded}
\item{which.Order}{for each of the given ICs, we order the observations (descending)
@@ -149,6 +180,9 @@
reduction by argument \code{which.lbs}, and ordering is according to the norm given by
\code{normtype(object)});
othervise we return \code{invisible()} as usual.}
+ \item{draw.nonlbl}{logical; should non-labelled observations be drawn?}
+ \item{cex.nonlbl}{character expansion(s) for non-labelled observations}
+ \item{pch.nonlbl}{plotting symbol(s) for non-labelled observations}
\item{\dots}{further arguments to be passed to \code{plot}}
}
\details{
@@ -166,7 +200,8 @@
and a "generated on <data>"-tag in case of \code{sub}.
Of course, if \code{main} / \code{inner} / \code{sub} are \code{character}, this
is used for the title; in case of \code{inner} it is then checked whether it
-has correct length. In all title arguments, the following patterns are substituted:
+has correct length. If argument \code{withSubst} is \code{TRUE}, in all title
+and axis lable arguments, the following patterns are substituted:
\describe{
\item{\code{"\%C1"},\code{"\%C2"},[\code{"\%C3"},][\code{"\%C4"}]}{class of argument
\code{obj<i>}, i=1,..4}
@@ -180,6 +215,13 @@
length 2*(number of plotted dimensions); in the case of longer length,
these are the values for \code{ylim} for the plotted dimensions of the IC,
one pair for each dimension.
+
+In addition, argument \code{\dots} may contain arguments \code{panel.first},
+\code{panel.last}, i.e., hook expressions to be evaluated at the very beginning
+and at the very end of each panel (within the then valid coordinates).
+To be able to use these hooks for each panel individually, they may also be
+lists of expressions (of the same length as the number of panels and
+run through in the same order as the panels).
}
%\value{}
Modified: pkg/RobAStBase/man/cutoff.Rd
===================================================================
--- pkg/RobAStBase/man/cutoff.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/cutoff.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -2,6 +2,7 @@
\alias{cutoff}
\alias{cutoff.sememp}
\alias{cutoff.chisq}
+\alias{cutoff.quant}
\title{Generating function(s) for class 'cutoff'}
\description{
@@ -11,8 +12,9 @@
cutoff(name = "empirical", body.fct0,
cutoff.quantile = 0.95,
norm = NormType(), QF, nsim = 100000)
-cutoff.sememp()
-cutoff.chisq()
+cutoff.sememp(cutoff.quantile = 0.95)
+cutoff.chisq(cutoff.quantile = 0.95)
+cutoff.quant(qfct)
}
\arguments{
\item{name}{argument for name slot of \code{cutoff} object}
@@ -26,6 +28,7 @@
normal and \eqn{Q} a corresponding quadratic form}
\item{QF}{ a quadratic (positive semidefinite, symmetric) matrix used
as quadratic form }
+ \item{qfct}{ a (nominal) quantile function }
}
\details{
\code{cutoff} generates a valid object of class \code{"cutoff"}.
@@ -47,6 +50,13 @@
\code{cutoff.chisq()} is a helper function generating the theoretical (asymptotic)
quantile of (the square root of) a (self-standardized) quadratic form, assuming multivariate
normality; i.e.; a corresponding quantile of a Chi-Square distribution.
+
+\code{cutoff.quant()} is a helper function generating the theoretical quantile
+corresponding to the quantile function \code{qfct}; if \code{qfct} is missing,
+it searches the caller environment for an object \code{..ICloc}, and if this
+exists it uses the respective model quantile function; the fallback is
+\code{qnorm}. At any rate, if there is an object \code{..trf} in the scope of
+the function it is used to transfer the quantile (after its evaluation).
}
\value{Object of class \code{"cutoff"}.}
\author{
Modified: pkg/RobAStBase/man/ddPlot-methods.Rd
===================================================================
--- pkg/RobAStBase/man/ddPlot-methods.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/ddPlot-methods.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -13,7 +13,7 @@
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jit.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -22,12 +22,12 @@
text.abline.y.x = NULL, text.abline.y.y = NULL,
text.abline.x.fmt.cx = "\%7.2f", text.abline.x.fmt.qx = "\%4.2f\%\%",
text.abline.y.fmt.cy = "\%7.2f", text.abline.y.fmt.qy = "\%4.2f\%\%",
- jitt.fac)
+ jit.fac, jit.tol = .Machine$double.eps,doplot = TRUE)
\S4method{ddPlot}{numeric}(data, dist.x = NormType(), dist.y = NormType(),
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jit.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -36,12 +36,12 @@
text.abline.y.x = NULL, text.abline.y.y = NULL,
text.abline.x.fmt.cx = "\%7.2f", text.abline.x.fmt.qx = "\%4.2f\%\%",
text.abline.y.fmt.cy = "\%7.2f", text.abline.y.fmt.qy = "\%4.2f\%\%",
- jitt.fac)
+ jit.fac, jit.tol=.Machine$double.eps, doplot = TRUE)
\S4method{ddPlot}{data.frame}(data, dist.x = NormType(), dist.y = NormType(),
cutoff.x, cutoff.y, ...,
cutoff.quantile.x = 0.95, cutoff.quantile.y = cutoff.quantile.x,
transform.x, transform.y = transform.x,
- id.n, lab.pts, adj, cex.idn,
+ id.n, cex.pts = 1,lab.pts, jit.pts = 0, alpha.trsp = NA, adj =0, cex.idn,
col.idn, lty.cutoff, lwd.cutoff, col.cutoff, text.abline = TRUE,
text.abline.x = NULL, text.abline.y = NULL,
cex.abline = par("cex"), col.abline = col.cutoff,
@@ -50,7 +50,7 @@
text.abline.y.x = NULL, text.abline.y.y = NULL,
text.abline.x.fmt.cx = "\%7.2f", text.abline.x.fmt.qx = "\%4.2f\%\%",
text.abline.y.fmt.cy = "\%7.2f", text.abline.y.fmt.qy = "\%4.2f\%\%",
- jitt.fac)
+ jit.fac, jit.tol=.Machine$double.eps, doplot = TRUE)
}
\arguments{
\item{data}{data coercable to \code{matrix}; the data at which to produce the \code{ddPlot}.}
@@ -69,7 +69,18 @@
distances of the \code{y} axis.}
\item{id.n}{a set of indices (or a corresponding logical vector); to select a subset
of the data in argument \code{data}.}
+ \item{cex.pts}{the corresponding \code{cex} argument for plotted points.}
\item{lab.pts}{a vector of labels for the (unsubsetted) \code{data}.}
+ \item{jit.pts}{the corresponding \code{jitter} argument for plotted points;
+ may be a vector of length 2 -- for separate factors for x- and y-coordinate.}
+ \item{alpha.trsp}{alpha transparency to be added ex post to colors
+ \code{col.pch} and \code{col.lbl}; if one-dim and NA all colors are
+ left unchanged. Otherwise, with usual recycling rules \code{alpha.trsp}
+ gets shorted/prolongated to length the data-symbols to be plotted.
+ Coordinates of this vector \code{alpha.trsp} with NA are left unchanged,
+ while for the remaining ones, the alpha channel in rgb space is set
+ to the respective coordinate value of \code{alpha.trsp}. The non-NA
+ entries must be integers in [0,255] (0 invisible, 255 opaque).}
\item{adj}{the corresponding argument for \code{\link[graphics]{text}} for
labelling the outliers.}
\item{cex.idn}{the corresponding \code{cex} argument for
@@ -108,7 +119,10 @@
\item{text.abline.x.fmt.qx}{format string to format cutoff probability in label in x direction.}
\item{text.abline.y.fmt.cy}{format string to format the cutoff value in label in y direction.}
\item{text.abline.y.fmt.qy}{format string to format cutoff probability in label in y direction.}
- \item{jitt.fac}{factor for jittering, see \code{jitter};}
+ \item{jit.fac}{factor for jittering, see \code{jitter};}
+ \item{jit.tol}{threshold for jittering: if distance between points is smaller
+ than \code{jit.tol}, points are considered replicates.}
+ \item{doplot}{logical; shall a plot be produced? if \code{FALSE} only the return values are produced.}
}
\details{
The \code{matrix}-method calls \code{.ddPlot.MatNtNtCoCo},
@@ -126,7 +140,7 @@
}
}
\value{
-a list with items
+a list (returned as \code{invisible()}) with items
\item{id.x}{the indices of (possibly transformed) data (within subset \code{id.n}) beyond the \code{x}-cutoff}
\item{id.y}{the indices of (possibly transformed) data (within subset \code{id.n}) beyond the \code{y}-cutoff}
\item{id.xy}{the indices of (possibly transformed) data (within subset \code{id.n}) beyond the \code{x}-cutoff and the \code{y}-cutoff}
Modified: pkg/RobAStBase/man/infoPlot.Rd
===================================================================
--- pkg/RobAStBase/man/infoPlot.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/infoPlot.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -16,18 +16,21 @@
main = FALSE, inner = TRUE, sub = FALSE,
col.inner = par("col.main"), cex.inner = 0.8,
bmar = par("mar")[1], tmar = par("mar")[3],
+ with.automatic.grid = TRUE,
with.legend = TRUE, legend = NULL, legend.bg = "white",
legend.location = "bottomright", legend.cex = 0.8,
- scaleX = FALSE, scaleX.fct, scaleX.inv,
+ x.vec = NULL, scaleX = FALSE, scaleX.fct, scaleX.inv,
scaleY = FALSE, scaleY.fct = pnorm, scaleY.inv=qnorm,
scaleN = 9, x.ticks = NULL, y.ticks = NULL,
mfColRow = TRUE, to.draw.arg = NULL,
- cex.pts = 1, col.pts = par("col"),
- pch.pts = 1, jitter.fac = 1, with.lab = FALSE,
+ cex.pts = 1, cex.pts.fun = NULL, col.pts = par("col"),
+ pch.pts = 1, jit.fac = 1, jit.tol = .Machine$double.eps, with.lab = FALSE,
lab.pts = NULL, lab.font = NULL, alpha.trsp = NA,
which.lbs = NULL, which.Order = NULL, return.Order = FALSE,
+ draw.nonlbl = TRUE, cex.nonlbl=0.3, pch.nonlbl=".",
ylab.abs = "absolute information",
- ylab.rel= "relative information")
+ ylab.rel= "relative information",
+ withSubst = TRUE)
}
\arguments{
\item{object}{object of class \code{"InfluenceCurve"} }
@@ -62,6 +65,9 @@
to the current setting of \code{cex}; as in
\code{\link[graphics]{par}}.}
\item{col.inner}{character or integer code; color for the inner title}
+ \item{with.automatic.grid}{logical; should a grid be plotted alongside
+ with the ticks of the axes, automatically? If \code{TRUE} a respective
+ call to \code{grid} in argument \code{panel.first} is ignored. }
\item{with.legend}{logical; shall a legend be plotted?}
\item{legend}{either \code{NULL} or a list of length (number of plotted panels)
of items which can be used as argument \code{legend} in
@@ -72,6 +78,15 @@
of such arguments, one for each plotted panel.}
\item{legend.bg}{background color for the legend}
\item{legend.cex}{magnification factor for the legend}
+ \item{x.vec}{a numeric vector of grid points to evaluate the influence curve;
+ by default, \code{x.vec} is \code{NULL}; then the grid is
+ produced automatically according to the distribution of the IC.
+ \code{x.vec} can be useful for usage with a rescaling of the
+ x-axis to avoid that the evaluation points be selected too
+ unevenly (i.e. on an equally spaced grid in the original scale,
+ but then, after rescaling non-equally).
+ The grid has to be specified in original scale; i.e.; when used
+ with rescaling, it should be chosen non-equally spaced. }
\item{scaleX}{logical; shall X-axis be rescaled (by default according to the cdf of
the underlying distribution)?}
\item{scaleY}{logical; shall Y-axis be rescaled for abs.info-plot
@@ -84,13 +99,17 @@
such that for any \code{x} in the domain,
\code{scaleX.inv(scaleX.fct(x))==x}; if \code{scaleX} is \code{TRUE}
and \code{scaleX.inv} is
- missing, the quantile function of the underlying observation distribution.}
+ missing, the quantile function of the underlying observation distribution. }
\item{scaleY.fct}{an isotone, vectorized function mapping the
range of the norm of the IC to [0,1]; defaulting
- to the cdf of \eqn{{\cal N}(0,1)}{N(0,1)}.}
+ to the cdf of \eqn{{\cal N}(0,1)}{N(0,1)};
+ can also be a list of functions with one list element for each
+ of the panels to be plot.}
\item{scaleY.inv}{an isotone, vectorized function mapping [0,1] into the range
of the norm of the IC; defaulting to the quantile function
- of \eqn{{\cal N}(0,1)}{N(0,1)}.}
+ of \eqn{{\cal N}(0,1)}{N(0,1)};
+ can also be a list of functions with one list element for each
+ of the panels to be plot.}
\item{scaleN}{integer; defaults to 9; on rescaled axes, number of x
and y ticks if drawn automatically;}
\item{x.ticks}{numeric; defaults to NULL; (then ticks are chosen automatically);
@@ -113,7 +132,19 @@
vector \code{"dim<dimnr>"}, \code{dimnr} running through
the number of rows of the trafo matrix.
}
+ \item{withSubst}{logical; if \code{TRUE} (default) pattern substitution for
+ titles and lables is used; otherwise no substitution is used. }
\item{cex.pts}{size of the points of the \code{data} argument plotted}
+ \item{cex.pts.fun}{rescaling function for the size of the points to be plotted;
+ either \code{NULL} (default), then \code{log(1+abs(x))} is used for each of
+ the rescalings, or a function which is then used for each of the
+ rescalings, or a list of functions; if it is a function or a list of
+ functions, if necessary it is recylced to length \code{2 * dim}
+ (where 2 is for the two pICs plotted, i.e., the classically optimal one and
+ argument \code{IC}, and \code{dim} is the number of
+ dimensions of the pICs to be plotted; in the index of this list,
+ the index for classical vs. \code{IC} is incremented first;
+ then \code{dim}.}
\item{col.pts}{color of the points of the \code{data} argument plotted}
\item{pch.pts}{symbol of the points of the \code{data} argument plotted}
\item{with.lab}{logical; shall labels be plotted to the observations?}
@@ -128,8 +159,10 @@
while for the remaining ones, the alpha channel in rgb space is set
to the respective coordinate value of \code{alpha.trsp}. The non-NA
entries must be integers in [0,255] (0 invisible, 255 opaque).}
- \item{jitter.fac}{jittering factor used in case of a \code{DiscreteDistribution}
+ \item{jit.fac}{jittering factor used in case of a \code{DiscreteDistribution}
for plotting points of the \code{data} argument in a jittered fashion.}
+ \item{jit.tol}{threshold for jittering: if distance between points is smaller
+ than \code{jit.tol}, points are considered replicates.}
\item{which.lbs}{either an integer vector with the indices of the observations
to be plotted into graph or \code{NULL} --- then no observation is excluded}
\item{which.Order}{we order the observations (descending) according to the norm given by
@@ -145,6 +178,9 @@
reduction by argument \code{which.lbs}, and ordering is according to the norm given by
\code{normtype(object)});
otherwise we return \code{invisible()} as usual.}
+ \item{draw.nonlbl}{logical; should non-labelled observations be drawn?}
+ \item{cex.nonlbl}{character expansion(s) for non-labelled observations}
+ \item{pch.nonlbl}{plotting symbol(s) for non-labelled observations}
\item{ylab.abs}{character; label to be used for y-axis in absolute information panel}
\item{ylab.rel}{character; label to be used for y-axis in relative information panel}
\item{\dots}{further parameters for \code{plot}}
@@ -170,7 +206,8 @@
and a "generated on <data>"-tag in case of \code{sub}.
Of course, if \code{main} / \code{inner} / \code{sub} are \code{character}, this
is used for the title; in case of \code{inner} it is then checked whether it
-has correct length. In all title arguments, the following patterns are substituted:
+has correct length. If argument \code{withSubst} is \code{TRUE}, in all title
+and axis lable arguments, the following patterns are substituted:
\describe{
\item{\code{"\%C"}}{class of argument \code{object}}
\item{\code{"\%A"}}{deparsed argument \code{object}}
@@ -195,6 +232,13 @@
The \code{\dots} argument may also contain an argument \code{withbox} which
if \code{TRUE} warrants that even if \code{xaxt} and \code{yaxt} both are
\code{FALSE}, a box is drawn around the respective panel.
+
+In addition, argument \code{\dots} may contain arguments \code{panel.first},
+\code{panel.last}, i.e., hook expressions to be evaluated at the very beginning
+and at the very end of each panel (within the then valid coordinates).
+To be able to use these hooks for each panel individually, they may also be
+lists of expressions (of the same length as the number of panels and
+run through in the same order as the panels).
}
%\value{}
\references{
Copied: pkg/RobAStBase/man/internal_GridHelpers.Rd (from rev 881, branches/robast-1.0/pkg/RobAStBase/man/internal_GridHelpers.Rd)
===================================================================
--- pkg/RobAStBase/man/internal_GridHelpers.Rd (rev 0)
+++ pkg/RobAStBase/man/internal_GridHelpers.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -0,0 +1,59 @@
+\name{internal_helpers_for_producing_grids_in_plots_RobAStBase}
+\alias{internal_helpers_for_producing_grids_in_plots_RobAStBase}
+\alias{.getDimsTD}
+\alias{.producePanelFirstS}
+
+\title{Internal / Helper functions of package RobAStBase for grids in plot functions}
+
+\description{
+These functions are internally used helper functions for \code{\link{plot}},
+\code{\link{infoPlot}} \code{\link{comparePlot}} in package \pkg{RobAStBase}.}
+
+\usage{
+.getDimsTD(L2Fam,to.draw.arg)
+.producePanelFirstS(panelFirst,IC,to.draw.arg, isInfoPlot=FALSE,
+ x.ticks, scaleX, scaleX.fct,
+ y.ticks, scaleY, scaleY.fct)
+}
+\arguments{
+ \item{L2Fam}{the model at which the plot is produced (of class \code{L2ParamFamily}).}
+ \item{to.draw.arg}{Either \code{NULL} (default;
+ everything is plotted) or a vector of either integers
+ (the indices of the subplots to be drawn) or characters
+ --- the names of the subplots to be drawn: these
+ names are to be chosen either among the row names of
+ the trafo matrix
+ \code{rownames(trafo(eval(x at CallL2Fam)@param))}
+ or if the last expression is \code{NULL} a
+ vector \code{"dim<dimnr>"}, \code{dimnr} running through
+ the number of rows of the trafo matrix.
+ }
+ \item{panelFirst}{argument \code{panel.first} to be mingled for grid plotting.}
+ \item{IC}{object of class \code{"InfluenceCurve"} }
+ \item{isInfoPlot}{logical; is this function to be used in \code{infoPlot} or
+ (\code{TRUE}) in another plot (\code{FALSE})? }
+ \item{x.ticks}{numeric: coordinates in original scale of user-given ticks on x-axis.}
+ \item{scaleX}{logical; shall X-axis be rescaled (by default according to the cdf of
+ the underlying distribution)?}
+ \item{scaleX.fct}{an isotone, vectorized function mapping the domain of the IC
+ to [0,1]; if \code{scaleX} is \code{TRUE} and \code{scaleX.fct} is
+ missing, the cdf of the underlying observation distribution.}
+ \item{y.ticks}{numeric: coordinates in original scale of user-given ticks on y-axis.}
+ \item{scaleY}{logical; shall Y-axis be rescaled (by default according to a probit scale)?}
+ \item{scaleY.fct}{an isotone, vectorized function mapping for each coordinate the
+ range of the respective coordinate of the IC
+ to [0,1]; defaulting to the cdf of \eqn{{\cal N}(0,1)}{N(0,1)}.}
+}
+\details{
+\code{.getDimsTD} computes the number of panels to be plotted.
+\code{.producePanelFirstS} produces an unevaluated expression to be
+used as argument \code{panel.first} in the diagnostic plots; i.e.;
+knowing the actual tickmarks of the axis at the time of evaluation,
+code is inserted to plot horizontal and vertical grid lines through
+these tickmarks.
+}
+
+
+\keyword{internal}
+\concept{utilities}
+\keyword{hplot}
Modified: pkg/RobAStBase/man/internal_plots.Rd
===================================================================
--- pkg/RobAStBase/man/internal_plots.Rd 2016-09-01 14:00:36 UTC (rev 883)
+++ pkg/RobAStBase/man/internal_plots.Rd 2016-09-01 14:11:24 UTC (rev 884)
@@ -6,6 +6,7 @@
\alias{.SelectOrderData}
\alias{.makedotsP}
\alias{.makedotsLowLevel}
+\alias{.cexscale}
\title{Internal / Helper functions of package RobAStBase for plot functions}
@@ -19,11 +20,13 @@
xlim, ylim, dots)
.plotRescaledAxis(scaleX, scaleX.fct, scaleX.inv, scaleY,scaleY.fct,
scaleY.inv, xlim, ylim, X, ypts = 400, n = 11,
+ finiteEndpoints = rep(FALSE,4),
x.ticks = NULL, y.ticks = NULL, withbox = TRUE)
.legendCoord(x, scaleX, scaleX.fct, scaleY, scaleY.fct)
.SelectOrderData(data, fct, which.lbs, which.Order)
.makedotsP(dots)
.makedotsLowLevel(dots)
+.cexscale(y, y1=y, maxcex=4,mincex=0.05,cex, fun=NULL)
}
\arguments{
\item{scaleX}{logical; shall X-axis be rescaled (by default according to the cdf of
@@ -51,6 +54,8 @@
scale).}
\item{ylim}{numeric vector of length 2: limits of the plotted y region (in original
scale).}
+ \item{finiteEndpoints}{a logical of length 4: are the unscaled \code{xlim[1]},
+ \code{xlim[2]}, \code{ylim[1]}, \code{ylim[2]} finite? }
\item{x.ticks}{numeric: coordinates in original scale of user-given ticks on x-axis.}
\item{y.ticks}{numeric: coordinates in original scale of user-given ticks on y-axis.}
\item{n}{integer: number of default ticks in x and y axis.}
@@ -75,6 +80,12 @@
\code{y.ticks} are both \code{NULL}, a respective box is drawn around the
panel; otherwise no box is drawn in this case. }
\item{dots}{a list; intended to be the \code{\dots} argument of \code{plot}. }
+ \item{y}{}
+ \item{y1}{}
+ \item{maxcex}{}
+ \item{mincex}{}
+ \item{cex}{}
+ \item{fun}{}
}
\details{
\code{.rescalefct} rescales, if necessary, x and y axis for use in plot
@@ -113,12 +124,27 @@
\code{data}, ie., the selected/thinned out data, \code{y}, ie., the
values of \code{fct(data)}, \code{ind}, ie., the indices of the selected data
in the original data (after possibly two selections), and \code{ind1} the
-indices of the data selected by \code{which.lbs} in the original data.
+indices of the data selected by \code{which.lbs} in the original data; in
+addition also the non selected data, \code{data.ns}, the respective
+y-values \code{y.ns} and the corresponding index elements \code{ind.ns} are
+returned as list items.
\code{.makedotsP} and \code{.makedotsLowLevel} manipulate the \code{\dots}
argument, deleting certain items and selecting items which can be digested by
\code{plot}, returning the manipulated list.
+
+\code{.cexscale}{rescales the point sizes of the points to be plotted;
+ the unscaled sizes are given in argument \code{y}, \code{y1} in
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/robast -r 884
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