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From: <ar...@us...> - 2008-06-30 22:29:39
|
Revision: 1299
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1299&view=rev
Author: arnima
Date: 2008-06-30 15:29:35 -0700 (Mon, 30 Jun 2008)
Log Message:
-----------
Simplified default 'unit' argument from c("KB","MB","bytes") to "KB".
Modified Paths:
--------------
trunk/gdata/R/env.R
trunk/gdata/R/ll.R
trunk/gdata/man/env.Rd
trunk/gdata/man/ll.Rd
Modified: trunk/gdata/R/env.R
===================================================================
--- trunk/gdata/R/env.R 2008-06-23 23:51:13 UTC (rev 1298)
+++ trunk/gdata/R/env.R 2008-06-30 22:29:35 UTC (rev 1299)
@@ -1,6 +1,4 @@
-# $Id$
-
-env <- function(unit=c("KB","MB","bytes"), digits=0)
+env <- function(unit="KB", digits=0)
{
get.object.size <- function(object.name, pos)
{
@@ -26,7 +24,7 @@
return(nobjects)
}
- unit <- match.arg(unit)
+ unit <- match.arg(unit, c("bytes","KB","MB"))
denominator <- switch(unit, "KB"=1024, "MB"=1024^2, 1)
size.vector <- sapply(seq(along=search()), get.environment.size)
size.vector <- round(size.vector/denominator, digits)
Modified: trunk/gdata/R/ll.R
===================================================================
--- trunk/gdata/R/ll.R 2008-06-23 23:51:13 UTC (rev 1298)
+++ trunk/gdata/R/ll.R 2008-06-30 22:29:35 UTC (rev 1299)
@@ -1,5 +1,5 @@
-ll <- function(pos=1, unit=c("KB","MB","bytes"), digits=0, dimensions=FALSE,
- function.dim="", sort.elements=FALSE, ...)
+ll <- function(pos=1, unit="KB", digits=0, dimensions=FALSE, function.dim="",
+ sort.elements=FALSE, ...)
{
get.object.classname <- function(object.name, pos)
{
@@ -29,7 +29,7 @@
return(size)
}
- unit <- match.arg(unit)
+ unit <- match.arg(unit, c("bytes","KB","MB"))
denominator <- switch(unit, "KB"=1024, "MB"=1024^2, 1)
if(is.character(pos)) # pos is an environment name
Modified: trunk/gdata/man/env.Rd
===================================================================
--- trunk/gdata/man/env.Rd 2008-06-23 23:51:13 UTC (rev 1298)
+++ trunk/gdata/man/env.Rd 2008-06-30 22:29:35 UTC (rev 1299)
@@ -7,7 +7,7 @@
Display name, number of objects, and size of all loaded environments.
}
\usage{
-env(unit=c("KB","MB","bytes"), digits=0)
+env(unit="KB", digits=0)
}
\arguments{
\item{unit}{required unit for displaying environment size: "bytes",
Modified: trunk/gdata/man/ll.Rd
===================================================================
--- trunk/gdata/man/ll.Rd 2008-06-23 23:51:13 UTC (rev 1298)
+++ trunk/gdata/man/ll.Rd 2008-06-30 22:29:35 UTC (rev 1299)
@@ -9,8 +9,8 @@
object, its elements are listed and described.
}
\usage{
-ll(pos=1, unit=c("KB","MB","bytes"), digits=0, dimensions=FALSE,
- function.dim="", sort.elements=FALSE, ...)
+ll(pos=1, unit="KB", digits=0, dimensions=FALSE, function.dim="",
+ sort.elements=FALSE, ...)
}
\arguments{
\item{pos}{environment position number, environment name, data frame,
@@ -39,8 +39,7 @@
}
\author{Arni Magnusson \email{arnima@u.washington.edu}, with a
- contribution by Jim Rogers
- \email{jam...@pf...}}
+ contribution by Jim Rogers \email{jam...@pf...}}
\seealso{
\code{\link{ls}} displays names of objects in a given environment.
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|
|
From: <wa...@us...> - 2008-06-16 14:18:51
|
Revision: 1296
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1296&view=rev
Author: warnes
Date: 2008-06-16 07:18:50 -0700 (Mon, 16 Jun 2008)
Log Message:
-----------
Add TODO list to gplots
Added Paths:
-----------
trunk/gplots/TODO
trunk/gplots/inst/TODO
Added: trunk/gplots/TODO
===================================================================
--- trunk/gplots/TODO (rev 0)
+++ trunk/gplots/TODO 2008-06-16 14:18:50 UTC (rev 1296)
@@ -0,0 +1 @@
+link inst/TODO
\ No newline at end of file
Property changes on: trunk/gplots/TODO
___________________________________________________________________
Name: svn:special
+ *
Added: trunk/gplots/inst/TODO
===================================================================
--- trunk/gplots/inst/TODO (rev 0)
+++ trunk/gplots/inst/TODO 2008-06-16 14:18:50 UTC (rev 1296)
@@ -0,0 +1,10 @@
+
+plot.lm2
+--------
+
+- Upgrade to match current plot.lm code
+- For predictor vs resid, use boxplot when predictor is a factor
+- Rug plot or histogram for residuals/fitted values in both dimensions
+- Confidence region for normal distribution with equivalent number of points on QQ plot
+- display "bad" cutoff line for cook's distance plot
+
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|
|
From: <wa...@us...> - 2008-06-14 21:03:54
|
Revision: 1295
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1295&view=rev
Author: warnes
Date: 2008-06-14 14:03:53 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
Minor changes to improve R CMD CHECK results
Modified Paths:
--------------
trunk/SII/R/reload.constants.R
trunk/SII/R/sii.excel.R
trunk/SII/man/critical.Rd
trunk/SII/man/sic.critical.Rd
Added Paths:
-----------
trunk/SII/man/undocumented.Rd
Modified: trunk/SII/R/reload.constants.R
===================================================================
--- trunk/SII/R/reload.constants.R 2008-06-14 20:51:59 UTC (rev 1294)
+++ trunk/SII/R/reload.constants.R 2008-06-14 21:03:53 UTC (rev 1295)
@@ -4,6 +4,8 @@
if(!require("gdata"))
stop("'gdata' package must be installed to run this function.")
+
+ read.xls <- gdata::read.xls
"critical" <- read.xls(
xls=file.path(xls.path,"SII_Constants.xls"),
Modified: trunk/SII/R/sii.excel.R
===================================================================
--- trunk/SII/R/sii.excel.R 2008-06-14 20:51:59 UTC (rev 1294)
+++ trunk/SII/R/sii.excel.R 2008-06-14 21:03:53 UTC (rev 1295)
@@ -15,7 +15,7 @@
if(matlab.spline)
{
- ispl <- interpSpline( THDI ~ freq )
+ ispl <- splines::interpSpline( THDI ~ freq )
THDI <- predict(ispl, sii.freqs)$y
THDI[sii.freqs<freq[1]] <- THDI[1]
}
Modified: trunk/SII/man/critical.Rd
===================================================================
--- trunk/SII/man/critical.Rd 2008-06-14 20:51:59 UTC (rev 1294)
+++ trunk/SII/man/critical.Rd 2008-06-14 21:03:53 UTC (rev 1295)
@@ -3,6 +3,7 @@
\alias{equal}
\alias{onethird}
\alias{octave}
+\alias{overall.spl}
\docType{data}
\title{Constants Tables for ANSI S3.5-1997 Speech Intelligibility Index
(SII)}
Modified: trunk/SII/man/sic.critical.Rd
===================================================================
--- trunk/SII/man/sic.critical.Rd 2008-06-14 20:51:59 UTC (rev 1294)
+++ trunk/SII/man/sic.critical.Rd 2008-06-14 21:03:53 UTC (rev 1295)
@@ -1,6 +1,6 @@
\name{sic.critical}
\alias{sic.critical}
-\alias{sic.threeoctave}
+\alias{sic.onethird}
\alias{sic.octave}
\docType{data}
\title{Alternative ANSI S3.5-1997 SII Transfer Function Weights}
@@ -10,7 +10,7 @@
}
\usage{
data(sic.critical)
-data(sic.threeoctave)
+data(sic.onethird)
data(sic.octave)
}
\format{
Added: trunk/SII/man/undocumented.Rd
===================================================================
--- trunk/SII/man/undocumented.Rd (rev 0)
+++ trunk/SII/man/undocumented.Rd 2008-06-14 21:03:53 UTC (rev 1295)
@@ -0,0 +1,13 @@
+\name{undocumented}
+\alias{sii.constants}
+\docType{data}
+\title{Undocuumented objects in package 'SII'}
+\description{
+ Undocuumented objects in package 'SII'
+}
+\usage{data(sii.constants)}
+\details{
+ This page notes objects containied in the 'SII' package that are not
+ intende for public use, hence are undocumented.
+}
+\keyword{datasets}
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|
|
From: <wa...@us...> - 2008-06-14 20:52:00
|
Revision: 1294
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1294&view=rev
Author: warnes
Date: 2008-06-14 13:51:59 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
Add funding to DESCRIPTION file
Modified Paths:
--------------
trunk/SII/DESCRIPTION
Modified: trunk/SII/DESCRIPTION
===================================================================
--- trunk/SII/DESCRIPTION 2008-06-14 20:48:11 UTC (rev 1293)
+++ trunk/SII/DESCRIPTION 2008-06-14 20:51:59 UTC (rev 1294)
@@ -17,6 +17,10 @@
The initial purpose of this package is to support use of SII as a
standard measure of severity of presbycusis (age-related of hearing
loss).
+ --
+ Development of this package was funded by the Center for Bioscience
+ Educationand Technology (CBET) of the Rochester Institute of
+ Technology (RIT).
Depends:
Recommends: splines, gdata
License: GPLv2
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|
|
From: <wa...@us...> - 2008-06-14 20:48:13
|
Revision: 1293
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1293&view=rev
Author: warnes
Date: 2008-06-14 13:48:11 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
Update package DESCRIPTION file.
Modified Paths:
--------------
trunk/SII/DESCRIPTION
Modified: trunk/SII/DESCRIPTION
===================================================================
--- trunk/SII/DESCRIPTION 2008-06-14 20:03:25 UTC (rev 1292)
+++ trunk/SII/DESCRIPTION 2008-06-14 20:48:11 UTC (rev 1293)
@@ -1,23 +1,23 @@
Package: SII
Type: Package
Title: Calculate ANSI S3.5-1997 Speech Intelligibility Index
-Version: 0.1.0
-Date: 2008-06-07
+Version: 0.1.1
+Date: 2008-06-14
Author: Gregory R. Warnes
Maintainer: Gregory R. Warnes <su...@ra...>
Description:
This package calculates ANSI S3.5-1997 Speech Intelligibility Index
(SII), which is a standard method for computing the intelligibility
- of speeck from acoustical measurments of speech and noise. This
+ of speech from acoustical measurements of speech and noise. This
package includes data frames corresponding to Tables 1 - 4 in the ANSI
- standard as well as a function utlilizing these tables and
- user-provided hearing threshold and noise level measurments to
+ standard as well as a function utilizing these tables and
+ user-provided hearing threshold and noise level measurements to
compute the SII score.
--
- The intial purpose of this package is to support use of SII as a
+ The initial purpose of this package is to support use of SII as a
standard measure of severity of presbycusis (age-related of hearing
loss).
Depends:
-Recommands: splines, gdata
+Recommends: splines, gdata
License: GPLv2
LazyLoad: yes
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|
|
From: <wa...@us...> - 2008-06-14 20:03:34
|
Revision: 1292
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1292&view=rev
Author: warnes
Date: 2008-06-14 13:03:25 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
Implement 'interpolate' as a separate argument, and when 'interpolate=TRUE' replace NA's in any provided measurement vector.
Modified Paths:
--------------
trunk/SII/R/sii.R
trunk/SII/man/sii.Rd
Modified: trunk/SII/R/sii.R
===================================================================
--- trunk/SII/R/sii.R 2008-06-14 20:01:31 UTC (rev 1291)
+++ trunk/SII/R/sii.R 2008-06-14 20:03:25 UTC (rev 1292)
@@ -5,7 +5,6 @@
loss,
freq,
method=c(
- "interpolate",
"critical",
"equal-contributing",
"one-third octave",
@@ -20,7 +19,8 @@
"ShortPassage",
"SPIN",
"CST"
- )
+ ),
+ interpolate=FALSE
)
{
## Assumptions:
@@ -28,7 +28,7 @@
## freq: If provided, frequencies in Hz at which speech, noise, and/or
## threshold values are measured. If missing, frequencies will
## corresponding to those utilized by the specified method.
- ## Note that, frequencies must be provided for method="interpolate"
+ ## Note that, frequencies must be provided if "interpolate=TRUE"
##
## speech: Speech level in dB at each frequency, or one of levels of
## stated vocal effort ("raised", "normal", "loud", "shout")
@@ -49,7 +49,6 @@
## Get the appropriate table of constants
data.name <- switch(method,
- "interpolate"="critical",
"critical"="critical",
"one-third octave"="onethird",
"equal-contributing"="equal",
@@ -79,8 +78,8 @@
## Handle missing freq
if(missing(freq))
- if(method=="interpolate")
- stop("`freq' must be specified when `method=\"interpolate\"'")
+ if(interpolate)
+ stop("`freq' must be specified when `interpolate=TRUE'")
else
freq <- table$fi
@@ -117,29 +116,13 @@
)
stop("`noise', `threshold', and `loss` must have the same length as `freq'.")
- ## Check for & handle missing values
- nas <- (is.na(noise) | is.na(threshold) | is.na(loss) | is.na(freq) )
+ ## Check for missing values
+ any.nas <- any(is.na(c(noise,threshold,loss,freq)) )
if(!const.speech)
- nas <- nas | is.na(speech)
+ any.nas <- any.nas || any(is.na(speech))
+ if(any.nas && !interpolate)
+ stop("Missing values only permitted when `interpolate=TRUE'")
- if(any(nas) )
- {
- if(method=="interpolate")
- {
- warning(sum(nas), " missing values omitted.")
- if(!const.speech)
- speech <- speech [!nas]
-
- noise <- noise [!nas]
- threshold <- threshold[!nas]
- loss <- loss [!nas]
- freq <- freq [!nas]
-
- }
- else
- stop("Missing values only permitted for method `interpolate'")
- }
-
## Sort values into frequency order
ord <- order(freq)
freq <- freq [ord]
@@ -155,30 +138,41 @@
retval <- list()
retval$call <- match.call()
retval$orig <- list( freq, speech, noise, threshold, loss )
+
- if(method=="interpolate")
+ if(interpolate)
{
- approx.l <- function(x,y)
- {
+
+ sii.freqs <- table[,"fi"]
+
+ approx.l <- function(obs.freq,value,target.freq)
+ {
+ nas <- is.na(value)
+ if(any(nas))
+ {
+ warning(sum(nas), " missing values ommitted")
+ value <- value[!nas]
+ obs.freq <- obs.freq[!nas]
+ }
+
tmp <- approx(
- log(x),
- y,
- log(sii.freqs),
+ x=log10(obs.freq),
+ y=value,
+ xout=log10(target.freq),
method="linear",
rule=2
)
tmp$y
}
-
- sii.freqs <- table[,"fi"]
+ #debug(approx.l)
## Interpolate unobserved frequencies
- noise <- approx.l(freq, noise)
- threshold <- approx.l(freq, threshold)
- loss <- approx.l(freq, loss)
+ noise <- approx.l(freq, noise, sii.freqs)
+ threshold <- approx.l(freq, threshold, sii.freqs)
+ loss <- approx.l(freq, loss, sii.freqs)
if(!const.speech)
- speech <- approx.l(freq, speech)
+ speech <- approx.l(freq, speech, sii.freqs)
freq <- sii.freqs
}
@@ -231,7 +225,6 @@
## 4.3.2.3 slope per octive of spread of masking, Ci
if(method=="critical" ||
- method=="interpolate" ||
method=="equal-contributing")
{
sii.tab$"Ci" <- -80 + 0.6*( sii.tab$"Bi" + 10*log10(table$"hi" - table$"li") )
@@ -242,7 +235,6 @@
}
if(method=="critical" ||
- method=="interpolate" ||
method=="equal-contributing")
{
Zifun <- function(i)
Modified: trunk/SII/man/sii.Rd
===================================================================
--- trunk/SII/man/sii.Rd 2008-06-14 20:01:31 UTC (rev 1291)
+++ trunk/SII/man/sii.Rd 2008-06-14 20:03:25 UTC (rev 1292)
@@ -12,10 +12,11 @@
\usage{
sii(speech = c("normal", "raised", "loud", "shout"),
noise, threshold, loss, freq,
- method = c("interpolate", "critical", "equal-contributing",
+ method = c("critical", "equal-contributing",
"one-third octave", "octave"),
importance = c("SII", "NNS", "CID22", "NU6", "DRT",
- "ShortPassage", "SPIN", "CST"))
+ "ShortPassage", "SPIN", "CST"),
+ interpolate=FALSE)
\method{print}{SII}(x, digits=2, ...)
\method{plot}{SII}(x, ...)
\method{summary}{SII}(object, digits=2, ...)
@@ -38,21 +39,24 @@
defaults to 0 dB for each frequency.}
\item{freq}{Vector of frequencies for which \code{speech},
\code{noise}, \code{threshold}, and/or \code{loss} are specified.
- If \code{method="interpolate"}, \code{freq} must be specified.
+ If \code{interpolate=TRUE}, \code{freq} must be specified.
Otherwise, it must either match the required value for SII
calculation method given by argument \code{method}, or be missing,
in which case it will default to the values required for the
specified method.}
\item{method}{A character string specifying the SII calculation
method ("critical", "one-third octave", "equal-contributing",
- "octave"), or \code{"interpolate"} in which case the critical-band
- method will be applied, with interpolation from the provided
- frequencies to the required 21 frequency values.}
+ "octave")}
\item{importance}{Either a numeric vector providing $F_i$, the
- transfer function (importance weights) at each frequency, or a character
- string indicating which transfer function to employ ("SII", "NNS",
- "CID22", "NU6", "DRT", "ShortPassage", "SPIN", "CST"). Defaults to
- the standard SII transfer function, \code{importance="SII"}.}
+ transfer function (importance weights) at each frequency, or a
+ character string indicating which transfer function to employ
+ ("SII", "NNS", "CID22", "NU6", "DRT", "ShortPassage", "SPIN",
+ "CST"). Defaults to the standard SII transfer function,
+ \code{importance="SII"}.}
+ \item{interpolate}{Logical flag indicating whether to interpolate
+ from the provide measurement values and frequencies to those
+ required by the specified method via linear interpolation on the log
+ scale.}
\item{object,x}{SII object}
\item{digits}{Number of digits to display}
\item{...}{Optional arguments to \code{print}, \code{summary}, and
@@ -78,13 +82,11 @@
Further, this implementation provides a mechanism for
interpolating/extrapolating available measurements to those required
- for calculating the critical band procedure (via the argument
- \code{method="interpolate"}). Interpolation is accomplished using
- linear interpolation (on log-scaled data) to the frequencies
- required for the critical-band SII procedure. Interpolation is
- performed (if necessary) for \code{noise}, \code{threshold}, and
- \code{loss}.
-
+ for the specified calculation procedure. When
+ \code{interpolate=TRUE}, required values for \code{speech},
+ \code{noise}, \code{threshold}, and \code{loss} will be computed
+ using linear interpolation (on log-scaled data). In this case,
+ missing values may be provided and will be appropriately interpolated.
}
\value{
The return value is an object of class SII, containing the following
@@ -196,7 +198,9 @@
speech="raised",
threshold=c(25,25,30,35,45,45,55,60),
freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="NU6"
+ method="critical",
+ importance="NU6",
+ interpolate=TRUE
)
sii.left
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From: <wa...@us...> - 2008-06-14 20:01:37
|
Revision: 1291
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1291&view=rev
Author: warnes
Date: 2008-06-14 13:01:31 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
Add SII to importance weight tables
Modified Paths:
--------------
trunk/SII/man/sic.critical.Rd
Modified: trunk/SII/man/sic.critical.Rd
===================================================================
--- trunk/SII/man/sic.critical.Rd 2008-06-14 19:59:29 UTC (rev 1290)
+++ trunk/SII/man/sic.critical.Rd 2008-06-14 20:01:31 UTC (rev 1291)
@@ -19,7 +19,8 @@
speech material:
\describe{
\item{\code{fi}}{Center frequency, Hz}
- \item{\code{NNS}}{NNS (various nonsense syllable tessz where
+ \item{\code{SII}}{Standard SII transfer function (weights)}
+ \item{\code{NNS}}{NNS (various nonsense syllable tests where
most of the English phonems occur equally often)}
\item{\code{CID22}}{CID-W22 (PB-words)}
\item{\code{NU6}}{NU6 monosyllables}
@@ -66,15 +67,21 @@
round(sic.critical,3)
## draw a comparison plot
-matplot(x=sic.critical[,1], y=sic.critical[,-1], type="o",
- xlab="Frequency, Hz", ylab="Weight",
- log="x")
+ngroup <- ncol(sic.critical)
+matplot(x=sic.critical[,1], y=sic.critical[,-1],
+ type="o",
+ xlab="Frequency, Hz",
+ ylab="Weight",
+ log="x",
+ lty=1:ngroup,
+ col=rainbow(ngroup)
+)
legend(
"topright",
legend=names(sic.critical)[-1],
- pch=1:ncol(sic.critical),
- lty=1:ncol(sic.critical),
- col=1:ncol(sic.critical)
+ pch=as.character(1:ngroup),
+ lty=1:ngroup,
+ col=rainbow(ngroup)
)
data(threeoctave)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-06-14 19:59:31
|
Revision: 1290
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1290&view=rev
Author: warnes
Date: 2008-06-14 12:59:29 -0700 (Sat, 14 Jun 2008)
Log Message:
-----------
Add SII to importance weight tables
Modified Paths:
--------------
trunk/SII/data/SII_Constants.xls
trunk/SII/data/critical.rda
trunk/SII/data/equal.rda
trunk/SII/data/octave.rda
trunk/SII/data/onethird.rda
trunk/SII/data/sic.critical.rda
trunk/SII/data/sic.octave.rda
trunk/SII/data/sic.onethird.rda
Modified: trunk/SII/data/SII_Constants.xls
===================================================================
(Binary files differ)
Modified: trunk/SII/data/critical.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/data/equal.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/data/octave.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/data/onethird.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/data/sic.critical.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/data/sic.octave.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/data/sic.onethird.rda
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-06-12 05:56:50
|
Revision: 1289
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1289&view=rev
Author: warnes
Date: 2008-06-11 22:56:39 -0700 (Wed, 11 Jun 2008)
Log Message:
-----------
More documentation, and some code cleanup
Modified Paths:
--------------
trunk/SII/DESCRIPTION
trunk/SII/NAMESPACE
trunk/SII/R/summary.SII.R
trunk/SII/data/sic.octave.rda
trunk/SII/man/SII-package.Rd
trunk/SII/man/critical.Rd
trunk/SII/man/sii.Rd
Added Paths:
-----------
trunk/SII/man/sic.critical.Rd
Removed Paths:
-------------
trunk/SII/R/sii.constants.Rd
trunk/SII/man/plot.SII.Rd
trunk/SII/man/print.SII.Rd
trunk/SII/man/sii.excel.Rd
Modified: trunk/SII/DESCRIPTION
===================================================================
--- trunk/SII/DESCRIPTION 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/DESCRIPTION 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,12 +1,12 @@
Package: SII
Type: Package
-Title: Calcluate ANSI S3.5-1997 Speech Intelligibility Index
+Title: Calculate ANSI S3.5-1997 Speech Intelligibility Index
Version: 0.1.0
Date: 2008-06-07
Author: Gregory R. Warnes
Maintainer: Gregory R. Warnes <su...@ra...>
Description:
- This package calculates ANSI S3.5-199 Speech Intelligibility Index
+ This package calculates ANSI S3.5-1997 Speech Intelligibility Index
(SII), which is a standard method for computing the intelligibility
of speeck from acoustical measurments of speech and noise. This
package includes data frames corresponding to Tables 1 - 4 in the ANSI
@@ -15,6 +15,9 @@
compute the SII score.
--
The intial purpose of this package is to support use of SII as a
- standard measure of the impact age-related of hearing loss.
+ standard measure of severity of presbycusis (age-related of hearing
+ loss).
+Depends:
+Recommands: splines, gdata
License: GPLv2
LazyLoad: yes
Modified: trunk/SII/NAMESPACE
===================================================================
--- trunk/SII/NAMESPACE 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/NAMESPACE 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,7 +1,10 @@
export(
- sii
+ sii,
+ plot.SII,
+ print.SII,
+ summary.SII
)
-s3method(plot, SII)
-s3method(print, SII)
-s3method(summary, SII)
+S3method(plot, SII)
+S3method(print, SII)
+S3method(summary, SII)
Deleted: trunk/SII/R/sii.constants.Rd
===================================================================
--- trunk/SII/R/sii.constants.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/R/sii.constants.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,39 +0,0 @@
-\name{sii.constants}
-\alias{sii.constants}
-\docType{data}
-\title{ ~~ data name/kind ... ~~}
-\description{
- ~~ A concise (1-5 lines) description of the dataset. ~~
-}
-\usage{data(sii.constants)}
-\format{
- A data frame with 21 observations on the following 12 variables.
- \describe{
- \item{\code{.NFreqLin}}{a numeric vector}
- \item{\code{.NFreqLog}}{a numeric vector}
- \item{\code{I.BandImp}}{a numeric vector}
- \item{\code{Ti'.THDN}}{a numeric vector}
- \item{\code{Ei.Raised}}{a numeric vector}
- \item{\code{Xi.Ref.Int.Nz}}{a numeric vector}
- \item{\code{Xi'.Int.Noise}}{a numeric vector}
- \item{\code{Di.Equiv.Dist}}{a numeric vector}
- \item{\code{Li.Distortion}}{a numeric vector}
- \item{\code{ki.Temp.Var}}{a numeric vector}
- \item{\code{Ai.BandAud}}{a numeric vector}
- \item{\code{Si.SII.band.}}{a numeric vector}
- }
-}
-\details{
- ~~ If necessary, more details than the __description__ above ~~
-}
-\source{
- ~~ reference to a publication or URL from which the data were obtained ~~
-}
-\references{
- ~~ possibly secondary sources and usages ~~
-}
-\examples{
-data(sii.constants)
-## maybe str(sii.constants) ; plot(sii.constants) ...
-}
-\keyword{datasets}
Modified: trunk/SII/R/summary.SII.R
===================================================================
--- trunk/SII/R/summary.SII.R 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/R/summary.SII.R 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,5 +1,5 @@
`summary.SII` <-
-function (x, digits = 2, ...)
+function (object, digits = 2, ...)
{
cat("\n")
cat("Speech Intellibility Index\n")
@@ -7,9 +7,9 @@
cat("\n")
cat("Call:\n")
cat("\n")
- print(x$call)
+ print(object$call)
cat("\n")
- methodStr <- switch(x$method,
+ methodStr <- switch(object$method,
"interpolate"="Interpolation + Critical Band",
"critical"="Critical band SII procedure",
"equal-contributing"="Equally-contrlbutlng (17 band) critical-band SII procedure ",
@@ -21,10 +21,10 @@
cat("\n")
cat("Calculation table:\n")
cat("\n")
- print(round(x$table, digits=digits))
+ print(object$table, digits=digits)
cat("\n")
- cat("SII:", round(x$sii, digits), "\n")
+ cat("SII:", round(object$sii, digits), "\n")
cat("\n")
- invisible(x)
+ invisible(object)
}
Modified: trunk/SII/data/sic.octave.rda
===================================================================
(Binary files differ)
Modified: trunk/SII/man/SII-package.Rd
===================================================================
--- trunk/SII/man/SII-package.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/man/SII-package.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -3,41 +3,46 @@
\alias{SII}
\docType{package}
\title{
-What the package does (short line)
-~~ package title ~~
+ Calculate ANSI S3.5-1997 Speech Intelligibility Index
}
\description{
-More about what it does (maybe more than one line)
-~~ A concise (1-5 lines) description of the package ~~
+This package calculates ANSI S3.5-199 Speech Intelligibility Index
+(SII), which is a standard method for computing the intelligibility
+of speeck from acoustical measurments of speech and noise. This
+package includes data frames corresponding to Tables 1 - 4 in the ANSI
+standard as well as a function utlilizing these tables and
+user-provided hearing threshold and noise level measurments to
+compute the SII score.
+
+
+The intial purpose of this package is to support use of SII as a
+standard measure of the impact age-related of hearing loss.
}
\details{
-\tabular{ll}{
-Package: \tab SII\cr
-Type: \tab Package\cr
-Version: \tab 1.0\cr
-Date: \tab 2008-06-07\cr
-License: \tab What license is it under?\cr
-LazyLoad: \tab yes\cr
}
-~~ An overview of how to use the package, including the most important ~~
-~~ functions ~~
-}
\author{
-Who wrote it
-
-Maintainer: Who to complain to <you...@so...>
-~~ The author and/or maintainer of the package ~~
+ Gregory R. Warnes \email{su...@ra...}
}
\references{
-~~ Literature or other references for background information ~~
+ANSI S3.5-1997, "American National Standard Methods for
+Calculation of the Speech Intelligibility Index" American National Stan-
+dards Institute, New York.
+
+Other software programs for calculating SII are available from
+\url{http://www.sii.to/html/programs.html}.
}
-~~ Optionally other standard keywords, one per line, from file KEYWORDS in ~~
-~~ the R documentation directory ~~
\keyword{ package }
-\seealso{
-~~ Optional links to other man pages, e.g. ~~
-~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
-}
\examples{
-~~ simple examples of the most important functions ~~
+## Example C.1 from ANSI S3.5-1997 Annex C
+sii.C1 <- sii(
+ speech = c(50.0, 40.0, 40.0, 30.0, 20.0, 0.0),
+ noise = c(70.0, 65.0, 45.0, 25.0, 1.0,-15.0),
+ threshold= c( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0),
+ method="octave"
+ )
+sii.C1 # rounded to 2 digits by default
+print(sii.C1$sii, digits=20) # full precision
+summary(sii.C1) # full details
+plot(sii.C1) # plot
+## The value given in the Standard is $0.504$.
}
Modified: trunk/SII/man/critical.Rd
===================================================================
--- trunk/SII/man/critical.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/man/critical.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -4,37 +4,77 @@
\alias{onethird}
\alias{octave}
\docType{data}
-\title{ ~~ data name/kind ... ~~}
+\title{Constants Tables for ANSI S3.5-1997 Speech Intelligibility Index
+ (SII)}
\description{
- ~~ A concise (1-5 lines) description of the dataset. ~~
+ Tables of constants for ANSI S3.5-1997 Speech Intelligibility Index
+ (SII)
}
-\usage{data(critical)}
+\usage{
+data(critical)
+data(equal)
+data(onethird)
+data(octave)
+data(overall.spl)
+}
+
\format{
- A data frame with 21 observations on the following 10 variables.
+ Each data frames has 6-21 observations and a subset of the following
+ variables:
\describe{
- \item{\code{fi}}{a numeric vector}
- \item{\code{li}}{a numeric vector}
- \item{\code{hi}}{a numeric vector}
- \item{\code{Ii}}{a numeric vector}
- \item{\code{normal}}{a numeric vector}
- \item{\code{raised}}{a numeric vector}
- \item{\code{loud}}{a numeric vector}
- \item{\code{shout}}{a numeric vector}
- \item{\code{Xi}}{a numeric vector}
- \item{\code{Fi}}{a numeric vector}
+ \item{\code{fi}}{Center frequency of SII band, Hz}
+ \item{\code{li}}{Lower limit of frequency band, Hz}
+ \item{\code{hi}}{Upper limit of frequency band, Hz}
+ \item{\code{Deltai}}{Band width adjustment, dB}
+ \item{\code{Ii}}{Band importance function}
+ \item{\code{normal}, \code{raised}, \code{loud} and
+ \code{shout}}{Standard spectrum levels for vocal effort levels
+ "normal", "raised", "loud", and "shout", respectively, dB}
+ \item{\code{Xi}}{Spectrum level of internal noise, dB}
+ \item{\code{Fi}}{Band importance function (weight)}
}
}
\details{
- ~~ If necessary, more details than the __description__ above ~~
+ These data objects provide constant tables 1 -- 4 from the ANSI
+ S3.5-1997.
+ \describe{
+ \item{\code{critical}}{Table 1: Critical band SII procedure
+ constants}
+ \item{\code{equal}}{Table 2:Equally contributing (17 band) critical
+ band SII}
+ \item{\code{onethird}}{Table 3: One-third octave band SII procedure
+ constants}
+ \item{\code{octave}}{Table 4: Octave band SII procedure constants}
+ \item{\code{overall.spl}}{Overall sound pressure level (SPL) for the
+ for vocal effort levels "normal", "raised", "loud", and "shout",
+ in dB}
+ }
}
\source{
- ~~ reference to a publication or URL from which the data were obtained ~~
+ANSI S3.5-1997, "American National Standard Methods for
+Calculation of the Speech Intelligibility Index" American National
+Standards Institute, New York.
}
\references{
- ~~ possibly secondary sources and usages ~~
+ANSI S3.5-1997, "American National Standard Methods for
+Calculation of the Speech Intelligibility Index" American National
+Standards Institute, New York.
}
\examples{
data(critical)
-## maybe str(critical) ; plot(critical) ...
+critical # show entire table
+
+data(equal)
+names(equal)
+equal$fi # extract just the frequency band centers
+
+data(onethird)
+barplot(onethird$Ii) # plot band importance function (weights)
+
+data(octave)
+round(octave, digits=2) # just 2 digits
+
+data(overall.spl)
+overall.spl
}
\keyword{datasets}
Deleted: trunk/SII/man/plot.SII.Rd
===================================================================
--- trunk/SII/man/plot.SII.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/man/plot.SII.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,63 +0,0 @@
-\name{plot.SII}
-\alias{plot.SII}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ ~~function to do ... ~~ }
-\description{
- ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-plot.SII(x, matlab, title, ...)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{x}{ ~~Describe \code{x} here~~ }
- \item{matlab}{ ~~Describe \code{matlab} here~~ }
- \item{title}{ ~~Describe \code{title} here~~ }
- \item{\dots}{ ~~Describe \code{\dots} here~~ }
-}
-\details{
- ~~ If necessary, more details than the description above ~~
-}
-\value{
- ~Describe the value returned
- If it is a LIST, use
- \item{comp1 }{Description of 'comp1'}
- \item{comp2 }{Description of 'comp2'}
- ...
-}
-\references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~
-
- ~Make other sections like Warning with \section{Warning }{....} ~
-}
-\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
-
-## The function is currently defined as
-function (x, matlab, title, ...)
-{
- plot(x = x$freq.orig, y = x$x.orig, col = "black", cex = 2,
- log = "x", xlab = "Frequency (Herz)", ylab = "Threshhold of Detection (dB)",
- ylim = c(1, 80), xlim = c(100, 8500))
- if (!missing(matlab))
- lines(sii.constants[, 1], matlab, type = "l", col = "red",
- lwd = 3)
- lines(x = sii.constants[, 1], y = x$table[, "T'i"], col = "blue",
- lwd = 2)
- abline(v = sii.constants[, 1], lty = 2)
- legend("topleft", legend = c("Measured data", "Matlab INTERP1(X, Y, XI, 'spline', 'extrap')",
- "R's approx(X,Y, XI, xout=XI,\n method='linear', rule=2)"),
- col = c("black", "red", "blue", "green", "orange", "magenta"),
- pch = c(1, NA, NA, NA, NA, NA), lty = c(NA, 1, 1, 1,
- 1, 1), lwd = c(NA, 3, 2, 2, 2, 2), bg = "white")
- title(title)
- }
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
Deleted: trunk/SII/man/print.SII.Rd
===================================================================
--- trunk/SII/man/print.SII.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/man/print.SII.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,48 +0,0 @@
-\name{print.SII}
-\alias{print.SII}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ ~~function to do ... ~~ }
-\description{
- ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-print.SII(x, digits = 2, ...)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{x}{ ~~Describe \code{x} here~~ }
- \item{digits}{ ~~Describe \code{digits} here~~ }
- \item{\dots}{ ~~Describe \code{\dots} here~~ }
-}
-\details{
- ~~ If necessary, more details than the description above ~~
-}
-\value{
- ~Describe the value returned
- If it is a LIST, use
- \item{comp1 }{Description of 'comp1'}
- \item{comp2 }{Description of 'comp2'}
- ...
-}
-\references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~
-
- ~Make other sections like Warning with \section{Warning }{....} ~
-}
-\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
-
-## The function is currently defined as
-function (x, digits = 2, ...)
-{
- print(unclass(round(x$sii, digits)))
- }
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
Added: trunk/SII/man/sic.critical.Rd
===================================================================
--- trunk/SII/man/sic.critical.Rd (rev 0)
+++ trunk/SII/man/sic.critical.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -0,0 +1,83 @@
+\name{sic.critical}
+\alias{sic.critical}
+\alias{sic.threeoctave}
+\alias{sic.octave}
+\docType{data}
+\title{Alternative ANSI S3.5-1997 SII Transfer Function Weights}
+\description{
+ Alternative ANSI S3.5-1997 Speech Intelligibility Index (SII) transfer
+ function weights for for various types of speech material.
+}
+\usage{
+data(sic.critical)
+data(sic.threeoctave)
+data(sic.octave)
+}
+\format{
+ Each data frame contains the following 8 variables, each
+ corresponding the the transfer function weights for a specific type of
+ speech material:
+ \describe{
+ \item{\code{fi}}{Center frequency, Hz}
+ \item{\code{NNS}}{NNS (various nonsense syllable tessz where
+ most of the English phonems occur equally often)}
+ \item{\code{CID22}}{CID-W22 (PB-words)}
+ \item{\code{NU6}}{NU6 monosyllables}
+ \item{\code{DRT}}{DRT (Diagnostic Rhyme Test)}
+ \item{\code{ShortPassage}}{short passages of easy reading material}
+ \item{\code{SPIN}}{SPIN monosyllables}
+ \item{\code{CST}}{Connected Speech Test}
+ }
+}
+\details{
+ \describe{
+ \item{\code{sic.critical}}{provides alternative weights for the
+ critical band SII procedure.}
+ \item{\code{sic.threeoctave}}{provides alternative weights for the
+ one-third octave frequency band SII procedure.}
+ \item{\code{octave}}{provides alternative weights for the
+ octave frequency band SII procedure.}
+ }
+}
+\section{note}{There is no table of alternative weights for the
+ equally-weighted SII band procedure as the weights for this method are
+ (by definition) constant across all bands.
+ }
+\source{
+ All values except the \code{CST} columns are from:
+
+ ANSI S3.5-1997, "American National Standard Methods for
+ Calculation of the Speech Intelligibility Index" American National
+ Standards Institute, New York.
+
+ Values in the \code{CST} columns are from:
+ \url{http://www.sii.to/CSTdata.txt}
+}
+\references{
+ ANSI S3.5-1997, "American National Standard Methods for
+ Calculation of the Speech Intelligibility Index" American National
+ Standards Institute, New York.
+}
+\examples{
+## Load the alternative weights for the critical band method
+data(sic.critical)
+
+## display the weights
+round(sic.critical,3)
+
+## draw a comparison plot
+matplot(x=sic.critical[,1], y=sic.critical[,-1], type="o",
+ xlab="Frequency, Hz", ylab="Weight",
+ log="x")
+legend(
+ "topright",
+ legend=names(sic.critical)[-1],
+ pch=1:ncol(sic.critical),
+ lty=1:ncol(sic.critical),
+ col=1:ncol(sic.critical)
+ )
+
+data(threeoctave)
+data(octave)
+}
+\keyword{datasets}
Modified: trunk/SII/man/sii.Rd
===================================================================
--- trunk/SII/man/sii.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/man/sii.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,172 +1,207 @@
\name{sii}
\alias{sii}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ ~~function to do ... ~~ }
+\alias{print.SII}
+\alias{plot.SII}
+\alias{summary.SII}
+\title{Compute ANSI S3.5-1997 Speech Intelligibility Index (SII)}
\description{
- ~~ A concise (1-5 lines) description of what the function does. ~~
+ Compute the Speech Intelligibility Index (SII) described by ANSI
+ specification S3.5-1997, including extensions for conductive
+ hearing loss.
}
\usage{
-sii(x, freq, noise, method = c("interpolate", "critical", "one-third octave", "equal-contributing", "octave"), voice = c("raised", "normal", "loud", "shout"))
+sii(speech = c("normal", "raised", "loud", "shout"),
+ noise, threshold, loss, freq,
+ method = c("interpolate", "critical", "equal-contributing",
+ "one-third octave", "octave"),
+ importance = c("SII", "NNS", "CID22", "NU6", "DRT",
+ "ShortPassage", "SPIN", "CST"))
+\method{print}{SII}(x, digits=2, ...)
+\method{plot}{SII}(x, ...)
+\method{summary}{SII}(object, digits=2, ...)
}
-%- maybe also 'usage' for other objects documented here.
\arguments{
- \item{x}{ ~~Describe \code{x} here~~ }
- \item{freq}{ ~~Describe \code{freq} here~~ }
- \item{noise}{ ~~Describe \code{noise} here~~ }
- \item{method}{ ~~Describe \code{method} here~~ }
- \item{voice}{ ~~Describe \code{voice} here~~ }
+ \item{speech}{Either a numeric vector providing $E'_i$, the equivalent
+ speech spectrum level (in dB) at each frequency, or a character
+ string indicating the stated vocal effort corresponding to one of
+ the standard standard speech spectrum levels ("normal", "raised",
+ "loud", "shout"). Defaults to \code{speech="normal"} correspoding to
+ the normal level of stated vocal effort. }
+ \item{noise}{A numeric vector providing $N'_i$, the equivalent
+ noise spectrum level (in dB) at each frequency. If missing,
+ defaults to -50 dB for each frequency.}
+ \item{threshold}{A numeric vector providing $T'_i$, the equivalent
+ hearing threshold level (in dB) at each frequency. If missing,
+ defaults to 0 dB for each frequency.}
+ \item{loss}{A numeric vector providing $J'_i$, the conductive hearing
+ loss level (in dB) at each frequency. If missing,
+ defaults to 0 dB for each frequency.}
+ \item{freq}{Vector of frequencies for which \code{speech},
+ \code{noise}, \code{threshold}, and/or \code{loss} are specified.
+ If \code{method="interpolate"}, \code{freq} must be specified.
+ Otherwise, it must either match the required value for SII
+ calculation method given by argument \code{method}, or be missing,
+ in which case it will default to the values required for the
+ specified method.}
+ \item{method}{A character string specifying the SII calculation
+ method ("critical", "one-third octave", "equal-contributing",
+ "octave"), or \code{"interpolate"} in which case the critical-band
+ method will be applied, with interpolation from the provided
+ frequencies to the required 21 frequency values.}
+ \item{importance}{Either a numeric vector providing $F_i$, the
+ transfer function (importance weights) at each frequency, or a character
+ string indicating which transfer function to employ ("SII", "NNS",
+ "CID22", "NU6", "DRT", "ShortPassage", "SPIN", "CST"). Defaults to
+ the standard SII transfer function, \code{importance="SII"}.}
+ \item{object,x}{SII object}
+ \item{digits}{Number of digits to display}
+ \item{...}{Optional arguments to \code{print}, \code{summary}, and
+ \code{plot} methods}
}
\details{
- ~~ If necessary, more details than the description above ~~
+ American National Standard ANSI S3.5-1997 ("Methods for Calculation of
+ the Speech Intelligibility Index") defines a method for computing a
+ physical measure that is highly correlated with the intelligibility
+ of speech as evaluated by speech perception tests given a group of
+ talkers and listeners. This measure is called the Speech
+ Intelligibility Index, or SII. The SII is calculated from acoustical
+ measurements of speech and noise.
+
+ The \code{sii} function implements ANSI S3.5-1997 as described in
+ the standard, without any attempt to optimize the performance. The
+ implementation does, however, include the extension for handling
+ conductive hearing loss from Annex A (utilizing the optional
+ \code{loss} argument, and for utilizing alternative band weights
+ (i.e. transfer function) appropriate for differing message contents
+ (e.g. types of speech) as described in Annex B or user-specified
+ band weights (utilizing the optional argument \code{importance}).
+
+ Further, this implementation provides a mechanism for
+ interpolating/extrapolating available measurements to those required
+ for calculating the critical band procedure (via the argument
+ \code{method="interpolate"}). Interpolation is accomplished using
+ linear interpolation (on log-scaled data) to the frequencies
+ required for the critical-band SII procedure. Interpolation is
+ performed (if necessary) for \code{noise}, \code{threshold}, and
+ \code{loss}.
+
}
\value{
- ~Describe the value returned
- If it is a LIST, use
- \item{comp1 }{Description of 'comp1'}
- \item{comp2 }{Description of 'comp2'}
- ...
+ The return value is an object of class SII, containing the following
+ components:
+ \item{call}{Function call used to generate the SII object}
+ \item{orig}{List containing original (pre-extrapolation) values for
+ \code{freq}, \code{speech}, \code{noise}, \code{threshold}, and
+ \code{loss}.}
+ \item{speech, noise, threshold, loss, and freq}{Values used in
+ calculations (extrapolated if necessary)}
+ \item{table}{SII calculation worksheet, containing columns
+ corresponding to both Table C.1 and C.2 in Annex C of the
+ standard. Table columns are
+ \describe{
+ \item{Fi}{Center frequency of SII band, Hz}
+ \item{E'i}{Spectrum level of equivalent speech, dB}
+ \item{N'i}{Spectrum level of equivalent noise, dB}
+ \item{T'i}{Equivalent hearing threshold level, dB}
+ \item{Vi}{Spectrum level for self-speech masking, dB}
+ \item{Bi}{Larger of the specrum levels for equivalent noise and
+ self-speech masking, dB}
+ \item{Ci}{Slope per octave (doubling of frequency) of the upward
+ spread of masking, dB/octave}
+ \item{Zi}{Spectrum level for equivalent masking, dB}
+ \item{Xi}{Spectrum level of internal noise, dB}
+ \item{X'i}{Spectrum level of equivalent internal noise, dB}
+ \item{Di}{Spectrum level for equivalent disturbance, dB}
+ \item{Ui}{Spectrum level of standard speech for normal vocal
+ effort, dB}
+ \item{Ji}{Equivalent hearing threshold due to conductive hearing
+ loss, dB}
+ \item{Li}{Speech level distortion factor, dB}
+ \item{Ki}{Temporary variable used in the calculation of the band
+ auditability function}
+ \item{Ai}{Band auditability function}
+ \item{Ii}{Band importance function}
+ \item{IiAi}{Product of the band importance function (Ii), and band
+ auditability function(Ai)}
+ }
+ }
+ \item{sii}{Calculated SII value}
}
-\references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~
+\references{
+ANSI S3.5-1997, "American National Standard Methods for
+Calculation of the Speech Intelligibility Index" American National
+Standards Institute, New York.
- ~Make other sections like Warning with \section{Warning }{....} ~
+Other software programs for calculating SII are available from
+\url{http://www.sii.to/html/programs.html}.
+
}
-\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
+\author{Gregory R. Warnes \email{gr...@ra...}}
+\seealso{ SII Constants: \code{\link{critical}}, and
+ \code{\link{sic.critical}} }
\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
-## The function is currently defined as
-function (x, freq, noise, method = c("interpolate", "critical",
- "one-third octave", "equal-contributing", "octave"), voice = c("raised",
- "normal", "loud", "shout"))
-{
- if (!(is.matrix(x) || is.data.frame(x)))
- x <- matrix(x, nrow = 1)
- method = match.arg(method)
- voice = match.arg(voice)
- if (method == "interpolate")
- data.name = "critical"
- else data.name = method
- table <- read.csv("SII_Table1.csv", skip = 3, header = TRUE,
- nrows = 21, check.names = FALSE)
- if (method == "interpolate") {
- if (missing(freq) || length(freq) != ncol(x))
- stop("`freq' must contain the frequencies corresponding to the measurements in `x'.")
- }
- else {
- if (missing(freq))
- freq <- table[, "fi"]
- else if (freq != table[, "fi"])
- stop("`freq' does not match frequencies specified in table ",
- data.name, ".")
- }
- if (missing(noise))
- noise <- rep(0, length(freq))
- nas <- is.na(x)
- if (any(nas)) {
- if (method == "interpolate") {
- x <- x[!nas]
- freq <- freq[!nas]
- noise <- noise[!nas]
- }
- else stop("NA's only permitted for method 'interpolate'")
- }
- ord <- order(freq)
- x <- x[ord]
- freq <- freq[ord]
- noise <- noise[ord]
- retval <- list()
- retval$call <- match.call()
- retval$x.orig <- x
- retval$freq.orig <- freq
- retval$noise.orig <- noise
- if (method == "interpolate") {
- approx.l <- function(x, y, xout, ...) {
- retval <- approx(log(x), y, log(xout), ...)
- retval$x <- xout
- retval
- }
- sii.freqs <- table[, "fi"]
- THDI <- approx.l(x = freq, y = x, method = "linear",
- xout = sii.freqs, rule = 2)$y
- noise <- approx.l(x = freq, y = noise, method = "linear",
- xout = sii.freqs, rule = 2)$y
- freq <- sii.freqs
- x <- THDI
- }
- col.names <- c("Fi", "E'i", "N'i", "T'i", "Vi", "Bi", "Ci",
- "Z'i", "Xi", "X'i", "Di", "Ui", "Li", "Ki", "Ai", "Ii",
- "IiAi")
- sii.tab <- matrix(nrow = length(freq), ncol = length(col.names))
- colnames(sii.tab) <- col.names
- rownames(sii.tab) <- 1:nrow(sii.tab)
- sii.tab[, "Fi"] <- freq
- sii.tab[, "E'i"] <- table[, voice]
- sii.tab[, "N'i"] <- noise
- sii.tab[, "T'i"] <- x
- if (method == "octave")
- sii.tab[, "Zi"] <- sii.tab[, "N'i"]
- else {
- sii.tab[, "Vi"] <- sii.tab[, "E'i"] - 24
- sii.tab[, "Bi"] <- pmax(sii.tab[, "N'i"], sii.tab[, "Vi"])
- if (method == "critical" || method == "interpolate" ||
- method == "equal-contributing") {
- sii.tab[, "Ci"] = -80 + 0.6 * (sii.tab[, "Bi"] +
- 10 * log10(table[, "fi.high"] - table[, "fi.low"]))
- Zifun <- function(i) {
- if (i > 1)
- inner <- sum(10^(0.1 * sii.tab[1:(i - 1), "Bi"] +
- 3.32 * sii.tab[1:(i - 1), "Ci"] * log10(table[i,
- "Fi"]/table[1:(i - 1), "Fi.high"])))
- else inner <- 0
- 10 * log10(10^(0.1 * sii.tab[i, "N'i"]) + inner)
- }
- sii.tab[, "Z'i"] = sapply(1:nrow(sii.tab), Zifun)
- }
- else {
- sii.tab[, "Ci"] = -80 + 0.6 * (sii.tab[, "Bi"] +
- 10 * log10(sii.tab[, "Fi"]) - 6.353)
- Zifun <- function(i) {
- if (i > 1)
- inner <- sum(10^(0.1 * sii.tab[1:(i - 1), "Bi"] +
- 3.32 * sii.tab[1:(i - 1), "Ci"] * log10(0.89 *
- table[i, "Fi"]/table[1:(i - 1), "Fi.high"])))
- else inner <- 0
- 10 * log10(10^(0.1 * sii.tab[i, "N'i"]) + inner)
- }
- sii.tab[, "Z'i"] = sapply(1:nrow(sii.tab), Zifun)
- }
- sii.tab[1, "Z'i"] <- sii.tab[1, "Bi"]
- }
- sii.tab[, "Xi"] <- table[, "Xi"]
- sii.tab[, "X'i"] <- sii.tab[, "T'i"] + sii.tab[, "Xi"]
- sii.tab[, "Di"] <- max(sii.tab[, "Z'i"], sii.tab[, "X'i"])
- sii.tab[, "Ui"] <- table[, "normal"]
- enforce.range <- function(x) {
- x[x < 0] <- 0
- x[x > 1] <- 1
- x
- }
- sii.tab[, "Li"] <- enforce.range(1 - (sii.tab[, "E'i"] -
- sii.tab[, "Ui"] - 10)/160)
- sii.tab[, "Ki"] <- enforce.range((sii.tab[, "E'i"] - sii.tab[,
- "Di"] + 15)/30)
- sii.tab[, "Ai"] <- sii.tab[, "Li"] * sii.tab[, "Ki"]
- sii.tab[, "Ii"] <- table[, "Ii"]
- sii.tab[, "IiAi"] <- table[, "Ii"] * sii.tab[, "Ai"]
- sii.val <- sum(sii.tab[, "IiAi"])
- retval$THDN <- x
- retval$freq <- freq
- retval$sii <- sii.val
- retval$table <- sii.tab
- class(retval) <- "SII"
- retval
- }
+## Example C.1 from ANSI S3.5-1997 Annex C
+sii.C1 <- sii(
+ speech = c(50.0, 40.0, 40.0, 30.0, 20.0, 0.0),
+ noise = c(70.0, 65.0, 45.0, 25.0, 1.0,-15.0),
+ threshold= c( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0),
+ method="octave"
+ )
+sii.C1 # rounded to 2 digits by default
+print(sii.C1$sii, digits=20) # full precision
+summary(sii.C1) # full details
+plot(sii.C1) # plot
+## The value given in the Standard is $0.504$.
+
+
+
+## Same calculation, but manually specify the frequencies
+## and importance function, and use default for threshold
+
+sii.C1 <- sii(
+ speech = c(50.0, 40.0, 40.0, 30.0, 20.0, 0.0),
+ noise = c(70.0, 65.0, 45.0, 25.0, 1.0,-15.0),
+ method="octave",
+ freq=c(250, 500, 1000, 2000, 4000, 8000),
+ importance=c(0.0617, 0.1671, 0.2373, 0.2648, 0.2142, 0.0549)
+ )
+sii.C1
+
+## Now perform the calculation using frequency weights for the Connected
+## Speech Test (CST)
+sii.CST <- sii(
+ speech = c(50.0, 40.0, 40.0, 30.0, 20.0, 0.0),
+ noise = c(70.0, 65.0, 45.0, 25.0, 1.0,-15.0),
+ method="octave",
+ importance="CST"
+ )
+round(sii.CST$table[,-c(5:7,13)],2)
+sii.CST$sii
+
+## Example C.2 from ANSI S3.5-1997 Annex C
+
+sii.C2 <- sii(
+ speech = rep(54.0, 18),
+ noise = c(40.0, 30.0, 20.0, rep(0, 18-3) ),
+ threshold= rep(0.0, 18),
+ method="one-third"
+ )
+sii.C2$table[1:3,1:8]
+sii.C2
+
+## Interpolation example, for 8 frequencies using NU6 importance
+## weight, default values for noise.
+sii.left <- sii(
+ speech="raised",
+ threshold=c(25,25,30,35,45,45,55,60),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="NU6"
+ )
+sii.left
+
+
}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
+
+\keyword{math}
+
Deleted: trunk/SII/man/sii.excel.Rd
===================================================================
--- trunk/SII/man/sii.excel.Rd 2008-06-12 00:29:28 UTC (rev 1288)
+++ trunk/SII/man/sii.excel.Rd 2008-06-12 05:56:39 UTC (rev 1289)
@@ -1,80 +0,0 @@
-\name{sii.excel}
-\alias{sii.excel}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ ~~function to do ... ~~ }
-\description{
- ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-sii.excel(THDI = c(25, 25, 30, 35, 45, 45, 55, 60), freq = c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000), matlab.spline = TRUE)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{THDI}{ ~~Describe \code{THDI} here~~ }
- \item{freq}{ ~~Describe \code{freq} here~~ }
- \item{matlab.spline}{ ~~Describe \code{matlab.spline} here~~ }
-}
-\details{
- ~~ If necessary, more details than the description above ~~
-}
-\value{
- ~Describe the value returned
- If it is a LIST, use
- \item{comp1 }{Description of 'comp1'}
- \item{comp2 }{Description of 'comp2'}
- ...
-}
-\references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~
-
- ~Make other sections like Warning with \section{Warning }{....} ~
-}
-\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
-
-## The function is currently defined as
-function (THDI = c(25, 25, 30, 35, 45, 45, 55, 60), freq = c(250,
- 500, 1000, 2000, 3000, 4000, 6000, 8000), matlab.spline = TRUE)
-{
- if (length(THDI) != length(freq))
- stop("THDI must have the same length as freq")
- sii.freqs <- sii.constants[, 1]
- if (matlab.spline) {
- ispl <- interpSpline(THDI ~ freq)
- THDI <- predict(ispl, sii.freqs)$y
- }
- else {
- approx.l <- function(x, y, xout, ...) {
- retval <- approx(log(x), y, log(xout), ...)
- retval$x <- xout
- retval
- }
- THDI <- approx.l(x = freq, y = THDI, method = "linear",
- xout = sii.freqs, rule = 2)$y
- }
- sii.tab <- sii.constants
- sii.tab[, c("Ti'.THDN", "Xi'.Int.Noise", "Di.Equiv.Dist",
- "ki.Temp.Var", "Ai.BandAud", "Si.SII.band.")] <- NA
- sii.tab[, "Ti'.THDN"] <- THDI
- sii.tab[, "Xi'.Int.Noise"] <- sii.tab[, "Ti'.THDN"] + sii.tab[,
- "Xi.Ref.Int.Nz"]
- sii.tab[, "Di.Equiv.Dist"] <- sii.tab[, "Xi'.Int.Noise"]
- sii.tab[, "ki.Temp.Var"] <- ifelse((sii.tab[, "Ei.Raised"] -
- sii.tab[, "Di.Equiv.Dist"] + 15)/30 > 1, 1, 0)
- sii.tab[, "Ai.BandAud"] <- sii.tab[, "ki.Temp.Var"]
- sii.tab[, "Si.SII.band."] <- sii.tab[, "I.BandImp"] * sii.tab[,
- "Ai.BandAud"]
- sii.val <- sum(sii.tab[, "Si.SII.band."])
- ret <- list(THDN = THDI, freq = freq, sii = sii.val, table = sii.tab)
- class(ret) <- "SII"
- ret
- }
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-06-12 00:29:32
|
Revision: 1288
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1288&view=rev
Author: warnes
Date: 2008-06-11 17:29:28 -0700 (Wed, 11 Jun 2008)
Log Message:
-----------
Update source code, improve documentation
Modified Paths:
--------------
trunk/SII/R/print.SII.R
trunk/SII/R/reload.constants.R
trunk/SII/R/sii.R
trunk/SII/R/sii.excel.R
Added Paths:
-----------
trunk/SII/R/summary.SII.R
Modified: trunk/SII/R/print.SII.R
===================================================================
--- trunk/SII/R/print.SII.R 2008-06-12 00:28:49 UTC (rev 1287)
+++ trunk/SII/R/print.SII.R 2008-06-12 00:29:28 UTC (rev 1288)
@@ -1,5 +1,7 @@
`print.SII` <-
function (x, digits = 2, ...)
{
- print(unclass(round(x$sii, digits)))
+ cat("\n")
+ cat("SII:", round(x$sii, digits), "\n")
+ cat("\n")
}
Modified: trunk/SII/R/reload.constants.R
===================================================================
--- trunk/SII/R/reload.constants.R 2008-06-12 00:28:49 UTC (rev 1287)
+++ trunk/SII/R/reload.constants.R 2008-06-12 00:29:28 UTC (rev 1288)
@@ -1,6 +1,10 @@
reload.constants <- function(xls.path,rda.path=xls.path)
{
+
+ if(!require("gdata"))
+ stop("'gdata' package must be installed to run this function.")
+
"critical" <- read.xls(
xls=file.path(xls.path,"SII_Constants.xls"),
sheet=1,
@@ -72,8 +76,8 @@
"sic.octave" <- read.xls(
xls=file.path(xls.path,"SII_Constants.xls"),
- sheet=4,
- skip=5,
+ sheet=7,
+ skip=3,
header=TRUE,
nrows=6,
check.names=FALSE,
Modified: trunk/SII/R/sii.R
===================================================================
--- trunk/SII/R/sii.R 2008-06-12 00:28:49 UTC (rev 1287)
+++ trunk/SII/R/sii.R 2008-06-12 00:29:28 UTC (rev 1288)
@@ -7,8 +7,8 @@
method=c(
"interpolate",
"critical",
+ "equal-contributing",
"one-third octave",
- "equal-contributing",
"octave"
),
importance=c(
@@ -59,16 +59,23 @@
table <- get(data.name)
## Get the correct importance functions
- importance=match.arg(importance)
- if(importance!="SII")
+ if(missing(importance) || is.character(importance) )
{
- sic.name <- paste("sic.",data.name, sep="")
- data(list=sic.name, package="SII")
- sic.table <- get(sic.name)
- table[,"Ii"] <- sic.table[[importance]]
+ importance=match.arg(importance)
+ if(importance!="SII")
+ {
+ sic.name <- paste("sic.",data.name, sep="")
+ data(list=sic.name, package="SII")
+ sic.table <- get(sic.name)
+ table[,"Ii"] <- sic.table[[importance]]
+ }
}
+ else
+ if(length(importance) != nrow(table))
+ stop("`importance' vector have length ", nrow(table), "for method `",method,"'.")
+ else
+ table[,"Ii"] <- importance
-
## Handle missing freq
if(missing(freq))
@@ -355,8 +362,9 @@
retval$threshold <- threshold
retval$loss <- loss
retval$freq <- freq
+ retval$method <- method
+ retval$table <- sii.tab
retval$sii <- sii.val
- retval$table <- sii.tab
class(retval) <- "SII"
Modified: trunk/SII/R/sii.excel.R
===================================================================
--- trunk/SII/R/sii.excel.R 2008-06-12 00:28:49 UTC (rev 1287)
+++ trunk/SII/R/sii.excel.R 2008-06-12 00:29:28 UTC (rev 1288)
@@ -4,6 +4,9 @@
matlab.spline=TRUE
)
{
+ if(!require("splines"))
+ stop("'splines' package must be installed to run this function.")
+
if(length(THDI) != length(freq))
stop("THDI must have the same length as freq")
Added: trunk/SII/R/summary.SII.R
===================================================================
--- trunk/SII/R/summary.SII.R (rev 0)
+++ trunk/SII/R/summary.SII.R 2008-06-12 00:29:28 UTC (rev 1288)
@@ -0,0 +1,30 @@
+`summary.SII` <-
+function (x, digits = 2, ...)
+{
+ cat("\n")
+ cat("Speech Intellibility Index\n")
+ cat("--------------------------\n")
+ cat("\n")
+ cat("Call:\n")
+ cat("\n")
+ print(x$call)
+ cat("\n")
+ methodStr <- switch(x$method,
+ "interpolate"="Interpolation + Critical Band",
+ "critical"="Critical band SII procedure",
+ "equal-contributing"="Equally-contrlbutlng (17 band) critical-band SII procedure ",
+ "one-third octave"="One-third octave band SII procedure",
+ "octave"="Octave band SII procedure"
+ )
+
+ cat("Method:", methodStr, "\n" )
+ cat("\n")
+ cat("Calculation table:\n")
+ cat("\n")
+ print(round(x$table, digits=digits))
+ cat("\n")
+ cat("SII:", round(x$sii, digits), "\n")
+ cat("\n")
+ invisible(x)
+}
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-06-12 00:28:50
|
Revision: 1287
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1287&view=rev
Author: warnes
Date: 2008-06-11 17:28:49 -0700 (Wed, 11 Jun 2008)
Log Message:
-----------
Add namespace file to hide private functions
Added Paths:
-----------
trunk/SII/NAMESPACE
Added: trunk/SII/NAMESPACE
===================================================================
--- trunk/SII/NAMESPACE (rev 0)
+++ trunk/SII/NAMESPACE 2008-06-12 00:28:49 UTC (rev 1287)
@@ -0,0 +1,7 @@
+export(
+ sii
+ )
+
+s3method(plot, SII)
+s3method(print, SII)
+s3method(summary, SII)
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|
|
From: <wa...@us...> - 2008-05-29 23:19:04
|
Revision: 1285
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1285&view=rev
Author: warnes
Date: 2008-05-29 16:19:00 -0700 (Thu, 29 May 2008)
Log Message:
-----------
Add newVersionAvailable() function to compare running and latest available R versions
Added Paths:
-----------
trunk/gtools/R/newVersionAvailable.R
Added: trunk/gtools/R/newVersionAvailable.R
===================================================================
--- trunk/gtools/R/newVersionAvailable.R (rev 0)
+++ trunk/gtools/R/newVersionAvailable.R 2008-05-29 23:19:00 UTC (rev 1285)
@@ -0,0 +1,28 @@
+newVersionAvailable <- function(quiet=FALSE)
+ {
+ page <- scan(file="http://cran.r-project.org/src/base/R-2", what="", quiet=TRUE)
+ matches <- grep("R-[0-9]\\.[0-9]+\\.[0-9]+", page, value=TRUE)
+ versionList <- gsub("^.*R-([0-9].[0-9]+.[0-9]+).*$","\\1",matches)
+ versionList <- numeric_version(versionList)
+ if( max(versionList) > getRversion() )
+ {
+ if(!quiet)
+ {
+ cat("A newer version of R is now available: ")
+ cat(max(versionList))
+ cat("\n")
+ }
+ invisible( max(versionList) )
+ }
+ else
+ {
+ if(!quiet)
+ {
+ cat("The latest version of R is installed: ")
+ cat(as.character(getRversion()))
+ cat("\n")
+ }
+ invisible( NULL );
+ }
+
+ }
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|
|
From: <wa...@us...> - 2008-05-26 19:15:47
|
Revision: 1284
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1284&view=rev
Author: warnes
Date: 2008-05-26 12:15:46 -0700 (Mon, 26 May 2008)
Log Message:
-----------
Update license specification
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2008-05-26 15:04:27 UTC (rev 1283)
+++ trunk/gtools/DESCRIPTION 2008-05-26 19:15:46 UTC (rev 1284)
@@ -6,4 +6,4 @@
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Maintainer: Gregory R. Warnes <wa...@bs...>
-License: LGPL 2.1
+License: LGPL-2.1
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|
|
From: <wa...@us...> - 2008-05-26 15:04:33
|
Revision: 1283
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1283&view=rev
Author: warnes
Date: 2008-05-26 08:04:27 -0700 (Mon, 26 May 2008)
Log Message:
-----------
Remove 'assert' man page
Removed Paths:
-------------
trunk/gtools/man/assert-deprecated.Rd
Deleted: trunk/gtools/man/assert-deprecated.Rd
===================================================================
--- trunk/gtools/man/assert-deprecated.Rd 2008-05-22 16:40:12 UTC (rev 1282)
+++ trunk/gtools/man/assert-deprecated.Rd 2008-05-26 15:04:27 UTC (rev 1283)
@@ -1,49 +0,0 @@
-\name{assert-deprecated}
-\alias{assert-deprecated}
-\alias{assert}
-\title{DEPRECATED: Generate an error if an expression is not true.}
-\description{
- Generate an error if an expression is not true.
-}
-\note{
- This function is deprecated in favor of \code{\link[base]{stopifnot}}
-}
-\usage{
-assert(FLAG)
-}
-\arguments{
- \item{FLAG}{ Expression that should evaluate to a boolean vector}
-}
-\details{
- Assert generate an error if its aregument does not evaluate to
- boolean (vector) containing only \code{TRUE} values. This is useful
- for defensinve programming as it provides a mechanism for checking
- that certain facts, the 'assertions', do in fact hold. Checking of
- 'assertions' is an important tool in the development of robust program
- code.
-}
-\value{
- None. Evaluated only for its side effect.
-}
-\author{Gregory R. Warnes \email{wa...@bs...} }
-\seealso{
- \code{\link[base]{stopifnot}}, \code{\link[base]{stop}},
- \code{\link[base]{warning}}
-}
-\examples{
-
-## Trivial example
-posSqrt <- function(x)
- {
- assert(x>=0)
- sqrt(x)
- }
-
-posSqrt(1:10) # works fine, no messages
-\dontrun{
-posSqrt(-5:5) # generates an error, since the asssertion is not met
-}
-
-
-}
-\keyword{programming}
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|
|
From: <wa...@us...> - 2008-05-22 16:40:14
|
Revision: 1282
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1282&view=rev
Author: warnes
Date: 2008-05-22 09:40:12 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Finish rename of assert.R to assert-depricated.Rd
Removed Paths:
-------------
trunk/gtools/man/assert.R
Deleted: trunk/gtools/man/assert.R
===================================================================
--- trunk/gtools/man/assert.R 2008-05-22 16:35:17 UTC (rev 1281)
+++ trunk/gtools/man/assert.R 2008-05-22 16:40:12 UTC (rev 1282)
@@ -1,49 +0,0 @@
-\name{assert-deprecated}
-\alias{assert-deprecated}
-\alias{assert}
-\title{DEPRECATED: Generate an error if an expression is not true.}
-\description{
- Generate an error if an expression is not true.
-}
-\note{
- This function is deprecated in favor of \code{\link[base]{stopifnot}}
-}
-\usage{
-assert(FLAG)
-}
-\arguments{
- \item{FLAG}{ Expression that should evaluate to a boolean vector}
-}
-\details{
- Assert generate an error if its aregument does not evaluate to
- boolean (vector) containing only \code{TRUE} values. This is useful
- for defensinve programming as it provides a mechanism for checking
- that certain facts, the 'assertions', do in fact hold. Checking of
- 'assertions' is an important tool in the development of robust program
- code.
-}
-\value{
- None. Evaluated only for its side effect.
-}
-\author{Gregory R. Warnes \email{wa...@bs...} }
-\seealso{
- \code{\link[base]{stopifnot}}, \code{\link[base]{stop}},
- \code{\link[base]{warning}}
-}
-\examples{
-
-## Trivial example
-posSqrt <- function(x)
- {
- assert(x>=0)
- sqrt(x)
- }
-
-posSqrt(1:10) # works fine, no messages
-\dontrun{
-posSqrt(-5:5) # generates an error, since the asssertion is not met
-}
-
-
-}
-\keyword{programming}
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|
|
From: <wa...@us...> - 2008-05-22 16:35:20
|
Revision: 1281
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1281&view=rev
Author: warnes
Date: 2008-05-22 09:35:17 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Add checkRVersion.R file
Added Paths:
-----------
trunk/gtools/R/checkRVersion.R
Added: trunk/gtools/R/checkRVersion.R
===================================================================
--- trunk/gtools/R/checkRVersion.R (rev 0)
+++ trunk/gtools/R/checkRVersion.R 2008-05-22 16:35:17 UTC (rev 1281)
@@ -0,0 +1,28 @@
+checkRVersion <- function(quiet=FALSE)
+ {
+ page <- scan(file="http://cran.r-project.org/src/base/R-2", what="", quiet=TRUE)
+ matches <- grep("R-[0-9]\\.[0-9]+\\.[0-9]+", page, value=TRUE)
+ versionList <- gsub("^.*R-([0-9].[0-9]+.[0-9]+).*$","\\1",matches)
+ versionList <- numeric_version(versionList)
+ if( max(versionList) > getRversion() )
+ {
+ if(!quiet)
+ {
+ cat("A newer version of R is now available: ")
+ cat(max(versionList))
+ cat("\n")
+ }
+ invisible( max(versionList) )
+ }
+ else
+ {
+ if(!quiet)
+ {
+ cat("The latest version of R is installed: ")
+ cat(as.character(getRversion()))
+ cat("\n")
+ }
+ invisible( NULL );
+ }
+
+ }
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|
|
From: <wa...@us...> - 2008-05-22 16:34:36
|
Revision: 1280
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1280&view=rev
Author: warnes
Date: 2008-05-22 09:34:35 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Rename again to get correct extension!
Added Paths:
-----------
trunk/gtools/man/assert-deprecated.Rd
Copied: trunk/gtools/man/assert-deprecated.Rd (from rev 1277, trunk/gtools/man/assert.R)
===================================================================
--- trunk/gtools/man/assert-deprecated.Rd (rev 0)
+++ trunk/gtools/man/assert-deprecated.Rd 2008-05-22 16:34:35 UTC (rev 1280)
@@ -0,0 +1,49 @@
+\name{assert-deprecated}
+\alias{assert-deprecated}
+\alias{assert}
+\title{DEPRECATED: Generate an error if an expression is not true.}
+\description{
+ Generate an error if an expression is not true.
+}
+\note{
+ This function is deprecated in favor of \code{\link[base]{stopifnot}}
+}
+\usage{
+assert(FLAG)
+}
+\arguments{
+ \item{FLAG}{ Expression that should evaluate to a boolean vector}
+}
+\details{
+ Assert generate an error if its aregument does not evaluate to
+ boolean (vector) containing only \code{TRUE} values. This is useful
+ for defensinve programming as it provides a mechanism for checking
+ that certain facts, the 'assertions', do in fact hold. Checking of
+ 'assertions' is an important tool in the development of robust program
+ code.
+}
+\value{
+ None. Evaluated only for its side effect.
+}
+\author{Gregory R. Warnes \email{wa...@bs...} }
+\seealso{
+ \code{\link[base]{stopifnot}}, \code{\link[base]{stop}},
+ \code{\link[base]{warning}}
+}
+\examples{
+
+## Trivial example
+posSqrt <- function(x)
+ {
+ assert(x>=0)
+ sqrt(x)
+ }
+
+posSqrt(1:10) # works fine, no messages
+\dontrun{
+posSqrt(-5:5) # generates an error, since the asssertion is not met
+}
+
+
+}
+\keyword{programming}
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|
|
From: <wa...@us...> - 2008-05-22 16:30:08
|
Revision: 1279
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1279&view=rev
Author: warnes
Date: 2008-05-22 09:30:01 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Update NEWS for 2.5.0
Modified Paths:
--------------
trunk/gtools/NEWS
Modified: trunk/gtools/NEWS
===================================================================
--- trunk/gtools/NEWS 2008-05-22 16:17:22 UTC (rev 1278)
+++ trunk/gtools/NEWS 2008-05-22 16:30:01 UTC (rev 1279)
@@ -1,16 +1,32 @@
-gtools SVN VERSION $Id$
------------------------
+gtools 2.5.0
+------------
-- Modify odd() and even() to use modulus operator instead of division.
- (Doesn't seem to change the results, but looks more elegant!)
+New features:
+- Add checkRVersion() function to determin if a newer version of R is
+ available.
+
+- Deprecated assert() in favor of base::stopifnot
+
+Bug fixes:
+
+- Fix bug in binsearch() identified by 2.6.0 R CMD CHECK
+
+Other changes:
+
+- Improve text explanation of how defmacro() and strmacro() differ from
+ function().
+
+- Update definitions of odd() and even() to use modulus operator
+ instead of division.
+
gtools 2.4.0
------------
- Add binsearch() function, previously in the genetics() package.
-gtoosl 2.3.1
+gtools 2.3.1
------------
- Add ask() function to prompt the user and collect a single response.
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|
|
From: <wa...@us...> - 2008-05-22 16:22:58
|
Revision: 1276
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1276&view=rev
Author: warnes
Date: 2008-05-22 09:15:21 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Add checkRVersion to NAMESPACE, and increment version in DESCRIPTION.
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/NAMESPACE
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2008-05-22 16:14:17 UTC (rev 1275)
+++ trunk/gtools/DESCRIPTION 2008-05-22 16:15:21 UTC (rev 1276)
@@ -1,7 +1,8 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 2.4.0
+Version: 2.5.0
+Date: 2008-05-22
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Maintainer: Gregory R. Warnes <wa...@bs...>
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2008-05-22 16:14:17 UTC (rev 1275)
+++ trunk/gtools/NAMESPACE 2008-05-22 16:15:21 UTC (rev 1276)
@@ -6,6 +6,7 @@
assert,
binsearch,
capture,
+ checkRVersion,
combinations,
ddirichlet,
defmacro,
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|
|
From: <wa...@us...> - 2008-05-22 16:17:26
|
Revision: 1278
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1278&view=rev
Author: warnes
Date: 2008-05-22 09:17:22 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Add man page for checkRVersion
Added Paths:
-----------
trunk/gtools/man/checkRVersion.Rd
Added: trunk/gtools/man/checkRVersion.Rd
===================================================================
--- trunk/gtools/man/checkRVersion.Rd (rev 0)
+++ trunk/gtools/man/checkRVersion.Rd 2008-05-22 16:17:22 UTC (rev 1278)
@@ -0,0 +1,44 @@
+\name{checkRVersion}
+\alias{checkRVersion}
+\title{Check if a newer version of R is available}
+\description{
+ Check if a newer version of R is available
+}
+\usage{
+checkRVersion(quiet = FALSE)
+}
+\arguments{
+ \item{quiet}{Logical indicating whether printed output should be supressed.}
+}
+\details{
+ This function accesses the R web site to discover the latest released
+ version of R. It then compares this version to the running version.
+ If the running version is the same as the latest version, it prints
+ the message, "The latest version of R is installed:" followed by the
+ version number, and returns NULL. If the running version is older
+ than the current version, it displays the message, "A newer version of
+ R is now available:" followed by the corresponding version number, and
+ returns the version number.
+
+ If \code{quiet=TRUE}, no printing is performed.
+
+}
+\value{
+ Either the version number of the latest version of R, if the running
+ version is less than the latest version, or NULL.
+}
+\author{Gregory R. Warnes \email{gre...@ro...>}}
+\note{
+ This function utilizes the internet to access the R project web
+ site. If internet access is unavailable, the function will fail.
+}
+\seealso{ \code{\link[base]{R.Version}} }
+\examples{
+
+checkRVersion()
+
+ver <- checkRVersion()
+print(ver)
+
+}
+\keyword{utilities}
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|
|
From: <wa...@us...> - 2008-05-22 16:17:00
|
Revision: 1277
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1277&view=rev
Author: warnes
Date: 2008-05-22 09:16:56 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Rename assert-deprecated.R to assert.R to meet R file name requirements.
Added Paths:
-----------
trunk/gtools/man/assert.R
Removed Paths:
-------------
trunk/gtools/man/assert-deprecated.R
Deleted: trunk/gtools/man/assert-deprecated.R
===================================================================
--- trunk/gtools/man/assert-deprecated.R 2008-05-22 16:15:21 UTC (rev 1276)
+++ trunk/gtools/man/assert-deprecated.R 2008-05-22 16:16:56 UTC (rev 1277)
@@ -1,49 +0,0 @@
-\name{assert-deprecated}
-\alias{assert-deprecated}
-\alias{assert}
-\title{DEPRECATED: Generate an error if an expression is not true.}
-\description{
- Generate an error if an expression is not true.
-}
-\note{
- This function is deprecated in favor of \code{\link[base]{stopifnot}}
-}
-\usage{
-assert(FLAG)
-}
-\arguments{
- \item{FLAG}{ Expression that should evaluate to a boolean vector}
-}
-\details{
- Assert generate an error if its aregument does not evaluate to
- boolean (vector) containing only \code{TRUE} values. This is useful
- for defensinve programming as it provides a mechanism for checking
- that certain facts, the 'assertions', do in fact hold. Checking of
- 'assertions' is an important tool in the development of robust program
- code.
-}
-\value{
- None. Evaluated only for its side effect.
-}
-\author{Gregory R. Warnes \email{wa...@bs...} }
-\seealso{
- \code{\link[base]{stopifnot}}, \code{\link[base]{stop}},
- \code{\link[base]{warning}}
-}
-\examples{
-
-## Trivial example
-posSqrt <- function(x)
- {
- assert(x>=0)
- sqrt(x)
- }
-
-posSqrt(1:10) # works fine, no messages
-\dontrun{
-posSqrt(-5:5) # generates an error, since the asssertion is not met
-}
-
-
-}
-\keyword{programming}
Copied: trunk/gtools/man/assert.R (from rev 1258, trunk/gtools/man/assert-deprecated.R)
===================================================================
--- trunk/gtools/man/assert.R (rev 0)
+++ trunk/gtools/man/assert.R 2008-05-22 16:16:56 UTC (rev 1277)
@@ -0,0 +1,49 @@
+\name{assert-deprecated}
+\alias{assert-deprecated}
+\alias{assert}
+\title{DEPRECATED: Generate an error if an expression is not true.}
+\description{
+ Generate an error if an expression is not true.
+}
+\note{
+ This function is deprecated in favor of \code{\link[base]{stopifnot}}
+}
+\usage{
+assert(FLAG)
+}
+\arguments{
+ \item{FLAG}{ Expression that should evaluate to a boolean vector}
+}
+\details{
+ Assert generate an error if its aregument does not evaluate to
+ boolean (vector) containing only \code{TRUE} values. This is useful
+ for defensinve programming as it provides a mechanism for checking
+ that certain facts, the 'assertions', do in fact hold. Checking of
+ 'assertions' is an important tool in the development of robust program
+ code.
+}
+\value{
+ None. Evaluated only for its side effect.
+}
+\author{Gregory R. Warnes \email{wa...@bs...} }
+\seealso{
+ \code{\link[base]{stopifnot}}, \code{\link[base]{stop}},
+ \code{\link[base]{warning}}
+}
+\examples{
+
+## Trivial example
+posSqrt <- function(x)
+ {
+ assert(x>=0)
+ sqrt(x)
+ }
+
+posSqrt(1:10) # works fine, no messages
+\dontrun{
+posSqrt(-5:5) # generates an error, since the asssertion is not met
+}
+
+
+}
+\keyword{programming}
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|
|
From: <wa...@us...> - 2008-05-22 16:14:19
|
Revision: 1275
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1275&view=rev
Author: warnes
Date: 2008-05-22 09:14:17 -0700 (Thu, 22 May 2008)
Log Message:
-----------
Remove broken SEE LSO reference
Modified Paths:
--------------
trunk/gtools/man/gtools-deprecated.Rd
Modified: trunk/gtools/man/gtools-deprecated.Rd
===================================================================
--- trunk/gtools/man/gtools-deprecated.Rd 2008-05-20 01:13:18 UTC (rev 1274)
+++ trunk/gtools/man/gtools-deprecated.Rd 2008-05-22 16:14:17 UTC (rev 1275)
@@ -19,6 +19,6 @@
\code{assert} is a deprecated synonym for \code{\link[base]{stopifnot}}.
}
\seealso{
- \code{\link{Deprecated}}, \code{\link{gtools-defunct}}
+ \code{\link{Deprecated}} }
}
\keyword{misc}
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|
|
From: <wa...@us...> - 2008-05-20 01:13:23
|
Revision: 1274
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1274&view=rev
Author: warnes
Date: 2008-05-19 18:13:18 -0700 (Mon, 19 May 2008)
Log Message:
-----------
Update man page to match recent changes to plot.lm2()
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/man/plot.lm2.Rd
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2008-05-20 01:08:55 UTC (rev 1273)
+++ trunk/gplots/DESCRIPTION 2008-05-20 01:13:18 UTC (rev 1274)
@@ -1,9 +1,9 @@
Package: gplots
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
-Depends: R (>= 1.9.0), gtools, gdata, stats, caTools
+Depends: R (>= 1.9.0), gtools, gdata, stats, caTools, grid
Recommends: datasets, grid
-Suggests: gtools, grid
+Suggests: gtools
Version: 2.7.0
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by (in alphabetical order):
Modified: trunk/gplots/man/plot.lm2.Rd
===================================================================
--- trunk/gplots/man/plot.lm2.Rd 2008-05-20 01:08:55 UTC (rev 1273)
+++ trunk/gplots/man/plot.lm2.Rd 2008-05-20 01:13:18 UTC (rev 1274)
@@ -7,14 +7,25 @@
Plots to assess the goodness of fit for the linear model objects
}
\usage{
- plot.lm2(x, which = 1:5, caption = c("Residuals vs Fitted",
- "Normal Q-Q plot", "Scale-Location plot",
- "Cook's distance plot"), panel = panel.smooth,
- sub.caption = deparse(x$call), main = "",
- ask = interactive() && nb.fig < length(which)
- && .Device != "postscript", ..., id.n = 3,
- labels.id = names(residuals(x)),
- cex.id = 0.75, band = TRUE, rug = TRUE)
+ plot.lm2(
+ x,
+ which = 1:5,
+ caption = c("Residuals vs Fitted", "Normal Q-Q plot",
+ "Scale-Location plot", "Cook's distance plot"),
+ panel = panel.smooth,
+ sub.caption = deparse(x$call),
+ main = "",
+ ask = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ id.n = 3,
+ labels.id = names(residuals(x)),
+ cex.id = 0.75,
+ band=TRUE,
+ rug=TRUE,
+ width=1/10,
+ max.n=5000
+ )
}
\arguments{
\item{x}{lm object}
@@ -39,16 +50,22 @@
\item{band}{logical vector indicating whether bandplot should also be plotted }
\item{rug}{logical vector indicating whether rug should be added to
the existing plot }
+ \item{width}{Fraction of the data to use for plot smooths}
+ \item{max.n}{Maximum number of points to display in plots}
}
\author{Gregory R. Warnes \email{wa...@bs...} and Nitin
Jain \email{nit...@pf...}}
\examples{
- ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
- trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
- group <- gl(2,10,20, labels=c("Ctl","Trt"))
- weight <- c(ctl, trt)
- x <- lm(weight ~ group)
- plot.lm2(x, which=1)
-plot.lm2(x, which=1:3)
+ctl <- rnorm(100, 4)
+trt <- rnorm(100, 4.5)
+group <- gl(2,100,200, labels=c("Ctl","Trt"))
+weight <- c(ctl, trt)
+wt.err <- rnorm(length(weight), mean=weight, sd=1/2)
+x <- lm(weight ~ group + wt.err)
+
+plot.lm2(x)
+
+plot.lm2(x, which=1, width=1/3)
+plot.lm2(x, which=1:3, widht=1/3)
}
\keyword{hplot}
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From: <wa...@us...> - 2008-05-20 01:08:59
|
Revision: 1273
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1273&view=rev
Author: warnes
Date: 2008-05-19 18:08:55 -0700 (Mon, 19 May 2008)
Log Message:
-----------
More work on documentation for venn()
Modified Paths:
--------------
trunk/gplots/man/venn.Rd
Modified: trunk/gplots/man/venn.Rd
===================================================================
--- trunk/gplots/man/venn.Rd 2008-05-20 01:07:28 UTC (rev 1272)
+++ trunk/gplots/man/venn.Rd 2008-05-20 01:08:55 UTC (rev 1273)
@@ -5,15 +5,19 @@
Plot Venn diagrams for up to 5 sets
}
\usage{
-venn(data, small = 0.7, showSetLogicLabel = FALSE, simplify = FALSE)
+venn(data, universe=NA, small=0.7, showSetLogicLabel=FALSE,
+ simplify=FALSE, show.plot=TRUE)
}
\arguments{
\item{data}{data to be plotted (see below)}
+ \item{universe}{??}
\item{small}{Character size of group labels}
\item{showSetLogicLabel}{Logical flag indicating whether the internal
group label should be displayed}
\item{simplify}{Logical flag indicating whether unobserved group
should be omitted.}
+ \item{show.plot}{Logical flag indicating whether the plot should be
+ displayed. If false, simply returns the group count matrix.}
}
\details{
\code{data} should be either a named list of vectors containing
@@ -27,7 +31,7 @@
The fist column contains observed counts, subsequent columns contain
0-1 indicators of group membership.
}
-\author{Steffen Moeller \email{ste...@gm...},
+\author{Steffen Moeller \email{steffen\_mo...@gm...},
with cleanup and packaging by Gregory R. Warnes
\email{gr...@ra...}.}
\examples{
@@ -57,7 +61,7 @@
## Omit un-observed groupings
-tmp <- venn(input, simplify=T)
+tmp <- venn(input, simplify=TRUE)
## show details
tmp
@@ -65,14 +69,7 @@
## Show internal binary group labels
venn(input, showSetLogicLabel=TRUE)
-## Omit un-observed groupings, and show internal binary group labels
-venn(input, simplify=T, showSetLogicLabel=TRUE)
-
-
-
-
+## Specify universe
+venn(input, universe=NULL, showSetLogicLabel=TRUE)
}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
+\keyword{hplot}
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From: <wa...@us...> - 2008-05-20 01:07:33
|
Revision: 1272
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1272&view=rev
Author: warnes
Date: 2008-05-19 18:07:28 -0700 (Mon, 19 May 2008)
Log Message:
-----------
Fix code/doc mismatch due to recent changes to bandplot()
Modified Paths:
--------------
trunk/gplots/R/bandplot.R
trunk/gplots/man/bandplot.Rd
Modified: trunk/gplots/R/bandplot.R
===================================================================
--- trunk/gplots/R/bandplot.R 2008-05-20 00:14:51 UTC (rev 1271)
+++ trunk/gplots/R/bandplot.R 2008-05-20 01:07:28 UTC (rev 1272)
@@ -9,7 +9,6 @@
sd.lwd=c(2,2,3,2,2),
sd.lty=c(2,1,1,1,2),
method="frac", width=1/5,
- use.runsd=TRUE,
n=50
)
{
Modified: trunk/gplots/man/bandplot.Rd
===================================================================
--- trunk/gplots/man/bandplot.Rd 2008-05-20 00:14:51 UTC (rev 1271)
+++ trunk/gplots/man/bandplot.Rd 2008-05-20 01:07:28 UTC (rev 1272)
@@ -28,8 +28,8 @@
}
\usage{
bandplot(x, y, ..., add = FALSE, sd = c(-2:2),
- sd.col = c("lightblue", "blue", "red", "blue", "lightblue"),
- sd.lwd = c(1, 2, 3, 2, 1), sd.lty = c(2, 1, 1, 1, 2),
+ sd.col=c("magenta", "blue", "red", "blue", "magenta"),
+ sd.lwd=c(2, 2, 3, 2, 2), sd.lty=c(2, 1, 1, 1, 2),
method = "frac", width = 1/5, n=50)
}
\arguments{
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