[Distr-commits] r996 - in branches/distr-2.6/pkg/distrMod: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 18 14:34:25 CET 2015
Author: ruckdeschel
Date: 2015-02-18 14:34:24 +0100 (Wed, 18 Feb 2015)
New Revision: 996
Modified:
branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R
branches/distr-2.6/pkg/distrMod/R/qqplot.R
branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R
branches/distr-2.6/pkg/distrMod/inst/NEWS
branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd
branches/distr-2.6/pkg/distrMod/man/qqplot.Rd
branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd
Log:
[distrMod] helper .isReplicated gains argument tol to be able to identify observations from a continuous distribution "too" close to each other, hence requiring jittering; jittering uses this tolerance now and is available for continuous distributions, too.
Modified: branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R
===================================================================
--- branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R 2015-02-18 13:34:24 UTC (rev 996)
@@ -610,10 +610,10 @@
sapply(x, function(y) length(which(fct(y,gapm)))>0)
}
-.isReplicated <- function(x){
+.isReplicated <- function(x, tol=.Machine$double.eps){
tx <- table(x)
rx <- as.numeric(names(tx[tx>1]))
- sapply(x, function(y) any(abs(y-rx)<.Machine$double.eps))
+ sapply(x, function(y) any(abs(y-rx)<tol))
}
.NotInSupport <- function(x,D){
Modified: branches/distr-2.6/pkg/distrMod/R/qqplot.R
===================================================================
--- branches/distr-2.6/pkg/distrMod/R/qqplot.R 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/R/qqplot.R 2015-02-18 13:34:24 UTC (rev 996)
@@ -22,7 +22,7 @@
oN <- oN0[which.Order]
x0 <- xys[oN,1]
y0 <- xys[oN,2]
-
+
col.lbl <- col.lbl[rx]
lab.pts <- lab.pts[rx]
cex.lbl <- cex.lbl[rx]
@@ -82,6 +82,8 @@
adj.lbl = NULL, ## adj parameter for the plotted observation labels
alpha.trsp = NA, ## alpha transparency to be added afterwards
jit.fac = 0, ## jittering factor used for discrete distributions
+ jit.tol = .Machine$double.eps, ## tolerance for jittering: if distance
+ #is smaller than jit.tol, points are considered replicates
check.NotInSupport = TRUE, ## shall we check if all x lie in support(y)
col.NotInSupport = "red", ## if preceding check TRUE color of x if not in support(y)
with.legend = TRUE, ## shall a legend be plotted
@@ -113,8 +115,8 @@
xcc))
}else function(inx)inx
xj <- x
- if(any(.isReplicated(x)))
- xj[.isReplicated(x)] <- jitter(x[.isReplicated(x)], factor=jit.fac)
+ if(any(.isReplicated(x, jit.tol))&&jit.fac>0)
+ xj[.isReplicated(x, jit.tol)] <- jitter(x[.isReplicated(x, jit.tol)], factor=jit.fac)
ord.x <- order(xj)
Modified: branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R
===================================================================
--- branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R 2015-02-18 13:34:24 UTC (rev 996)
@@ -57,6 +57,8 @@
adj.lbl = NULL, ## adj parameter for the plotted observation labels
alpha.trsp = NA, ## alpha transparency to be added afterwards
jit.fac = 0, ## jittering factor used for discrete distributions
+ jit.tol = .Machine$double.eps, ## tolerance for jittering: if distance
+ #is smaller than jit.tol, points are considered replicates
check.NotInSupport = TRUE, ## shall we check if all x lie in support(y)
col.NotInSupport = "red", ## if preceding check TRUE color of x if not in support(y)
with.legend = TRUE, ## shall a legend be plotted
@@ -106,8 +108,8 @@
}
xj <- sort(x)
- if(any(.isReplicated(x))&&jit.fac>0)
- xj[.isReplicated(x)] <- jitter(x[.isReplicated(x)], factor=jit.fac)
+ if(any(.isReplicated(x, jit.tol))&&jit.fac>0)
+ xj[.isReplicated(x, jit.tol)] <- jitter(x[.isReplicated(x, jit.tol)], factor=jit.fac)
xj <- sort(xj)
ord.x <- order(xj)
Modified: branches/distr-2.6/pkg/distrMod/inst/NEWS
===================================================================
--- branches/distr-2.6/pkg/distrMod/inst/NEWS 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/inst/NEWS 2015-02-18 13:34:24 UTC (rev 996)
@@ -41,11 +41,15 @@
* now by default has datax = TRUE
* fixed issue with labeling
* issues with datax fixed
+ * gains argument jit.tol to allow jittering to take place also for
+ continuous observations, if observations are "too" close to each other
+ returnlevelplot
* similar as qqplot as to additional methods
* returnlevelplot now gains an argument threshold for POT
* set datax argument in case it is missing in returnlevelplot ...
* issues with datax fixed
+ * gains argument jit.tol to allow jittering to take place also for
+ continuous observations, if observations are "too" close to each other
+ new internal method .checkEstClassForParamFamily-method to be called
immediately before returning an Estimate object (in functions Estimator(),
MCEstimator(), MDEstimator(), MLEstimator()); this allows to return an
@@ -55,6 +59,7 @@
"MCEstimate" and "GEVEstimate", so that a diag-method for
"GEVEstimate" becomes available for this class.
+ enhanced imports in DESCRIPTION by explicating second order imports
++ helper function .isReplicated gains an optional argument tol
BUGFIXES:
Modified: branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd
===================================================================
--- branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd 2015-02-18 13:34:24 UTC (rev 996)
@@ -26,8 +26,9 @@
\details{
\code{.labelprep} prepares the labels for later output:
-first we (optionally) select some indices among \code{x} according
-to \code{which.lbs}, then orders both \code{x} and \code{y} according to the
+first some indices among \code{x} according
+to \code{which.lbs} are (optionally) selected,
+then orders both \code{x} and \code{y} according to the
order of the remaining (optionally transformed by \code{order.traf}) values of
\code{x} (decreasing); finally only the order statistics (w.r.t. the preceding
ordering) as specified in \code{which.Order} are returned;
Modified: branches/distr-2.6/pkg/distrMod/man/qqplot.Rd
===================================================================
--- branches/distr-2.6/pkg/distrMod/man/qqplot.Rd 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/man/qqplot.Rd 2015-02-18 13:34:24 UTC (rev 996)
@@ -10,7 +10,7 @@
ylab = deparse(substitute(y)),
..., width = 10, height = 5.5, withSweave = getdistrOption("withSweave"),
mfColRow = TRUE, n.CI = n, withLab = FALSE, lab.pts = NULL, which.lbs = NULL,
- which.Order = NULL, order.traf = NULL,
+ which.Order = NULL, order.traf = NULL,
col.IdL = "red", lty.IdL = 2, lwd.IdL = 2, alpha.CI = .95,
exact.pCI = (n<100), exact.sCI = (n<100), nosym.pCI = FALSE,
col.pCI = "orange", lty.pCI = 3, lwd.pCI = 2, pch.pCI = par("pch"),
@@ -19,7 +19,7 @@
cex.sCI = par("cex"), added.points.CI = TRUE,
cex.pch = par("cex"), col.pch = par("col"),
cex.lbl = par("cex"), col.lbl = par("col"), adj.lbl = NULL,
- alpha.trsp = NA, jit.fac = 0,
+ alpha.trsp = NA, jit.fac = 0, jit.tol = .Machine$double.eps,
check.NotInSupport = TRUE, col.NotInSupport = "red",
with.legend = TRUE, legend.bg = "white",
legend.pos = "topleft", legend.cex = 0.8,
@@ -107,7 +107,9 @@
while for the remaining ones, the alpha channel in rgb space is set
to the respective coordinate value of \code{alpha.trsp}. The non-NA
entries must be integers in [0,255] (0 invisible, 255 opaque).}
-\item{jit.fac}{jittering factor used for discrete distributions}
+\item{jit.fac}{jittering factor used for discrete distributions.}
+\item{jit.tol}{threshold for jittering: if distance between points is smaller
+ than \code{jit.tol}, points are considered replicates.}
\item{check.NotInSupport}{logical; shall we check if all \code{x}-quantiles lie
in \code{support(y)}?}
\item{col.NotInSupport}{logical; if preceding check \code{TRUE} color of
Modified: branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd
===================================================================
--- branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd 2015-02-18 13:22:31 UTC (rev 995)
+++ branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd 2015-02-18 13:34:24 UTC (rev 996)
@@ -13,7 +13,7 @@
main = "",
..., width = 10, height = 5.5, withSweave = getdistrOption("withSweave"),
mfColRow = TRUE, n.CI = n, withLab = FALSE, lab.pts = NULL, which.lbs = NULL,
- which.Order = NULL, order.traf = NULL,
+ which.Order = NULL, order.traf = NULL,
col.IdL = "red", lty.IdL = 2, lwd.IdL = 2, alpha.CI = .95,
exact.pCI = (n<100), exact.sCI = (n<100), nosym.pCI = FALSE,
col.pCI = "orange", lty.pCI = 3, lwd.pCI = 2, pch.pCI = par("pch"),
@@ -22,7 +22,7 @@
cex.sCI = par("cex"), added.points.CI = TRUE,
cex.pch = par("cex"), col.pch = par("col"),
cex.lbl = par("cex"), col.lbl = par("col"), adj.lbl = NULL,
- alpha.trsp = NA, jit.fac = 0,
+ alpha.trsp = NA, jit.fac = 0, jit.tol = .Machine$double.eps,
check.NotInSupport = TRUE, col.NotInSupport = "red",
with.legend = TRUE, legend.bg = "white",
legend.pos = "topleft", legend.cex = 0.8,
@@ -120,7 +120,9 @@
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{jit.fac}{jittering factor used for discrete distributions}
+\item{jit.fac}{jittering factor used for discrete distributions.}
+\item{jit.tol}{threshold for jittering: if distance between points is smaller
+ than \code{jit.tol}, points are considered replicates.}
\item{check.NotInSupport}{logical; shall we check if all \code{x}-quantiles lie
in \code{support(y)}?}
\item{col.NotInSupport}{logical; if preceding check \code{TRUE} color of
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