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From: <wa...@us...> - 2014-03-01 20:15:08
|
Revision: 1776
http://sourceforge.net/p/r-gregmisc/code/1776
Author: warnes
Date: 2014-03-01 20:15:05 +0000 (Sat, 01 Mar 2014)
Log Message:
-----------
Fix cut-and-paste error.
Modified Paths:
--------------
trunk/gtools/tests/test_mixedorder.R
Modified: trunk/gtools/tests/test_mixedorder.R
===================================================================
--- trunk/gtools/tests/test_mixedorder.R 2014-03-01 20:12:46 UTC (rev 1775)
+++ trunk/gtools/tests/test_mixedorder.R 2014-03-01 20:15:05 UTC (rev 1776)
@@ -5,7 +5,7 @@
"Asprin 100mg/day", "Acetomycin 100mg/day",
"Acetomycin 1000mg/day")
-stopifnot( mixedorder(tmp)==c(4, 5, 1, 2, 3 ))
+stopifnot( mixedorder(Treatment)==c(5, 6, 2, 3, 4, 1) )
x <- rev(c("AA 0.50 ml", "AA 1.5 ml", "AA 500 ml", "AA 1500 ml",
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|
|
From: <wa...@us...> - 2014-03-01 20:12:49
|
Revision: 1775
http://sourceforge.net/p/r-gregmisc/code/1775
Author: warnes
Date: 2014-03-01 20:12:46 +0000 (Sat, 01 Mar 2014)
Log Message:
-----------
Update files for gtools 3.3.1 release
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/inst/NEWS
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2014-03-01 20:02:08 UTC (rev 1774)
+++ trunk/gtools/DESCRIPTION 2014-03-01 20:12:46 UTC (rev 1775)
@@ -1,8 +1,8 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.3.0
-Date: 2014-02-11
+Version: 3.3.1
+Date: 2014-03-01
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
License: LGPL-2.1
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2014-03-01 20:02:08 UTC (rev 1774)
+++ trunk/gtools/inst/NEWS 2014-03-01 20:12:46 UTC (rev 1775)
@@ -1,3 +1,15 @@
+gtools 3.3.1 - 2014-03-01
+-------------------------
+
+Bug fixes:
+
+- 'mixedorder' (and hence 'mixedsort') not properly handling
+ single-character strings between numbers, so that '1a2' was being
+ handled as a single string rather than being properly handled as
+ c('1', 'a', '2').
+
+
+
gtools 3.3.0 - 2014-02-11
-------------------------
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|
|
From: <wa...@us...> - 2014-03-01 20:02:10
|
Revision: 1774
http://sourceforge.net/p/r-gregmisc/code/1774
Author: warnes
Date: 2014-03-01 20:02:08 +0000 (Sat, 01 Mar 2014)
Log Message:
-----------
Fix bug in gtools::mixedorder regular expression for regognizing numbers. (Periods weren't escaped).
Modified Paths:
--------------
trunk/gtools/R/mixedsort.R
Added Paths:
-----------
trunk/gtools/tests/test_mixedorder.R
Modified: trunk/gtools/R/mixedsort.R
===================================================================
--- trunk/gtools/R/mixedsort.R 2014-02-11 17:44:04 UTC (rev 1773)
+++ trunk/gtools/R/mixedsort.R 2014-03-01 20:02:08 UTC (rev 1774)
@@ -17,7 +17,7 @@
if( is.numeric(x) )
return( order(x) )
-
+
delim="\\$\\@\\$"
numeric <- function(x)
@@ -37,7 +37,7 @@
if(length(which.blanks) >0)
x[ which.blanks ] <- -Inf
-
+
if(length(which.nas) >0)
x[ which.nas ] <- Inf
@@ -47,7 +47,7 @@
####
# find and mark numbers in the form of +1.23e+45.67
- delimited <- gsub("([+-]{0,1}[0-9]+.{0,1}[0-9]*([eE][\\+\\-]{0,1}[0-9]+.{0,1}[0-9]*){0,1})",
+ delimited <- gsub("([+-]{0,1}[0-9]+\\.{0,1}[0-9]*([eE][\\+\\-]{0,1}[0-9]+\\.{0,1}[0-9]*){0,1})",
paste(delim,"\\1",delim,sep=""), x)
# separate out numbers
@@ -90,7 +90,7 @@
t(rank.character) +
apply(matrix(rank.numeric),2,max,na.rm=TRUE)
)
-
+
rank.overall <- ifelse(is.na(rank.character),rank.numeric,rank.character)
order.frame <- as.data.frame(rank.overall)
Added: trunk/gtools/tests/test_mixedorder.R
===================================================================
--- trunk/gtools/tests/test_mixedorder.R (rev 0)
+++ trunk/gtools/tests/test_mixedorder.R 2014-03-01 20:02:08 UTC (rev 1774)
@@ -0,0 +1,27 @@
+library(gtools)
+
+## Examples from man page
+Treatment <- c("Control", "Asprin 10mg/day", "Asprin 50mg/day",
+ "Asprin 100mg/day", "Acetomycin 100mg/day",
+ "Acetomycin 1000mg/day")
+
+stopifnot( mixedorder(tmp)==c(4, 5, 1, 2, 3 ))
+
+
+x <- rev(c("AA 0.50 ml", "AA 1.5 ml", "AA 500 ml", "AA 1500 ml",
+ "EXP 1", "AA 1e3 ml", "A A A", "1 2 3 A", "NA", NA, "1e2",
+ "", "-", "1A", "1 A", "100", "100A", "Inf"))
+
+stopifnot( mixedorder(x)==c(7, 11, 4, 5, 3, 8, 2, 1, 6, 12, 18, 17, 16, 13, 15, 14, 10, 9) )
+
+## Bug reported by Aaron Taudt on 2014-03-01
+
+tmp <- c("uniresult_simulated_H3k27ac_binsize_200_chr1.RData",
+ "uniresult_simulated_H3k27me3_binsize_200_chr1.RData",
+ "uniresult_simulated_H3k36me3_binsize_200_chr1.RData",
+ "uniresult_simulated_H3k4me3_binsize_200_chr1.RData",
+ "uniresult_simulated_H3k9me3_binsize_200_chr1.RData")
+
+stopifnot( mixedorder(tmp)==c(4, 5, 1, 2, 3) )
+
+
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|
|
From: <wa...@us...> - 2014-02-11 17:44:06
|
Revision: 1773
http://sourceforge.net/p/r-gregmisc/code/1773
Author: warnes
Date: 2014-02-11 17:44:04 +0000 (Tue, 11 Feb 2014)
Log Message:
-----------
Create and use locate copy of tools:::.split_op_version.
Modified Paths:
--------------
trunk/gtools/R/clean_up_dependencies2.R
Modified: trunk/gtools/R/clean_up_dependencies2.R
===================================================================
--- trunk/gtools/R/clean_up_dependencies2.R 2014-02-11 17:25:33 UTC (rev 1772)
+++ trunk/gtools/R/clean_up_dependencies2.R 2014-02-11 17:44:04 UTC (rev 1773)
@@ -1,5 +1,21 @@
.clean_up_dependencies2 <- function (x, installed, available)
{
+
+ .split_op_version <- function (x)
+ {
+ pat <- "^([^\\([:space:]]+)[[:space:]]*\\(([^\\)]+)\\).*"
+ x1 <- sub(pat, "\\1", x)
+ x2 <- sub(pat, "\\2", x)
+ if (x2 != x1) {
+ pat <- "[[:space:]]*([[<>=!]+)[[:space:]]+(.*)"
+ version <- sub(pat, "\\2", x2)
+ if (!grepl("^r", version))
+ version <- package_version(version)
+ list(name = x1, op = sub(pat, "\\1", x2), version = version)
+ }
+ else list(name = x1)
+ }
+
.split_dependencies <- function(x) {
.split2 <- function(x) {
x <- sub("[[:space:]]+$", "", x)
@@ -8,7 +24,7 @@
x <- x[names(x) != "R"]
x <- x[nzchar(x)]
x <- x[!duplicated(names(x))]
- lapply(x, tools:::.split_op_version)
+ lapply(x, .split_op_version)
}
if (!any(nzchar(x)))
return(list())
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|
|
From: <wa...@us...> - 2014-02-11 17:25:36
|
Revision: 1772
http://sourceforge.net/p/r-gregmisc/code/1772
Author: warnes
Date: 2014-02-11 17:25:33 +0000 (Tue, 11 Feb 2014)
Log Message:
-----------
Update for gtools 3.3.0.
Modified Paths:
--------------
trunk/gtools/inst/NEWS
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2014-02-11 17:19:16 UTC (rev 1771)
+++ trunk/gtools/inst/NEWS 2014-02-11 17:25:33 UTC (rev 1772)
@@ -1,12 +1,21 @@
-gtools 3.2.2 - 2014-01-14
+gtools 3.3.0 - 2014-02-11
-------------------------
+New features:
+
+- Add the getDependencies() function to return a list of dependencies
+ for the specified package(s). Includes arguments to control whether
+ these dependencies should be constructed using information from
+ locally installed packages ('installed', default is TRUE), avilable
+ CRAN packages ('available', default is TRUE) and whether to include
+ base ('base', default=FALSE) and recommended ('recommended', default
+ is FALSE) packages.
+
Bug fixes:
- binsearch() was returning the wrong endpoint & value when the found
value was at the upper endpoint.
-
gtools 3.2.1 - 2014-01-13
-------------------------
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|
|
From: <wa...@us...> - 2014-02-11 17:19:19
|
Revision: 1771
http://sourceforge.net/p/r-gregmisc/code/1771
Author: warnes
Date: 2014-02-11 17:19:16 +0000 (Tue, 11 Feb 2014)
Log Message:
-----------
Fix arguments
Modified Paths:
--------------
trunk/gtools/man/getDependencies.Rd
Modified: trunk/gtools/man/getDependencies.Rd
===================================================================
--- trunk/gtools/man/getDependencies.Rd 2014-02-11 17:17:42 UTC (rev 1770)
+++ trunk/gtools/man/getDependencies.Rd 2014-02-11 17:19:16 UTC (rev 1771)
@@ -31,7 +31,7 @@
packages that are included in the R installation. Defaults to
FALSE.
}
- \item{base}{Logical indicating whether to include dependencies on
+ \item{recommended}{Logical indicating whether to include dependencies on
recommended packages that are included in the R
installation. Defaults to
FALSE.
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|
|
From: <wa...@us...> - 2014-02-11 17:17:45
|
Revision: 1770
http://sourceforge.net/p/r-gregmisc/code/1770
Author: warnes
Date: 2014-02-11 17:17:42 +0000 (Tue, 11 Feb 2014)
Log Message:
-----------
Update arguments to match code.
Modified Paths:
--------------
trunk/gtools/man/getDependencies.Rd
Modified: trunk/gtools/man/getDependencies.Rd
===================================================================
--- trunk/gtools/man/getDependencies.Rd 2014-02-11 17:14:08 UTC (rev 1769)
+++ trunk/gtools/man/getDependencies.Rd 2014-02-11 17:17:42 UTC (rev 1770)
@@ -8,11 +8,11 @@
}
\usage{
getDependencies(pkgs,
- dependencies=NA,
- installed=TRUE,
- available=TRUE,
- base=FALSE,
- recommended=FALSE)
+ dependencies = c("Depends", "Imports", "LinkingTo"),
+ installed=TRUE,
+ available=TRUE,
+ base=FALSE,
+ recommended=FALSE)
}
\arguments{
\item{pkgs}{character vector of package names}
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|
|
From: <wa...@us...> - 2014-02-11 17:14:12
|
Revision: 1769
http://sourceforge.net/p/r-gregmisc/code/1769
Author: warnes
Date: 2014-02-11 17:14:08 +0000 (Tue, 11 Feb 2014)
Log Message:
-----------
Add getDependencies() function to return a list of package dependencies.
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/NAMESPACE
Added Paths:
-----------
trunk/gtools/R/clean_up_dependencies2.R
trunk/gtools/R/getDependencies.R
trunk/gtools/man/getDependencies.Rd
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2014-01-14 19:43:17 UTC (rev 1768)
+++ trunk/gtools/DESCRIPTION 2014-02-11 17:14:08 UTC (rev 1769)
@@ -1,8 +1,8 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.2.2
-Date: 2014-01-14
+Version: 3.3.0
+Date: 2014-02-11
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
License: LGPL-2.1
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2014-01-14 19:43:17 UTC (rev 1768)
+++ trunk/gtools/NAMESPACE 2014-02-11 17:14:08 UTC (rev 1769)
@@ -13,6 +13,7 @@
even,
foldchange,
foldchange2logratio,
+ getDependencies,
inv.logit,
invalid,
keywords,
Added: trunk/gtools/R/clean_up_dependencies2.R
===================================================================
--- trunk/gtools/R/clean_up_dependencies2.R (rev 0)
+++ trunk/gtools/R/clean_up_dependencies2.R 2014-02-11 17:14:08 UTC (rev 1769)
@@ -0,0 +1,68 @@
+.clean_up_dependencies2 <- function (x, installed, available)
+{
+ .split_dependencies <- function(x) {
+ .split2 <- function(x) {
+ x <- sub("[[:space:]]+$", "", x)
+ x <- unique(sub("^[[:space:]]*(.*)", "\\1", x))
+ names(x) <- sub("^([[:alnum:].]+).*$", "\\1", x)
+ x <- x[names(x) != "R"]
+ x <- x[nzchar(x)]
+ x <- x[!duplicated(names(x))]
+ lapply(x, tools:::.split_op_version)
+ }
+ if (!any(nzchar(x)))
+ return(list())
+ unlist(lapply(strsplit(x, ","), .split2), FALSE, FALSE)
+ }
+ x <- x[!is.na(x)]
+ if (!length(x))
+ return(list(character(), character()))
+ xx <- .split_dependencies(x)
+ if (!length(xx))
+ return(list(character(), character()))
+ pkgs <- installed[, "Package"]
+ have <- sapply(xx, function(x) {
+ if (length(x) == 3L) {
+ if (!x[[1L]] %in% pkgs)
+ return(FALSE)
+ if (x[[2L]] != ">=")
+ return(TRUE)
+ current <- as.package_version(installed[pkgs == x[[1L]],
+ "Version"])
+ target <- as.package_version(x[[3L]])
+ eval(parse(text = paste("any(current", x$op, "target)")))
+ }
+ else x[[1L]] %in% pkgs
+ })
+ xx <- xx[!have]
+ if (!length(xx))
+ return(list(character(), character()))
+ pkgs <- row.names(available)
+ canget <- miss <- character()
+ for (i in seq_along(xx)) {
+ x <- xx[[i]]
+ if (length(x) == 3L) {
+ if (!x[[1L]] %in% pkgs) {
+ miss <- c(miss, x[[1L]])
+ next
+ }
+ if (x[[2L]] != ">=") {
+ canget <- c(canget, x[[1L]])
+ next
+ }
+ current <- as.package_version(available[pkgs == x[[1L]],
+ "Version"])
+ target <- as.package_version(x[[3L]])
+ res <- eval(parse(text = paste("any(current", x$op,
+ "target)")))
+ if (res)
+ canget <- c(canget, x[[1L]])
+ else miss <- c(miss, paste0(x[[1L]], " (>= ", x[[3L]],
+ ")"))
+ }
+ else if (x[[1L]] %in% pkgs)
+ canget <- c(canget, x[[1L]])
+ else miss <- c(miss, x[[1L]])
+ }
+ list(canget, miss)
+}
Added: trunk/gtools/R/getDependencies.R
===================================================================
--- trunk/gtools/R/getDependencies.R (rev 0)
+++ trunk/gtools/R/getDependencies.R 2014-02-11 17:14:08 UTC (rev 1769)
@@ -0,0 +1,96 @@
+## This function determines the dependencies for the specified
+## package, exluding only packages found in "base".
+getDependencies <- function (pkgs,
+ dependencies = c("Depends", "Imports", "LinkingTo"),
+ installed=TRUE,
+ available=TRUE,
+ base=FALSE,
+ recommended=FALSE)
+{
+ pkgs.in = pkgs
+ if (is.null(dependencies))
+ return(unique(pkgs))
+ dep2 <- c("Depends", "Imports", "LinkingTo")
+
+
+ if(installed && !available)
+ all.packages <- installed.packages()
+ else if (available && !installed)
+ all.packages <- available.packages()
+ else
+ all.packages <- as.matrix(smartbind(##
+ installed.packages(),
+ available.packages()
+ ))
+ rownames(all.packages) <- all.packages[,"Package"]
+
+ p0 <- unique(pkgs)
+ miss <- !p0 %in% row.names(all.packages)
+ if (sum(miss)) {
+ warning(sprintf(ngettext(sum(miss), "package %s is not available (for %s)",
+ "packages %s are not available (for %s)"), paste(sQuote(p0[miss]),
+ collapse = ", "), sub(" *\\(.*", "", R.version.string)),
+ domain = NA, call. = FALSE)
+ if (sum(miss) == 1L && !is.na(w <- match(tolower(p0[miss]),
+ tolower(row.names(all.packages))))) {
+ warning(sprintf("Perhaps you meant %s ?", sQuote(row.names(all.packages)[w])),
+ call. = FALSE, domain = NA)
+ }
+ flush.console()
+ }
+
+ ## Whether to exclude base and recommended packages
+ if(!base || !recommended)
+ {
+ priority <- NULL
+ if(!base) priority <- c("base", priority)
+ if(!recommended) priority <- c("recommended", priority)
+ installed <- installed.packages(priority=priority)
+ }
+ else
+ installed <- installed.packages()[FALSE,]
+
+ p0 <- p0[!miss]
+
+ p1 <- p0
+ not_avail <- character()
+ repeat {
+ deps <- apply(all.packages[p1, dependencies, drop = FALSE],
+ 1L, function(x) paste(x[!is.na(x)], collapse = ", "))
+
+ res <- .clean_up_dependencies2(
+ deps,
+ installed=installed,
+ all.packages)
+ not_avail <- c(not_avail, res[[2L]])
+ deps <- unique(res[[1L]])
+ deps <- deps[!deps %in% c("R", pkgs)]
+ if (!length(deps))
+ break
+ pkgs <- c(deps, pkgs)
+ p1 <- deps
+ if (!is.null(dep2)) {
+ dependencies <- dep2
+ dep2 <- NULL
+ }
+ }
+ if (length(not_avail)) {
+ not_avail <- unique(not_avail)
+ warning(sprintf(ngettext(length(not_avail),
+ "dependency %s is not available",
+ "dependencies %s are not available"),
+ paste(sQuote(not_avail),
+ collapse = ", ")),
+ domain = NA,
+ call. = FALSE,
+ immediate. = TRUE)
+ flush.console()
+ }
+ pkgs <- unique(pkgs)
+ pkgs <- pkgs[pkgs %in% row.names(all.packages)]
+ p0 <- pkgs
+
+
+ p0[ ! p0 %in% pkgs.in ]
+}
+
Added: trunk/gtools/man/getDependencies.Rd
===================================================================
--- trunk/gtools/man/getDependencies.Rd (rev 0)
+++ trunk/gtools/man/getDependencies.Rd 2014-02-11 17:14:08 UTC (rev 1769)
@@ -0,0 +1,81 @@
+\name{getDependencies}
+\alias{getDependencies}
+\title{
+ Get package dependencies
+}
+\description{
+ Get package dependencies
+}
+\usage{
+getDependencies(pkgs,
+ dependencies=NA,
+ installed=TRUE,
+ available=TRUE,
+ base=FALSE,
+ recommended=FALSE)
+}
+\arguments{
+ \item{pkgs}{character vector of package names}
+ \item{dependencies}{character vector of dependency types to include.
+ Choices are "Depends", "Imports", "LinkingTo", "Suggests",
+ and "Enhances". Defaults to \code{c("Depends", "Imports",
+ "LinkingTo")}.
+ }
+ \item{installed}{Logical indicating whether to pull dependency
+ information from installed packages. Defaults to TRUE.
+ }
+ \item{available}{Logical indicating whether to pull dependency
+ information from available packages. Defaults to TRUE.
+ }
+ \item{base}{Logical indicating whether to include dependencies on base
+ packages that are included in the R installation. Defaults to
+ FALSE.
+ }
+ \item{base}{Logical indicating whether to include dependencies on
+ recommended packages that are included in the R
+ installation. Defaults to
+ FALSE.
+ }
+}
+\details{
+ This function recursively constructs the list of dependencies for the
+ packages given by \code{pkgs}. By default, the dependency information
+ is extracted from both installed and available packages. As a
+ consequence, it works both for local and CRAN packages.
+}
+\value{
+ A character vector of package names.
+}
+\note{
+ If \code{available=TRUE} R will attempt to access the currently
+ selected CRAN repository, prompting for one if necessary.
+ }
+\author{
+ Gregory R. Warnes email{gr...@wa...} based on the non exported
+ \code{utils:::getDependencies} and
+ \code{utils:::.clean_up_dependencies2}.
+}
+\seealso{
+ \code{\link{installed.packages}},
+ \code{\link{available.packages}}
+}
+\examples{
+## A locally installed package
+getDependencies("MASS", installed=TRUE, available=FALSE)
+
+\dontrun{
+## A package on CRAN
+getDependencies("gregmisc", installed=FALSE, available=TRUE)
+}
+
+## Show base and recommended dependencies
+getDependencies("MASS", available=FALSE, base=TRUE, recommended=TRUE)
+
+\dontrun{
+## Download the set of packages necessary to support a local package
+deps <- getDependencies("MyLocalPackage", available=FALSE)
+download.packages(deps, destdir="./R_Packages")
+}
+
+}
+\keyword{utilities}
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|
|
From: <wa...@us...> - 2014-01-14 19:43:20
|
Revision: 1768
http://sourceforge.net/p/r-gregmisc/code/1768
Author: warnes
Date: 2014-01-14 19:43:17 +0000 (Tue, 14 Jan 2014)
Log Message:
-----------
Update for bug-fix release
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/inst/NEWS
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2014-01-14 19:37:16 UTC (rev 1767)
+++ trunk/gtools/DESCRIPTION 2014-01-14 19:43:17 UTC (rev 1768)
@@ -1,10 +1,9 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.2.0
-Date: 2014-01-11
+Version: 3.2.2
+Date: 2014-01-14
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
-Imports: gdata
License: LGPL-2.1
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2014-01-14 19:37:16 UTC (rev 1767)
+++ trunk/gtools/inst/NEWS 2014-01-14 19:43:17 UTC (rev 1768)
@@ -1,3 +1,20 @@
+gtools 3.2.2 - 2014-01-14
+-------------------------
+
+Bug fixes:
+
+- binsearch() was returning the wrong endpoint & value when the found
+ value was at the upper endpoint.
+
+
+gtools 3.2.1 - 2014-01-13
+-------------------------
+
+Bug fixes:
+
+- Resolve circular dependency with gdata
+
+
gtools 3.2.0 - 2014-01-11
-------------------------
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|
|
From: <wa...@us...> - 2014-01-14 19:37:19
|
Revision: 1767
http://sourceforge.net/p/r-gregmisc/code/1767
Author: warnes
Date: 2014-01-14 19:37:16 +0000 (Tue, 14 Jan 2014)
Log Message:
-----------
Add test file for binsearch() function.
Added Paths:
-----------
trunk/gtools/tests/
trunk/gtools/tests/test_binsearch.R
Added: trunk/gtools/tests/test_binsearch.R
===================================================================
--- trunk/gtools/tests/test_binsearch.R (rev 0)
+++ trunk/gtools/tests/test_binsearch.R 2014-01-14 19:37:16 UTC (rev 1767)
@@ -0,0 +1,64 @@
+library(gtools)
+
+##############################
+### Examples from man page ###
+##############################
+
+### Toy examples
+
+# search for x=10
+s <- binsearch( function(x) x-10, range=c(0,20) )
+stopifnot(s$where==10)
+
+# search for x=10.1
+s <- binsearch( function(x) x-10.1, range=c(0,20) )
+stopifnot( s$where==c(10,11) )
+
+### Classical toy example
+
+# binary search for the index of 'M' among the sorted letters
+fun <- function(X) ifelse(LETTERS[X] > 'M', 1,
+ ifelse(LETTERS[X] < 'M', -1, 0 ) )
+
+s = binsearch( fun, range=1:26 )
+stopifnot( LETTERS[s$where]=="M")
+
+##################################
+### Test boundary contiditions ###
+##################################
+
+s = binsearch(fun = function(x) x-10, range=c(1,10) )
+with(s, stopifnot(where==10, value==0, flag=="Found") )
+
+s = binsearch(fun = function(x) x-1, range=c(1,10) )
+with(s, stopifnot(where==1, value==0, flag=="Found") )
+
+
+checkWarning <- function( expr )
+ {
+ myEnv <- environment()
+
+ catchWarning <- function(w) {
+ assign("warningValue", w, pos=myEnv)
+ invokeRestart("muffleWarning")
+ }
+
+ retval <- withCallingHandlers(expr = expr,
+ warning = catchWarning)
+
+
+ if( !exists("warningValue", where=myEnv, inherits=FALSE) )
+ stop("Expected a warning message")
+ }
+
+checkWarning( s <- binsearch(fun = function(x) x-10, range=c(1,9) ) )
+with(s, stopifnot(where==9, value==-1, flag=="Upper Boundary" ) )
+
+checkWarning( s <- binsearch(fun = function(x) x-1, range=c(2,10) ) )
+with(s, stopifnot(where==2, value==1, flag=="Lower Boundary" ) )
+
+
+
+
+
+
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|
|
From: <wa...@us...> - 2014-01-14 15:56:46
|
Revision: 1766
http://sourceforge.net/p/r-gregmisc/code/1766
Author: warnes
Date: 2014-01-14 15:56:41 +0000 (Tue, 14 Jan 2014)
Log Message:
-----------
Fixed bug where binsearch() returned the wrong endpoint & value when the found value was at the upper endpoint.
Modified Paths:
--------------
trunk/gtools/R/binsearch.R
Modified: trunk/gtools/R/binsearch.R
===================================================================
--- trunk/gtools/R/binsearch.R 2014-01-13 18:16:51 UTC (rev 1765)
+++ trunk/gtools/R/binsearch.R 2014-01-14 15:56:41 UTC (rev 1766)
@@ -51,7 +51,7 @@
cat("fun(center)=",val,"\n")
}
-
+
if( val==target )
{
val.lo <- val.hi <- val
@@ -75,9 +75,9 @@
cat("new hi=",hi,"\n")
cat("--------------\n")
}
-
+
}
-
+
# Create return value
retval <- list()
retval$call <- match.call()
@@ -116,8 +116,8 @@
else if( val.hi==target )
{
retval$flag="Found"
- retval$where=lo
- retval$value=val.lo
+ retval$where=hi
+ retval$value=val.hi
}
else
{
@@ -125,10 +125,10 @@
retval$where=c(lo, hi)
retval$value=c(val.lo, val.hi)
}
-
+
return(retval)
}
-
-
+
+
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|
From: <wa...@us...> - 2014-01-13 18:16:54
|
Revision: 1765
http://sourceforge.net/p/r-gregmisc/code/1765
Author: warnes
Date: 2014-01-13 18:16:51 +0000 (Mon, 13 Jan 2014)
Log Message:
-----------
Fix typo
Modified Paths:
--------------
trunk/gtools/man/smartbind.Rd
Modified: trunk/gtools/man/smartbind.Rd
===================================================================
--- trunk/gtools/man/smartbind.Rd 2014-01-11 23:39:09 UTC (rev 1764)
+++ trunk/gtools/man/smartbind.Rd 2014-01-13 18:16:51 UTC (rev 1765)
@@ -1,6 +1,6 @@
\name{smartbind}
\alias{smartbind}
-\title{Efficient rbind of data framesy, even if the column names don't match}
+\title{Efficient rbind of data frames, even if the column names don't match}
\description{
Efficient rbind of data frames, even if the column names don't match
}
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|
From: <wa...@us...> - 2014-01-11 23:39:12
|
Revision: 1764
http://sourceforge.net/p/r-gregmisc/code/1764
Author: warnes
Date: 2014-01-11 23:39:09 +0000 (Sat, 11 Jan 2014)
Log Message:
-----------
Update for gtools release 3.2.0
Modified Paths:
--------------
trunk/gtools/inst/NEWS
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2014-01-11 23:38:29 UTC (rev 1763)
+++ trunk/gtools/inst/NEWS 2014-01-11 23:39:09 UTC (rev 1764)
@@ -1,3 +1,25 @@
+gtools 3.2.0 - 2014-01-11
+-------------------------
+
+New features:
+
+- The keywords() function now accepts a function or function name as
+ an argument and will return the list of keywords associated with the
+ named function.
+
+- New function stars.pval() which will generate p-value significance
+ symbols ('***', '**', etc.)
+
+Bug fixes:
+
+- R/mixedsort.R: mixedorder() was failing to correctly handle numbers
+ including decimals due to a faulty regular expression.
+
+Other changes:
+
+- capture() and sprint() are now defunct.
+
+
gtools 3.1.1 - 2013-11-06
-------------------------
@@ -30,7 +52,7 @@
- The function 'addLast()' has been deprecated because it directly
manipulates the global environment, which is expressly prohibited by
- the CRAN policies.
+ the CRAN policies.
- A new function, 'lastAdd()' has been created to replace 'addLast()'.
The name has been changed because the two functions require
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|
From: <wa...@us...> - 2014-01-11 23:38:32
|
Revision: 1763
http://sourceforge.net/p/r-gregmisc/code/1763
Author: warnes
Date: 2014-01-11 23:38:29 +0000 (Sat, 11 Jan 2014)
Log Message:
-----------
fixes for R CMD check
Modified Paths:
--------------
trunk/gtools/man/gtools-defunct.Rd
Modified: trunk/gtools/man/gtools-defunct.Rd
===================================================================
--- trunk/gtools/man/gtools-defunct.Rd 2014-01-11 23:24:20 UTC (rev 1762)
+++ trunk/gtools/man/gtools-defunct.Rd 2014-01-11 23:38:29 UTC (rev 1763)
@@ -2,20 +2,13 @@
\alias{gtools-defunct}
\alias{assert}
\alias{addLast}
+\alias{capture}
+\alias{sprint}
\title{Defunct Functions in package \code{gtools}}
\description{
The functions or variables listed here are no longer part of
package \code{gtools}.
}
-\usage{
-assert(FLAG)
-addLast(fun)
-capture(
-}
-%\arguments{
-% \item{FLAG}{ Expression that should evaluate to a boolean vector}
-% \item{fun}{Function to be called.}
-%}
\details{
\itemize{
\item{ \code{assert} is a defunct synonym for
@@ -23,13 +16,13 @@
\item{ \code{addLast} has been replaced by \code{lastAdd}, which has
the same purpose but appled using different syntax. }
\item{ \code{capture} and \code{capture.output} have been removed in
- favor of \code{capture.output} from the \code{base} package.}
+ favor of \code{capture.output} from the \code{utils} package.}
}
}
\seealso{
\code{\link[base]{Defunct}},
\code{\link[base]{stopifnot}},
\code{\link[gtools]{lastAdd}},
- \code{\link[base]{capture.output}
+ \code{\link[utils]{capture.output}}
}
\keyword{misc}
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|
From: <wa...@us...> - 2014-01-11 23:24:23
|
Revision: 1762
http://sourceforge.net/p/r-gregmisc/code/1762
Author: warnes
Date: 2014-01-11 23:24:20 +0000 (Sat, 11 Jan 2014)
Log Message:
-----------
Fixes for gtools release 3.2.0
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/NAMESPACE
trunk/gtools/R/keywords.R
trunk/gtools/man/gtools-defunct.Rd
trunk/gtools/man/stars.pval.Rd
Added Paths:
-----------
trunk/gtools/R/defunct.R
Removed Paths:
-------------
trunk/gtools/R/capture.R
trunk/gtools/man/capture.Rd
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/DESCRIPTION 2014-01-11 23:24:20 UTC (rev 1762)
@@ -1,9 +1,10 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.1.1
-Date: 2013-11-06
+Version: 3.2.0
+Date: 2014-01-11
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
+Imports: gdata
License: LGPL-2.1
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/NAMESPACE 2014-01-11 23:24:20 UTC (rev 1762)
@@ -34,4 +34,3 @@
stars.pval,
strmacro
)
-
Deleted: trunk/gtools/R/capture.R
===================================================================
--- trunk/gtools/R/capture.R 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/R/capture.R 2014-01-11 23:24:20 UTC (rev 1762)
@@ -1,44 +0,0 @@
-# $Id$
-#
-# $Log$
-# Revision 1.4 2004/01/21 04:31:25 warnes
-# - Mark sprint() as depreciated.
-# - Replace references to sprint with capture.output()
-# - Use match.arg for halign and valign arguments to textplot.default.
-# - Fix textplot.character so that a vector of characters is properly
-# displayed. Previouslt, character vectors were plotted on top of each
-# other.
-#
-# Revision 1.3 2003/11/10 22:11:13 warnes
-#
-# - Add files contributed by Arni Magnusson
-# <arnima@u.washington.edu>. As well as some of my own.
-#
-# Revision 1.2 2003/04/04 13:45:21 warnes
-#
-# - Allow optional arguments to sprint to be passed to print
-#
-# Revision 1.1 2003/04/02 22:28:32 warnes
-#
-# - Added file 'capture.R' containing capture() and sprint().
-#
-#
-
-capture <- function( expression, collapse="\n")
- {
- .Deprecated("capture.output", "base", )
-
- resultText <- capture.output( expression )
-
- return( paste( c(resultText, ""), collapse=collapse, sep="" ) )
- # the reason for c(result, "") is so that we get the line
- # terminator on the last line of output. Otherwise, it just shows
- # up between the lines.
- }
-
-
-sprint <- function(x,...)
- {
- .Deprecated("capture.output", "base")
- capture(print(x,...))
- }
Copied: trunk/gtools/R/defunct.R (from rev 1761, trunk/gtools/R/capture.R)
===================================================================
--- trunk/gtools/R/defunct.R (rev 0)
+++ trunk/gtools/R/defunct.R 2014-01-11 23:24:20 UTC (rev 1762)
@@ -0,0 +1,6 @@
+capture <- function( expression, collapse="\n")
+ .Defunct("capture.output", "base")
+
+sprint <- function(x,...)
+ .Defunct("capture.output", "base")
+
Modified: trunk/gtools/R/keywords.R
===================================================================
--- trunk/gtools/R/keywords.R 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/R/keywords.R 2014-01-11 23:24:20 UTC (rev 1762)
@@ -8,6 +8,15 @@
}
else
{
+
+ ## Local copy of trim.character to avoid cyclic dependency with gdata ##
+ trim <- function(s)
+ {
+ s <- sub(pattern="^[[:blank:]]+", replacement="", x=s)
+ s <- sub(pattern="[[:blank:]]+$", replacement="", x=s)
+ s
+ }
+
kw <- scan(file=file, what=character(), sep="\n", quiet=TRUE)
kw <- grep("&", kw, value=TRUE)
kw <- gsub("&[^&]*$","", kw)
Deleted: trunk/gtools/man/capture.Rd
===================================================================
--- trunk/gtools/man/capture.Rd 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/man/capture.Rd 2014-01-11 23:24:20 UTC (rev 1762)
@@ -1,51 +0,0 @@
-\name{capture}
-\alias{capture}
-\alias{sprint}
-\title{Capture printed output of an R expression in a string}
-\description{
-Capture printed output of an R expression in a string
-}
-\usage{
-capture(expression, collapse = "\n")
-sprint(x,...)
-}
-\arguments{
- \item{expression}{R expression whose output will be captured.}
- \item{collapse}{Character used to join output lines. Defaults to
- "\\n". Use \code{NULL} to return a vector of individual output lines.}
- \item{x}{Object to be printed}
- \item{...}{Optional parameters to be passed to \code{\link{print}} }
-}
-\details{
- The \code{capture} function uses \code{\link{sink}} to capture the
- printed results generated by \code{expression}.
-
- The function \code{sprint} uses \code{capture} to redirect the
- results of calling \code{\link{print}} on an object to a string.
-}
-\value{
- A character string, or if \code{collapse==NULL} a vector of character
- strings containing the printed output from the R expression.
-}
-\section{WARNING}{R 1.7.0+ includes \code{capture.output}, which
- duplicates the functionality of \code{capture}. Thus, \code{capture}
- is depreciated.}
-\author{Gregory R. Warnes \email{gr...@wa...} }
-\seealso{
- \code{\link[session]{texteval}},
- \code{\link{capture.output}}
-}
-\examples{
-
-# capture the results of a loop
-loop.text <- capture( for(i in 1:10) cat("i=",i,"\n") )
-loop.text
-
-# put regression summary results into a string
-data(iris)
-reg <- lm( Sepal.Length ~ Species, data=iris )
-summary.text <- sprint( summary(reg) )
-cat(summary.text)
-}
-\keyword{print}
-\keyword{IO}
Modified: trunk/gtools/man/gtools-defunct.Rd
===================================================================
--- trunk/gtools/man/gtools-defunct.Rd 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/man/gtools-defunct.Rd 2014-01-11 23:24:20 UTC (rev 1762)
@@ -2,29 +2,34 @@
\alias{gtools-defunct}
\alias{assert}
\alias{addLast}
-\title{Deprecated Functions in the gtools package}
+\title{Defunct Functions in package \code{gtools}}
\description{
- These functions are no longer available in gtools.
+ The functions or variables listed here are no longer part of
+ package \code{gtools}.
}
\usage{
assert(FLAG)
addLast(fun)
+capture(
}
-\arguments{
- \item{FLAG}{ Expression that should evaluate to a boolean vector}
- \item{fun}{Function to be called.}
-}
+%\arguments{
+% \item{FLAG}{ Expression that should evaluate to a boolean vector}
+% \item{fun}{Function to be called.}
+%}
\details{
\itemize{
\item{ \code{assert} is a defunct synonym for
- \code{\link[base]{stopifnot}}. }
+ \code{\link[base]{stopifnot}}. }
\item{ \code{addLast} has been replaced by \code{lastAdd}, which has
- the same purpose but appled using different syntax. }
+ the same purpose but appled using different syntax. }
+ \item{ \code{capture} and \code{capture.output} have been removed in
+ favor of \code{capture.output} from the \code{base} package.}
}
}
\seealso{
- \code{\link[base]{Defunct}}
- \code{\link[base]{stopifnot}}
- \code{\link[gtools]{lastAdd}}
+ \code{\link[base]{Defunct}},
+ \code{\link[base]{stopifnot}},
+ \code{\link[gtools]{lastAdd}},
+ \code{\link[base]{capture.output}
}
\keyword{misc}
Modified: trunk/gtools/man/stars.pval.Rd
===================================================================
--- trunk/gtools/man/stars.pval.Rd 2013-12-23 18:48:15 UTC (rev 1761)
+++ trunk/gtools/man/stars.pval.Rd 2014-01-11 23:24:20 UTC (rev 1762)
@@ -36,9 +36,7 @@
}
\examples{
p.val <- c(0.0004, 0.0015, 0.013, 0.044, 0.067, 0.24)
-stars.pval(x)
+stars.pval(p.val)
}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
\keyword{misc}
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|
|
From: <wa...@us...> - 2013-12-23 18:48:18
|
Revision: 1761
http://sourceforge.net/p/r-gregmisc/code/1761
Author: warnes
Date: 2013-12-23 18:48:15 +0000 (Mon, 23 Dec 2013)
Log Message:
-----------
Extend the keywords() function to return keywords associated with a specified topic via 'keywords(topic)'.
Modified Paths:
--------------
trunk/gtools/R/keywords.R
trunk/gtools/man/keywords.Rd
Modified: trunk/gtools/R/keywords.R
===================================================================
--- trunk/gtools/R/keywords.R 2013-12-23 16:08:10 UTC (rev 1760)
+++ trunk/gtools/R/keywords.R 2013-12-23 18:48:15 UTC (rev 1761)
@@ -1,5 +1,33 @@
-keywords <- function( ... )
+keywords <- function( topic )
{
+
file <- file.path(R.home("doc"),"KEYWORDS")
- file.show(file, ...)
+ if(missing(topic))
+ {
+ file.show(file)
+ }
+ else
+ {
+ kw <- scan(file=file, what=character(), sep="\n", quiet=TRUE)
+ kw <- grep("&", kw, value=TRUE)
+ kw <- gsub("&[^&]*$","", kw)
+ kw <- gsub("&+"," ", kw)
+ kw <- na.omit(trim(kw))
+
+ ischar <- tryCatch(is.character(topic) && length(topic) ==
+ 1L, error = identity)
+ if (inherits(ischar, "error"))
+ ischar <- FALSE
+ if (!ischar)
+ topic <- deparse(substitute(topic))
+
+ item <- paste("^",topic,"$", sep="")
+
+ topics <- function(k) help.search(keyword=k)$matches[,"topic"]
+ matches <- lapply(kw, topics)
+ names(matches) <- kw
+
+ tmp <- unlist(lapply( matches, function(m) grep(item, m, value=TRUE) ))
+ names(tmp)
+ }
}
Modified: trunk/gtools/man/keywords.Rd
===================================================================
--- trunk/gtools/man/keywords.Rd 2013-12-23 16:08:10 UTC (rev 1760)
+++ trunk/gtools/man/keywords.Rd 2013-12-23 18:48:15 UTC (rev 1761)
@@ -5,21 +5,24 @@
List valid keywords for R man pages
}
\usage{
-keywords(...)
+keywords(topic)
}
\arguments{
- \item{\dots}{Optional argumenst to pass to show.file()}
+ \item{topic}{object or man page topic}
}
\details{
- This function simply determines the path \$RHOME/doc/KEYWORDS and calls
- show.file() to display it.
+ If \code{topic} is provided, return a list of the keywords associated
+ with \code{topic}. Otherwise, display the list of valid R keywords
+ from the R doc/KEYWORDS file.
}
-\value{
- Nothing of interest.
-}
\author{Gregory R. Warnes \email{gr...@wa...}}
\seealso{ \code{\link[utils]{help}} }
\examples{
+## Show all valid R keywords
keywords()
+
+## Show keywords associated with the 'merge' function
+keywords(merge)
+keywords("merge")
}
\keyword{documentation}
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|
|
From: <wa...@us...> - 2013-12-23 16:08:13
|
Revision: 1760
http://sourceforge.net/p/r-gregmisc/code/1760
Author: warnes
Date: 2013-12-23 16:08:10 +0000 (Mon, 23 Dec 2013)
Log Message:
-----------
Add keyword.
Modified Paths:
--------------
trunk/gtools/man/stars.pval.Rd
Modified: trunk/gtools/man/stars.pval.Rd
===================================================================
--- trunk/gtools/man/stars.pval.Rd 2013-12-23 16:04:03 UTC (rev 1759)
+++ trunk/gtools/man/stars.pval.Rd 2013-12-23 16:08:10 UTC (rev 1760)
@@ -40,5 +40,5 @@
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
+\keyword{misc}
+
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|
From: <wa...@us...> - 2013-12-23 16:04:06
|
Revision: 1759
http://sourceforge.net/p/r-gregmisc/code/1759
Author: warnes
Date: 2013-12-23 16:04:03 +0000 (Mon, 23 Dec 2013)
Log Message:
-----------
Add stars.pval() function to convert p-values into significance symbols.
Modified Paths:
--------------
trunk/gtools/NAMESPACE
Added Paths:
-----------
trunk/gtools/R/stars.pval.R
trunk/gtools/man/stars.pval.Rd
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2013-12-18 14:33:28 UTC (rev 1758)
+++ trunk/gtools/NAMESPACE 2013-12-23 16:04:03 UTC (rev 1759)
@@ -31,6 +31,7 @@
setTCPNoDelay,
smartbind,
sprint,
+ stars.pval,
strmacro
)
Added: trunk/gtools/R/stars.pval.R
===================================================================
--- trunk/gtools/R/stars.pval.R (rev 0)
+++ trunk/gtools/R/stars.pval.R 2013-12-23 16:04:03 UTC (rev 1759)
@@ -0,0 +1,8 @@
+stars.pval <- function(p.value)
+ {
+ unclass(
+ symnum(p.value, corr = FALSE, na = FALSE,
+ cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
+ symbols = c("***", "**", "*", ".", " "))
+ )
+ }
Added: trunk/gtools/man/stars.pval.Rd
===================================================================
--- trunk/gtools/man/stars.pval.Rd (rev 0)
+++ trunk/gtools/man/stars.pval.Rd 2013-12-23 16:04:03 UTC (rev 1759)
@@ -0,0 +1,44 @@
+\name{stars.pval}
+\alias{stars.pval}
+\title{
+Generate significance stars from p-values
+}
+\description{
+ Generate significance stars (e.g. '***', '**', '*', '+') from
+ p-values using R's standard definitions.
+}
+\usage{
+stars.pval(p.value)
+}
+\arguments{
+ \item{p.value}{numeric vector of p-values}
+}
+\details{
+ Mapping from p-value ranges to symbols:
+ \describe{
+ \item{0 - 0.001}{'***'}
+ \item{0.001 - 0.01}{'**'}
+ \item{0.01 - 0.05}{'*'}
+ \item{0.05 - 0.1}{'+'}
+ \item{0.1 - 1.0}{'' (No symbol)}
+ }
+}
+\value{
+ A character vector containing the same number of elements as
+ \code{p-value}, with an attribute "legend" providing the conversion
+ pattern.
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link[stats]{symnum}}
+}
+\examples{
+p.val <- c(0.0004, 0.0015, 0.013, 0.044, 0.067, 0.24)
+stars.pval(x)
+}
+% 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: <ar...@us...> - 2013-12-18 14:33:31
|
Revision: 1758
http://sourceforge.net/p/r-gregmisc/code/1758
Author: arnima
Date: 2013-12-18 14:33:28 +0000 (Wed, 18 Dec 2013)
Log Message:
-----------
Retain original list order unless sort=FALSE; also stop if unnamed list
Modified Paths:
--------------
trunk/gdata/R/ll.R
Modified: trunk/gdata/R/ll.R
===================================================================
--- trunk/gdata/R/ll.R 2013-12-16 19:58:56 UTC (rev 1757)
+++ trunk/gdata/R/ll.R 2013-12-18 14:33:28 UTC (rev 1758)
@@ -29,13 +29,21 @@
return(size)
}
+ ## 1 Set unit, denominator, original.rank
unit <- match.arg(unit, c("bytes","KB","MB"))
denominator <- switch(unit, "KB"=1024, "MB"=1024^2, 1)
+ original.rank <- NULL
+ ## 2 Detect what 'pos' is like, then get class, size, dim
if(is.character(pos)) # pos is an environment name
pos <- match(pos, search())
if(is.list(pos)) # pos is a list-like object
+ {
+ if(is.null(names(pos)))
+ stop("All elements of a list must be named")
+ original.rank <- rank(names(pos))
pos <- as.environment(pos)
+ }
if(length(ls(pos,...)) == 0) # pos is an empty environment
{
object.frame <- data.frame()
@@ -66,6 +74,12 @@
object.frame <- cbind(object.frame,
Dim=sapply(ls(pos,...),get.object.dim,pos=pos))
}
+
+ ## 3 Retain original order of list elements
+ if(!sort && !is.null(original.rank))
+ object.frame <- object.frame[original.rank,]
+
+ ## 4 Filter results given class
if(!is.null(class))
{
include <- object.frame$Class %in% class
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-12-16 19:59:00
|
Revision: 1757
http://sourceforge.net/p/r-gregmisc/code/1757
Author: warnes
Date: 2013-12-16 19:58:56 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
Trim will now remove all types of leading/trailing whitespace by using
the [:blank:] character class.
Modified Paths:
--------------
trunk/gdata/R/trim.R
Modified: trunk/gdata/R/trim.R
===================================================================
--- trunk/gdata/R/trim.R 2013-12-07 16:12:05 UTC (rev 1756)
+++ trunk/gdata/R/trim.R 2013-12-16 19:58:56 UTC (rev 1757)
@@ -8,8 +8,8 @@
trim.character <- function(s, recode.factor=TRUE, ...)
{
- s <- sub(pattern="^ +", replacement="", x=s)
- s <- sub(pattern=" +$", replacement="", x=s)
+ s <- sub(pattern="^[[:blank:]]+", replacement="", x=s)
+ s <- sub(pattern="[[:blank:]]+$", replacement="", x=s)
s
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-12-07 16:12:09
|
Revision: 1756
http://sourceforge.net/p/r-gregmisc/code/1756
Author: warnes
Date: 2013-12-07 16:12:05 +0000 (Sat, 07 Dec 2013)
Log Message:
-----------
Remove spurious '<' character
Modified Paths:
--------------
trunk/SII/vignettes/SII.Rnw
Modified: trunk/SII/vignettes/SII.Rnw
===================================================================
--- trunk/SII/vignettes/SII.Rnw 2013-12-07 16:00:09 UTC (rev 1755)
+++ trunk/SII/vignettes/SII.Rnw 2013-12-07 16:12:05 UTC (rev 1756)
@@ -728,7 +728,7 @@
t(round(tab,2))
@
-<<<ComparisonFigure2,fig=TRUE>>=
+<<ComparisonFigure2,fig=TRUE>>=
compare.plot(sii.right, matlab=matlab, title="Spline method comparison, Right Ear")
@
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-12-07 16:00:16
|
Revision: 1755
http://sourceforge.net/p/r-gregmisc/code/1755
Author: warnes
Date: 2013-12-07 16:00:09 +0000 (Sat, 07 Dec 2013)
Log Message:
-----------
Move sii.constants out of data/ and into R/sysdata.Rda so it becomes part of the package namespace. Remove the now unneeded 'undocumented' man page that listed it.
Modified Paths:
--------------
trunk/SII/R/sii.excel.R
trunk/SII/vignettes/SII.Rnw
trunk/SII/vignettes/SII.pdf
Added Paths:
-----------
trunk/SII/R/sysdata.rda
Removed Paths:
-------------
trunk/SII/data/sii.constants.rda
trunk/SII/man/undocumented.Rd
Modified: trunk/SII/R/sii.excel.R
===================================================================
--- trunk/SII/R/sii.excel.R 2013-12-06 22:24:10 UTC (rev 1754)
+++ trunk/SII/R/sii.excel.R 2013-12-07 16:00:09 UTC (rev 1755)
@@ -10,9 +10,6 @@
if(length(THDI) != length(freq))
stop("THDI must have the same length as freq")
- ## Load constants into *this* environment
- data(sii.constants, package="SII", envir=parent.frame())
-
# Interpolate unobserved frequencies
sii.freqs <- sii.constants[,1]
Copied: trunk/SII/R/sysdata.rda (from rev 1752, trunk/SII/data/sii.constants.rda)
===================================================================
(Binary files differ)
Deleted: trunk/SII/data/sii.constants.rda
===================================================================
(Binary files differ)
Deleted: trunk/SII/man/undocumented.Rd
===================================================================
--- trunk/SII/man/undocumented.Rd 2013-12-06 22:24:10 UTC (rev 1754)
+++ trunk/SII/man/undocumented.Rd 2013-12-07 16:00:09 UTC (rev 1755)
@@ -1,13 +0,0 @@
-\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}
Modified: trunk/SII/vignettes/SII.Rnw
===================================================================
--- trunk/SII/vignettes/SII.Rnw 2013-12-06 22:24:10 UTC (rev 1754)
+++ trunk/SII/vignettes/SII.Rnw 2013-12-07 16:00:09 UTC (rev 1755)
@@ -492,10 +492,9 @@
THDI=c(25,25,30,35,45,45,55,60)
freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
-data(sii.constants)
-sii.freqs <- sii.constants[,1]
+sii.freqs <- SII:::sii.constants[,1]
-xlist <- sort(c(sii.constants[, 1], freq))
+xlist <- sort(c(SII:::sii.constants[, 1], freq))
ylist <- rep(NA, length=length(xlist))
names(ylist) <- xlist
ylist[ as.character(freq) ] <- THDI
@@ -527,15 +526,15 @@
plot(x=freq, y=THDI, col="black", cex=2, log=if(logx) "x" else "",
xlab="Frequency (Herz)", ylab="Threshhold of Detection (dB)",
xlim=range(sii.freqs), ylim=c(20,60) )
- lines(sii.constants[, 1], sii.constants[, "Ti'.THDN"], col="red", lwd=3)
+ lines(SII:::sii.constants[, 1], SII:::sii.constants[, "Ti'.THDN"], col="red", lwd=3)
abline(v=sii.freqs,lty=3)
}
tmp()
- lines( x=sii.constants[, 1], y=ispl, col="blue", lwd=2)
+ lines( x=SII:::sii.constants[, 1], y=ispl, col="blue", lwd=2)
if(separate) tmp()
- lines( x=sii.constants[, 1], y=ispl.l, col="cyan", lwd=2)
+ lines( x=SII:::sii.constants[, 1], y=ispl.l, col="cyan", lwd=2)
if(separate) tmp()
lines( spline (x=freq, y=THDI), col="green", lwd=2)
@@ -663,12 +662,12 @@
## comparison of our interpolation and matlab's
tab <- cbind(
- matlab=sii.constants[,"Ti'.THDN"],
+ matlab=SII:::sii.constants[,"Ti'.THDN"],
R =sii.left$table[,"T'i"],
delta =NA
)
tab[,3] <- tab[,1] - tab[,2]
-rownames(tab) <- sii.constants[,".NFreqLin"]
+rownames(tab) <- SII:::sii.constants[,".NFreqLin"]
t(round(tab,2))
@
@@ -676,7 +675,7 @@
compare.plot <- function(x, matlab, title)
{
plot(x)
- lines(sii.constants[,".NFreqLin"],
+ lines(SII:::sii.constants[,".NFreqLin"],
matlab,
type="l", col="red", lwd=3)
@@ -698,7 +697,7 @@
<<ComparisonFigure1,fig=TRUE>>=
-compare.plot(sii.left, matlab=sii.constants[, "Ti'.THDN"], title="Spline method comparison, Left Ear")
+compare.plot(sii.left, matlab=SII:::sii.constants[, "Ti'.THDN"], title="Spline method comparison, Left Ear")
@
@@ -725,7 +724,7 @@
delta =NA
)
tab[,3] <- tab[,1] - tab[,2]
-rownames(tab) <- sii.constants[,".NFreqLin"]
+rownames(tab) <- SII:::sii.constants[,".NFreqLin"]
t(round(tab,2))
@
Modified: trunk/SII/vignettes/SII.pdf
===================================================================
--- trunk/SII/vignettes/SII.pdf 2013-12-06 22:24:10 UTC (rev 1754)
+++ trunk/SII/vignettes/SII.pdf 2013-12-07 16:00:09 UTC (rev 1755)
@@ -9,18 +9,15 @@
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endstream
endobj
115 0 obj <<
@@ -277,25 +274,31 @@
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/N 100
/First 793
-/Length 1879
+/Length 1877
/Filter /FlateDecode
>>
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|
From: <wa...@us...> - 2013-12-06 22:24:14
|
Revision: 1754
http://sourceforge.net/p/r-gregmisc/code/1754
Author: warnes
Date: 2013-12-06 22:24:10 +0000 (Fri, 06 Dec 2013)
Log Message:
-----------
Update pdf file
Modified Paths:
--------------
trunk/SII/vignettes/SII.pdf
Modified: trunk/SII/vignettes/SII.pdf
===================================================================
--- trunk/SII/vignettes/SII.pdf 2013-12-06 22:09:14 UTC (rev 1753)
+++ trunk/SII/vignettes/SII.pdf 2013-12-06 22:24:10 UTC (rev 1754)
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|
From: <wa...@us...> - 2013-12-06 22:09:18
|
Revision: 1753
http://sourceforge.net/p/r-gregmisc/code/1753
Author: warnes
Date: 2013-12-06 22:09:14 +0000 (Fri, 06 Dec 2013)
Log Message:
-----------
rename package directories to match current CRAN standards
Added Paths:
-----------
trunk/SII/tests/
trunk/SII/vignettes/
trunk/SII/vignettes/SII.Rnw
Removed Paths:
-------------
trunk/SII/inst/doc/
trunk/SII/test/
trunk/SII/vignettes/SII.Rnw
Deleted: trunk/SII/vignettes/SII.Rnw
===================================================================
--- trunk/SII/inst/doc/SII.Rnw 2013-10-21 23:33:29 UTC (rev 1744)
+++ trunk/SII/vignettes/SII.Rnw 2013-12-06 22:09:14 UTC (rev 1753)
@@ -1,913 +0,0 @@
-% \VignetteIndexEntry{Calculate ANSI S3.5-1997 Speech Intelligibility Index}
-% \VignetteDepends{SII, gdata, xtable, splines}
-% \VignetteKeyword{Speech Intelligibility Index}
-%
-\documentclass[letterpaper]{article}
-\usepackage{Rd}
-\usepackage{Sweave}
-\usepackage[margin=1.0in]{geometry}
-\usepackage{hyperref}
-\parskip=11pt
-\parindent=0mm
-\usepackage{graphicx}
-
-%\usepackage{makeidx}
-%\makeindex{}
-
-%------------------------------------------------------------
-% newcommand
-%------------------------------------------------------------
-\newcommand{\scscst}{\scriptscriptstyle}
-\newcommand{\scst}{\scriptstyle}
-\newcommand{\Robject}[1]{{\texttt{#1}}}
-\newcommand{\Rfunction}[1]{{\texttt{#1}}}
-\newcommand{\Rclass}[1]{\textit{#1}}
-\newcommand{\Rpackage}[1]{\textit{#1}}
-\newcommand{\Rexpression}[1]{\texttt{#1}}
-\newcommand{\Rmethod}[1]{{\texttt{#1}}}
-\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
-%---
-
-
-\setkeys{Gin}{width=\textwidth}
-
-\title{
- Calculating Speech Intelligibility Index (SII) using R
-}
-\author{
- Gregory R. Warnes, Ph.D. \\
- Random Technologies LLC.
- }
-
-\begin{document}
-\maketitle
-
-This document describes the calculation of Speech Intelligibility
-Index (SII) using R. The core calculations have been encapsulated as
-an R add-on package named ``SII'', which, once installed, can be
-loaded thusly:
-
-<<load.package>>=
-library(SII)
-@
-
-\section{SII constant tables}
-
-The R package includes constant tables 1 -- 4 from the ANSI S3.5-1997
-text. These can be loaded via
-<<load.data>>=
-## Table 1: Critical band SII procedure constants
-data("critical")
-head(critical)
-
-## Table 2:Equally contributing (17 band) critical band SII
-## procedure constants
-data("equal")
-
-## Table 3: One-third octave band SII procedure constants
-data("onethird")
-
-## Table 4: Octave band SII procedure constants
-data("octave")
-
-## Overall SPL constants
-data("overall.spl")
-overall.spl
-@
-
-It also includes constant tables for alternative transfer functions
-corresponding to different types of message content, tables B.1 --
-B.3. These tables have been augmented with the corresponding values
-for the Connected Speech Test (CST) as given by
-\url{http://www.sii.to/CSTdata.txt}. These tables can be loaded via:
-<<load.alternative.data>>=
-## Table B.1: Critical band importance functions for various speech tests.
-data(sic.critical)
-head(sic.critical)
-
-## Table B.2: One-third octave band importance functions for various speech tests.
-data(sic.onethird)
-
-## Table B.3: Octave band importance functions for various speech tests.
-data(sic.octave)
-@
-
-With the alternative transfer functions available, it becomes easy to
-generate a nice graphical comparison of the functions:
-<<sicplot,fig=TRUE,width=12,height=6>>=
-data(sic.critical)
-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=as.character(1:ngroup),
- lty=1:ngroup,
- col=rainbow(ngroup)
- )
-
-@
-
-\section{Calculating SII}
-
-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 the specified procedure (via the argument
-\code{interpolate=TRUE}). Interpolation is accomplished using linear
-interpolation (on log-scaled data) to the frequencies required for the
-specified SII procedure. Interpolation is performed (if necessary)
-for \code{speech}, \code{noise}, \code{threshold}, and \code{loss}.
-
-The \code{sii} function has the following header:
-<<header>>=
-args(sii)
-@
-
-Where the arguments are:
-\begin{description}
- \item[speech] Speech spectrum level, as a standard level name
- ("normal", "raised", "loud", or "shout")or a vector of values, in dB
- \item[noise] Noise spectrum level, in dB
- \item[threshold] Hearing threshold level, in dB
- \item[loss] Conductive hearing loss level, in dB
- \item[freq] Frequencies at which values are provided (required if
- interpolate=TRUE)
- \item[method] SII calculation method, one of "critical",
- "equal-contributing", "one-third octave", "octave".
- \item[importance] Transfer function (importance weights), as a
- standard SII measurement name ("SII", "NNS", "CID22", "NU6", "DRT",
- "ShortPassage", "SPIN", or "CST")
- \item[interpolate] Flag indicating whether to interpolate
- from the provide measurement values and frequencies to those
- required by the specified method
-\end{description}
-
-For a detailed description of the arguments see the \Rfunction{sii}
-manual page in appendix \ref{man.pages}.
-
-\subsection{Example C.1 from ANSI S3.5-1997 Annex C}
-
-<<ExampleC.1>>=
-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"
- #, importance="SII"
- #, importance=octave$Ii
- , importance="CST"
- )
-round(sii.C1$table[,-c(5:7,13)],2)
-sii.C1$sii
-@
-
-The value given in the Standard is $0.504$.
-
-\subsection{Example C.2 from ANSI S3.5-1997 Annex C}
-
-<<ExampleC.1>>=
-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$table[1:3,1:8]
-sii.C2$sii
-@
-
-The standard shows the first three rows in the table as
-
-\begin{center}
-\begin{tabular}{rrrrrrrrr}
- \hline
- & Fi & E'i & N'i & T'i & Vi & Bi & Ci & Zi \\
- \hline
- 1 & 160 & 54.00 & 40.00 & 0.00 & 30.00 & 40.00 & $-$46.59\footnote{Typo in the standard document} & 40.00 \\
- 2 & 200 & 54.00 & 30.00 & 0.00 & 30.00 & 30.00 & $-$52.01 & 34.66 \\
- 3 & 250 & 54.00 & 20.00 & 0.00 & 30.00 & 30.00 & $-$51.42 & 25.04 \\
- \hline
-\end{tabular}
-\end{center}
-
-
-\subsection{Interpolation Example}
-
-<<ExampleC.1>>=
-sii.C1 <- sii(
- speech = c(50.0, 40.0, 40.0, 30.0, 20.0, 0.0),
- noise = c(70.0, 65.0, 45.0, 25.0, 1.0,-15.0),
- threshold= c( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0),
- method="octave"
- #, importance="SII"
- #, importance=octave$Ii
- , importance="CST"
- )
-round(sii.C1$table[,-c(5:7,13)],2)
-sii.C1$sii
-@
-
-The value given in the Standard is $0.504$.
-
-
-\subsection{Calculating SII for a set of patients}
-
-First, we need to load the patient information table
-<<LoadData, eval=FALSE>>=
-library(gdata)
-patInfo <- read.xls("../AI subject list.xls")
-@
-
-Check that we got the data properly read in:
-<<ExamineData, eval=FALSE>>=
-## Information about variables
-str(patInfo)
-@
-
-<<ExamineData, eval=FALSE>>=
-## First 6 rows
-head(patInfo)
-@
-
-Create some useful variables:
-<<vars, eval=FALSE>>=
-## measured frequencies
-freq <- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
-
-## columns containing frequencies for the right/left ear
-rt.cols <- paste("PTR",freq, sep="")
-lt.cols <- paste("PTL",freq, sep="")
-
-rt.vals <- patInfo[,rt.cols]
-lt.vals <- patInfo[,lt.cols]
-@
-
-Handle missing value encoding
-<<missing, eval=FALSE>>=
-rt.vals[rt.vals==-888] <- NA
-lt.vals[rt.vals==-888] <- NA
-@
-
-Now, construct a utility function to handle an individual patient's
-SII calculation using the arguments we want.
-<<fun, eval=FALSE>>=
-fun <- function(X)
- {
- ret <- try(
- sii(X,
- speech="raised",
- threshold=c(15,15,20,25,35,35,45,50),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="SII",
- interpolate=TRUE
- )$sii
- )
- if("try-error" %in% class(ret))
- return(NA)
- else
- return(ret)
- }
-
-## Test it
-fun( rt.vals[1,] )
-@
-
-
-Now apply it for the right and left ears:
-<<CalculateSII, eval=FALSE>>=
-sii.right <- apply(rt.vals, 1, fun )
-
-sii.left <- apply(lt.vals, 1, fun )
-@
-
-Now add theses back onto our table:
-<<AddSIIToTable, eval=FALSE>>=
-patInfo$"SII.right" <- sii.right
-patInfo$"SII.left" <- sii.left
-
-tail(patInfo)
-@
-
-And save to a file:
-<<SavePatInfo, eval=FALSE>>=
-write.table(patInfo,
- file="../AI subject list-SII.xls",
- row.names=FALSE,
- sep="\t"
- )
-@
-
-Now define a function to do all of this with a single call
-
-<<SIIFileFun, eval=FALSE>>=
-sii.dina <- function(infile, outfile, verbose=TRUE)
- {
- if(verbose)
- cat("\nLoading data file '", infile, "'...\n", sep="")
- ## Load the data
- library(gdata)
- patInfo <- read.xls(infile)
-
- ## measured frequencies
- freq <- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
-
- if(verbose)
- cat("\nExtracting hearing thresholds...\n")
-
- ## columns containing frequencies for the right/left ear
- rt.cols <- paste("PTR",freq, sep="")
- lt.cols <- paste("PTL",freq, sep="")
-
- rt.vals <- patInfo[,rt.cols]
- lt.vals <- patInfo[,lt.cols]
-
- ## Handle missing code '-888'
- rt.vals[rt.vals==-888] <- NA
- lt.vals[rt.vals==-888] <- NA
-
- ## define function to compute SII with our defaults
- fun <- function(X)
- {
- ret <- try(
- sii(X,
- speech="raised",
- threshold=c(15,15,20,25,35,35,45,50),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="SII",
- interpolate=TRUE
- )$sii #$
- )
- if("try-error" %in% class(ret))
- return(NA)
- else
- return(ret)
- }
-
- ## Calculate SII
- if(verbose)
- cat("\nCalculating right ear SII...\n")
- sii.right <- apply(rt.vals, 1, fun )
- if(verbose)
- cat("\nCalculating left ear SII...\n")
- sii.left <- apply(lt.vals, 1, fun )
-
- ## Add back onto the table
- patInfo$"SII.right" <- sii.right
- patInfo$"SII.left" <- sii.left
-
- if(verbose)
- cat("\nWriting new data table as '", outfile, "'...\n", sep="")
-
- ## Save file
- write.table(patInfo,
- file=outfile,
- row.names=FALSE,
- sep="\t"
- )
-
- if(verbose)
- cat("\nDone.\n\n")
- }
-@
-
-Try it out:
-
-<<RunFun, eval=FALSE>>=
-sii.dina(infile="../AI subject list.xls",
- outfile="../AI subject list-SII.xls")
-@
-
-
-Just for kicks, compare the original AI, and our computed sii values:
-<<CompareAItoSII,results=tex, eval=FALSE>>=
-library(xtable)
-xt <- xtable(patInfo[,c("AI","SII.right","SII.left")],
- caption="Comparison of original AI and new right and left SII values \\label{table}",
- digits=2)
-print(xt)
-@
-
-<<PlotAIandSII,fig=TRUE, eval=FALSE>>=
-## put histograms on the diagonal
-panel.hist <- function(x, ...)
- {
- usr <- par("usr"); on.exit(par(usr))
- par(usr = c(usr[1:2], 0, 1.5) )
- h <- hist(x, plot = FALSE)
- breaks <- h$breaks; nB <- length(breaks)
- y <- h$counts; y <- y/max(y)
- rect(breaks[-nB], 0, breaks[-1], y, col="cyan", ...)
- }
-pairs.2 <- function(x)
- pairs(x,
- panel=panel.smooth,
- cex = 1.5,
- pch = 24,
- bg="light blue",
- diag.panel=panel.hist,
- cex.labels = 2,
- font.labels=2
- )
-
-
-pairs.2(patInfo[,c("AI","SII.right","SII.left")])
-@
-
-
-\clearpage
-\appendix
-
-\section{SII Help Pages}\label{man.pages}
-
-<<echo=FALSE,results=tex>>=
-latexhelp <- function(topics, package=NULL)
- {
- if(missing(topics) && missing(package))
- stop("Help on what?")
- else if (missing(topics))
- {
- callObj <- call("library", help=package)
- topicStrings <- eval(callObj)$info[[2]]
- topicStrings <- lapply( topicStrings, strsplit, split=" ")
- topicStrings <- sapply( topicStrings, function(x) x[[1]][1])
- topicStrings <- topicStrings[topicStrings > " "]
- topics <- topicStrings
- }
-
- for(topic in topics)
- {
- if(!is.character(topic))
- topic <- deparse(substitute(topic))
-
- callObj <- call("help", topic=topic, package=package)
-
- ## Get the file path
- help.file<- as.character(eval(callObj))
-
- ## Get R to translate it to latex and display it
- tools::Rd2latex(utils:::.getHelpFile(help.file))
-
- ## new page
- cat("\n")
- cat("\\clearpage")
- cat("\n")
- }
- }
-
-
-tmp <- function (x, ...)
-{
-}
-
-latexhelp(package="SII")
-
-@
-
-\clearpage
-
-\section{Interpolation}
-
-Do some experimentation to determine how to best perform
-interpolation/extrapolation from the small set of frequencies where
-hearing sensitivity was measured to the set of frequencies necessary
-for the calculation of SII:
-<<splineFit>>=
-
-THDI=c(25,25,30,35,45,45,55,60)
-freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
-
-data(sii.constants)
-sii.freqs <- sii.constants[,1]
-
-xlist <- sort(c(sii.constants[, 1], freq))
-ylist <- rep(NA, length=length(xlist))
-names(ylist) <- xlist
-ylist[ as.character(freq) ] <- THDI
-@
-
-<<interSpline>>=
-library(splines)
-ispl <- interpSpline( THDI ~ freq )
-ispl <- predict(ispl, sii.freqs)$y
-
-ispl.l <- interpSpline( THDI ~ log(freq) )
-ispl.l <- predict(ispl.l, log(sii.freqs) )$y
-
-approx.l <- function(x,y,xout,...)
- {
- retval <- approx(log(x), y, log(xout), ...)
- retval$x <- xout
- retval
- }
-
-@
-
-<<Spline_comparison_function, echo=FALSE>>=
-doplot <- function(logx=FALSE, separate=FALSE)
- {
- if(separate)
- layout( cbind( c(1,2,3,7), c(4,5,6,7) ))
- tmp <- function() {
- plot(x=freq, y=THDI, col="black", cex=2, log=if(logx) "x" else "",
- xlab="Frequency (Herz)", ylab="Threshhold of Detection (dB)",
- xlim=range(sii.freqs), ylim=c(20,60) )
- lines(sii.constants[, 1], sii.constants[, "Ti'.THDN"], col="red", lwd=3)
- abline(v=sii.freqs,lty=3)
- }
-
- tmp()
- lines( x=sii.constants[, 1], y=ispl, col="blue", lwd=2)
-
- if(separate) tmp()
- lines( x=sii.constants[, 1], y=ispl.l, col="cyan", lwd=2)
-
- if(separate) tmp()
- lines( spline (x=freq, y=THDI), col="green", lwd=2)
-
- if(separate) tmp()
- lines( spline (x=freq, y=THDI, method="natural", xout=sii.freqs), col="orange", lwd=2)
-
- if(separate) tmp()
- lines( approx (x=freq, y=THDI, method="linear", xout=sii.freqs, rule=2), col="magenta", lwd=2)
-
- if(separate) tmp()
- lines( approx.l(x=freq, y=THDI, method="linear", xout=sii.freqs, rule=2), col="brown", lwd=3)
-
- if(separate) plot.new()
- legend(if(separate) "center" else { if(logx) "topleft" else "bottomright" },
- legend=c(
- "Measured data",
- "Matlab INTERP1(X, Y, XI, 'spline', 'extrap')",
- "R's predict( interSpline(X,Y), XI )",
- "R's predict( interSpline(log(X),Y), log(XI) )",
- "R's spline(x, y)",
- "R's spline(x, y, method='natural')",
- "R's approx(x, y, method='linear')",
- "R's approx(x, y, method='linear') (on log scale)",
- "Frequencies used for SII calculation"
- ),
- col=c("black", "red", "blue","cyan","green","orange","magenta","brown", "black"),
- pch=c( 1, NA, NA, NA, NA, NA, NA, NA, NA),
- lty=c( NA, 1, 1, 1, 1, 1, 1, 1, 3),
- lwd=c( NA, 3, 2, 2, 2, 2, 2, 2, 1),
- bg="white",
- cex=if(separate) 1.25 else 0.75,
- ncol=if(separate) 2 else 1
- )
- if(separate)
- layout( 1 )
- title(paste("Spline method comparison\n", if(logx)"(log scale)"else"(natural scale)", "\n"))
-
- }
-@
-
-<<natural_scale_one_plot, fig=TRUE, width=8, height=8>>=
-doplot(FALSE, FALSE)
-@
-
-<<natural_scale_separate_plots, fig=TRUE, width=8, height=11>>=
-doplot(FALSE, TRUE)
-@
-
-<<log_scale_one_plot, fig=TRUE, width=8, height=8>>=
-doplot(TRUE, FALSE)
-@
-
-
-<<log_scale_separate_plots, fig=TRUE, width=8, height=11>>=
-doplot(TRUE, TRUE)
-@
-
-
-
-\section{SII function definition}
-
-\subsection{Excel to R translation}
-
-First, I have defined an R function that simply translates the Excel
-code into R:
-
-<<SII:::sii.excel>>=
-args(SII:::sii.excel)
-@
-
-\subsection{R code written from the ANSI S3.5-1997}
-
-
-Second, I implemented the SII calculation following the text of the
-standard. This code is more general and quite a bit more complex.
-
-<<sii>>=
-args(sii)
-@
-
-\subsection{Utility functions}
-
-I also defined a utility function to nicely print the output.
-
-<<sii.print>>=
-
-@
-
-In order to make it easy to maintain the SII contants. A single
-Microsoft Excel file, \verb+\data\SII_Constants.xls+ is included in the
-SII \verb+data+ directory containing the complete set of SII contants,
-where each tab corresponds to one Table from the standard.
-
-<<show.reload.constants>>=
-SII:::reload.constants
-@
-
-The package mainainer may use it as :
-<<run.reload.constants, eval=FALSE>>=
-SII:::reload.constants(xls.path="./SII/extdata")
-@
-
-The SII package must then be rebuilt and reinstalled for the updated
-contants to become available.
-
-
-\section{Tests}
-
-
-\subsection{Compare interpolation details for example data}
-
-
-\subsubsection{Left Ear}
-
-<<ComparisonTable1>>=
-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",
- interpolate=TRUE
- )
-
-
-## comparison of our interpolation and matlab's
-tab <- cbind(
- matlab=sii.constants[,"Ti'.THDN"],
- R =sii.left$table[,"T'i"],
- delta =NA
- )
-tab[,3] <- tab[,1] - tab[,2]
-rownames(tab) <- sii.constants[,".NFreqLin"]
-t(round(tab,2))
-@
-
-<<<plot.sii, show=FALSE>>=
-compare.plot <- function(x, matlab, title)
- {
- plot(x)
- lines(sii.constants[,".NFreqLin"],
- matlab,
- type="l", col="red", lwd=3)
-
- legend("topleft",
- legend=c(
- "Measured data",
- "Matlab INTERP1(X, Y, XI, 'spline', 'extrap')",
- "R's approx(X,Y, XI, xout=XI,\n method='linear', rule=2)"
- ),
- col=c("black", "red","blue","green","orange","magenta"),
- pch=c( 1, NA, 2, NA, NA, NA),
- lty=c( NA, 1, 1, 1, 1, 1),
- lwd=c( NA, 3, 2, 2, 2, 2),
- bg="white"
- )
- title(title)
- }
-@
-
-<<ComparisonFigure1,fig=TRUE>>=
-
-compare.plot(sii.left, matlab=sii.constants[, "Ti'.THDN"], title="Spline method comparison, Left Ear")
-
-@
-
-\subsubsection{Right Ear}
-
-<<ComparisonTable2>>=
-# comparison of our interpolation and matlab's
-
-matlab <- c(15.00, 15.00, 13.34, 14.27, 16.06, 17.82, 19.18, 20.00,
- 20.26, 20.54, 21.44, 23.36, 26.93, 31.38, 34.63, 35.13,
- 35.00, 38.29, 43.98, 48.80, 49.58)
-
-sii.right <- sii(
- speech="raised",
- threshold=c(15,15,20,25,35,35,45,50),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="NU6",
- interpolate=TRUE
- )
-
-tab <- cbind(
- matlab=matlab,
- R =sii.right$table [,"T'i"],
- delta =NA
- )
-tab[,3] <- tab[,1] - tab[,2]
-rownames(tab) <- sii.constants[,".NFreqLin"]
-t(round(tab,2))
-@
-
-<<<ComparisonFigure2,fig=TRUE>>=
-compare.plot(sii.right, matlab=matlab, title="Spline method comparison, Right Ear")
-@
-
-
-\subsection{Comparison with Excel implementation}
-
-Test the SII function using the example data from the Excel worksheet:
-
-\begin{itemize}
- \item Left ear example
-
- Excel code: $0.43$.
-
- ``Translated'' R code:
-<<<sii.left.old>>=
-SII:::sii.excel(
- c(25,25,30,35,45,45,55,60),
- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
- )
-@
-
-
- New R code:
-<<sii.left>>=
-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",
- interpolate=TRUE
- )
-sii.left
-@
-
-
- \item Right ear example
-
- Excel worksheet: $0.72$.
-
- ``Translated'' R code:
-<<<sii.right.old>>=
-SII:::sii.excel(
- c(15,15,20,25,35,35,45,50),
- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
- )
-@
-
- New R code:
-<<sii.right>>=
-sii.right <- sii(
- speech="raised",
- threshold=c(15,15,20,25,35,35,45,50),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="NU6",
- interpolate=TRUE
- )
-sii.right
-@
-
- \item Best possible score (No detectible threshold)
-
- Excel Spreadsheet: $0.9887$
-
- ``Translated'' R code:
-<<<sii.best.old>>=
-SII:::sii.excel(
- rep(0,8),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
- )
-@
-
-
- New R code:
-<<sii.best>>=
-sii.best <- sii(
- threshold=rep(0,8),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- interpolate=TRUE
- )
-sii.best
-@
-
- \item Worst possible score (No detectible threshold)
-
- Excel Spreadsheet: $0.00$
-
- ``Translated'' R code:
-<<<sii.worst.old>>=
-SII:::sii.excel(
- rep(100,8),
- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
- )
-@
-
-
- New R code:
-<<sii.worst>>=
-sii.worst <- sii(
- threshold=rep(100,8),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- interpolate=TRUE
- )
-sii.worst
-@
-
-
-\end{itemize}
-
-\subsection{Test handling of missing values}
-
-<<sii.missing>>=
-sii.worst <- sii(
- threshold=c(NA, rep(100,7)),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- interpolate=TRUE
- )
-sii.worst
-@
-
-<<sii.missing>>=
-sii.right <- sii(
- speech="raised",
- threshold=c(0,15,15,20,25,35,35,45,50),
- freq=c(NA, 250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="NU6",
- interpolate=TRUE
- )
-sii.right
-@
-
-<<sii.all.missing>>=
-## This should fail, because there is no data!
-sii.NONE <- try(
- sii(
- threshold=rep(NA,8),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- interpolate=TRUE
- )
- )
-sii.NONE
-@
-
-
-
-<<sii.missing>>=
-sii.right <- sii(
- speech="raised",
- threshold=c(15,15,20,NA,35,35,45,50),
- freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
- importance="NU6",
- interpolate=TRUE
- )
-sii.right
-@
-
-<<missing.C.1>>=
-sii.C1.NA <- sii(
- speech = c(50.0, 40.0, 40.0, NA, 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, NA, 0.0),
- freq = c( 250, 500, 1000, 2000, 4000, 8000),
- method="octave",
- importance="CST",
- interpolate=TRUE
- )
-sii.C1
-sii.C1.NA
-@
-
-
-
-\section{Final cleanup}
-
-Save the data we created here for debugging purposes:
-<<save data>>=
-save.image("SII-Code.Rda")
-@
-
-%\printindex{}
-
-\end{document}
Copied: trunk/SII/vignettes/SII.Rnw (from rev 1750, trunk/SII/inst/doc/SII.Rnw)
===================================================================
--- trunk/SII/vignettes/SII.Rnw (rev 0)
+++ trunk/SII/vignettes/SII.Rnw 2013-12-06 22:09:14 UTC (rev 1753)
@@ -0,0 +1,913 @@
+% \VignetteIndexEntry{Calculate ANSI S3.5-1997 Speech Intelligibility Index}
+% \VignetteDepends{SII, gdata, xtable, splines}
+% \VignetteKeyword{Speech Intelligibility Index}
+%
+\documentclass[letterpaper]{article}
+\usepackage{Rd}
+\usepackage{Sweave}
+\usepackage[margin=1.0in]{geometry}
+\usepackage{hyperref}
+\parskip=11pt
+\parindent=0mm
+\usepackage{graphicx}
+
+%\usepackage{makeidx}
+%\makeindex{}
+
+%------------------------------------------------------------
+% newcommand
+%------------------------------------------------------------
+\newcommand{\scscst}{\scriptscriptstyle}
+\newcommand{\scst}{\scriptstyle}
+\newcommand{\Robject}[1]{{\texttt{#1}}}
+\newcommand{\Rfunction}[1]{{\texttt{#1}}}
+\newcommand{\Rclass}[1]{\textit{#1}}
+\newcommand{\Rpackage}[1]{\textit{#1}}
+\newcommand{\Rexpression}[1]{\texttt{#1}}
+\newcommand{\Rmethod}[1]{{\texttt{#1}}}
+\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
+%---
+
+
+\setkeys{Gin}{width=\textwidth}
+
+\title{
+ Calculating Speech Intelligibility Index (SII) using R
+}
+\author{
+ Gregory R. Warnes, Ph.D. \\
+ Gregory R. Warnes Consulting
+ }
+
+\begin{document}
+\maketitle
+
+This document describes the calculation of Speech Intelligibility
+Index (SII) using R. The core calculations have been encapsulated as
+an R add-on package named ``SII'', which, once installed, can be
+loaded thusly:
+
+<<load.package>>=
+library(SII)
+@
+
+\section{SII constant tables}
+
+The R package includes constant tables 1 -- 4 from the ANSI S3.5-1997
+text. These can be loaded via
+<<load.data>>=
+## Table 1: Critical band SII procedure constants
+data("critical")
+head(critical)
+
+## Table 2:Equally contributing (17 band) critical band SII
+## procedure constants
+data("equal")
+
+## Table 3: One-third octave band SII procedure constants
+data("onethird")
+
+## Table 4: Octave band SII procedure constants
+data("octave")
+
+## Overall SPL constants
+data("overall.spl")
+overall.spl
+@
+
+It also includes constant tables for alternative transfer functions
+corresponding to different types of message content, tables B.1 --
+B.3. These tables have been augmented with the corresponding values
+for the Connected Speech Test (CST) as given by
+\url{http://www.sii.to/CSTdata.txt}. These tables can be loaded via:
+<<load.alternative.data>>=
+## Table B.1: Critical band importance functions for various speech tests.
+data(sic.critical)
+head(sic.critical)
+
+## Table B.2: One-third octave band importance functions for various speech tests.
+data(sic.onethird)
+
+## Table B.3: Octave band importance functions for various speech tests.
+data(sic.octave)
+@
+
+With the alternative transfer functions available, it becomes easy to
+generate a nice graphical comparison of the functions:
+<<sicplot,fig=TRUE,width=12,height=6>>=
+data(sic.critical)
+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=as.character(1:ngroup),
+ lty=1:ngroup,
+ col=rainbow(ngroup)
+ )
+
+@
+
+\section{Calculating SII}
+
+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 the specified procedure (via the argument
+\code{interpolate=TRUE}). Interpolation is accomplished using linear
+interpolation (on log-scaled data) to the frequencies required for the
+specified SII procedure. Interpolation is performed (if necessary)
+for \code{speech}, \code{noise}, \code{threshold}, and \code{loss}.
+
+The \code{sii} function has the following header:
+<<header>>=
+args(sii)
+@
+
+Where the arguments are:
+\begin{description}
+ \item[speech] Speech spectrum level, as a standard level name
+ ("normal", "raised", "loud", or "shout")or a vector of values, in dB
+ \item[noise] Noise spectrum level, in dB
+ \item[threshold] Hearing threshold level, in dB
+ \item[loss] Conductive hearing loss level, in dB
+ \item[freq] Frequencies at which values are provided (required if
+ interpolate=TRUE)
+ \item[method] SII calculation method, one of "critical",
+ "equal-contributing", "one-third octave", "octave".
+ \item[importance] Transfer function (importance weights), as a
+ standard SII measurement name ("SII", "NNS", "CID22", "NU6", "DRT",
+ "ShortPassage", "SPIN", or "CST")
+ \item[interpolate] Flag indicating whether to interpolate
+ from the provide measurement values and frequencies to those
+ required by the specified method
+\end{description}
+
+For a detailed description of the arguments see the \Rfunction{sii}
+manual page in appendix \ref{man.pages}.
+
+\subsection{Example C.1 from ANSI S3.5-1997 Annex C}
+
+<<ExampleC.1>>=
+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"
+ #, importance="SII"
+ #, importance=octave$Ii
+ , importance="CST"
+ )
+round(sii.C1$table[,-c(5:7,13)],2)
+sii.C1$sii
+@
+
+The value given in the Standard is $0.504$.
+
+\subsection{Example C.2 from ANSI S3.5-1997 Annex C}
+
+<<ExampleC.1>>=
+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$table[1:3,1:8]
+sii.C2$sii
+@
+
+The standard shows the first three rows in the table as
+
+\begin{center}
+\begin{tabular}{rrrrrrrrr}
+ \hline
+ & Fi & E'i & N'i & T'i & Vi & Bi & Ci & Zi \\
+ \hline
+ 1 & 160 & 54.00 & 40.00 & 0.00 & 30.00 & 40.00 & $-$46.59\footnote{Typo in the standard document} & 40.00 \\
+ 2 & 200 & 54.00 & 30.00 & 0.00 & 30.00 & 30.00 & $-$52.01 & 34.66 \\
+ 3 & 250 & 54.00 & 20.00 & 0.00 & 30.00 & 30.00 & $-$51.42 & 25.04 \\
+ \hline
+\end{tabular}
+\end{center}
+
+
+\subsection{Interpolation Example}
+
+<<ExampleC.1>>=
+sii.C1 <- sii(
+ speech = c(50.0, 40.0, 40.0, 30.0, 20.0, 0.0),
+ noise = c(70.0, 65.0, 45.0, 25.0, 1.0,-15.0),
+ threshold= c( 0.0, 0.0, 0.0, 0.0, 0.0, 0.0),
+ method="octave"
+ #, importance="SII"
+ #, importance=octave$Ii
+ , importance="CST"
+ )
+round(sii.C1$table[,-c(5:7,13)],2)
+sii.C1$sii
+@
+
+The value given in the Standard is $0.504$.
+
+
+\subsection{Calculating SII for a set of patients}
+
+First, we need to load the patient information table
+<<LoadData, eval=FALSE>>=
+library(gdata)
+patInfo <- read.xls("../AI subject list.xls")
+@
+
+Check that we got the data properly read in:
+<<ExamineData, eval=FALSE>>=
+## Information about variables
+str(patInfo)
+@
+
+<<ExamineData, eval=FALSE>>=
+## First 6 rows
+head(patInfo)
+@
+
+Create some useful variables:
+<<vars, eval=FALSE>>=
+## measured frequencies
+freq <- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+
+## columns containing frequencies for the right/left ear
+rt.cols <- paste("PTR",freq, sep="")
+lt.cols <- paste("PTL",freq, sep="")
+
+rt.vals <- patInfo[,rt.cols]
+lt.vals <- patInfo[,lt.cols]
+@
+
+Handle missing value encoding
+<<missing, eval=FALSE>>=
+rt.vals[rt.vals==-888] <- NA
+lt.vals[rt.vals==-888] <- NA
+@
+
+Now, construct a utility function to handle an individual patient's
+SII calculation using the arguments we want.
+<<fun, eval=FALSE>>=
+fun <- function(X)
+ {
+ ret <- try(
+ sii(X,
+ speech="raised",
+ threshold=c(15,15,20,25,35,35,45,50),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="SII",
+ interpolate=TRUE
+ )$sii
+ )
+ if("try-error" %in% class(ret))
+ return(NA)
+ else
+ return(ret)
+ }
+
+## Test it
+fun( rt.vals[1,] )
+@
+
+
+Now apply it for the right and left ears:
+<<CalculateSII, eval=FALSE>>=
+sii.right <- apply(rt.vals, 1, fun )
+
+sii.left <- apply(lt.vals, 1, fun )
+@
+
+Now add theses back onto our table:
+<<AddSIIToTable, eval=FALSE>>=
+patInfo$"SII.right" <- sii.right
+patInfo$"SII.left" <- sii.left
+
+tail(patInfo)
+@
+
+And save to a file:
+<<SavePatInfo, eval=FALSE>>=
+write.table(patInfo,
+ file="../AI subject list-SII.xls",
+ row.names=FALSE,
+ sep="\t"
+ )
+@
+
+Now define a function to do all of this with a single call
+
+<<SIIFileFun, eval=FALSE>>=
+sii.dina <- function(infile, outfile, verbose=TRUE)
+ {
+ if(verbose)
+ cat("\nLoading data file '", infile, "'...\n", sep="")
+ ## Load the data
+ library(gdata)
+ patInfo <- read.xls(infile)
+
+ ## measured frequencies
+ freq <- c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+
+ if(verbose)
+ cat("\nExtracting hearing thresholds...\n")
+
+ ## columns containing frequencies for the right/left ear
+ rt.cols <- paste("PTR",freq, sep="")
+ lt.cols <- paste("PTL",freq, sep="")
+
+ rt.vals <- patInfo[,rt.cols]
+ lt.vals <- patInfo[,lt.cols]
+
+ ## Handle missing code '-888'
+ rt.vals[rt.vals==-888] <- NA
+ lt.vals[rt.vals==-888] <- NA
+
+ ## define function to compute SII with our defaults
+ fun <- function(X)
+ {
+ ret <- try(
+ sii(X,
+ speech="raised",
+ threshold=c(15,15,20,25,35,35,45,50),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="SII",
+ interpolate=TRUE
+ )$sii #$
+ )
+ if("try-error" %in% class(ret))
+ return(NA)
+ else
+ return(ret)
+ }
+
+ ## Calculate SII
+ if(verbose)
+ cat("\nCalculating right ear SII...\n")
+ sii.right <- apply(rt.vals, 1, fun )
+ if(verbose)
+ cat("\nCalculating left ear SII...\n")
+ sii.left <- apply(lt.vals, 1, fun )
+
+ ## Add back onto the table
+ patInfo$"SII.right" <- sii.right
+ patInfo$"SII.left" <- sii.left
+
+ if(verbose)
+ cat("\nWriting new data table as '", outfile, "'...\n", sep="")
+
+ ## Save file
+ write.table(patInfo,
+ file=outfile,
+ row.names=FALSE,
+ sep="\t"
+ )
+
+ if(verbose)
+ cat("\nDone.\n\n")
+ }
+@
+
+Try it out:
+
+<<RunFun, eval=FALSE>>=
+sii.dina(infile="../AI subject list.xls",
+ outfile="../AI subject list-SII.xls")
+@
+
+
+Just for kicks, compare the original AI, and our computed sii values:
+<<CompareAItoSII,results=tex, eval=FALSE>>=
+library(xtable)
+xt <- xtable(patInfo[,c("AI","SII.right","SII.left")],
+ caption="Comparison of original AI and new right and left SII values \\label{table}",
+ digits=2)
+print(xt)
+@
+
+<<PlotAIandSII,fig=TRUE, eval=FALSE>>=
+## put histograms on the diagonal
+panel.hist <- function(x, ...)
+ {
+ usr <- par("usr"); on.exit(par(usr))
+ par(usr = c(usr[1:2], 0, 1.5) )
+ h <- hist(x, plot = FALSE)
+ breaks <- h$breaks; nB <- length(breaks)
+ y <- h$counts; y <- y/max(y)
+ rect(breaks[-nB], 0, breaks[-1], y, col="cyan", ...)
+ }
+pairs.2 <- function(x)
+ pairs(x,
+ panel=panel.smooth,
+ cex = 1.5,
+ pch = 24,
+ bg="light blue",
+ diag.panel=panel.hist,
+ cex.labels = 2,
+ font.labels=2
+ )
+
+
+pairs.2(patInfo[,c("AI","SII.right","SII.left")])
+@
+
+
+\clearpage
+\appendix
+
+\section{SII Help Pages}\label{man.pages}
+
+<<echo=FALSE,results=tex>>=
+latexhelp <- function(topics, package=NULL)
+ {
+ if(missing(topics) && missing(package))
+ stop("Help on what?")
+ else if (missing(topics))
+ {
+ callObj <- call("library", help=package)
+ topicStrings <- eval(callObj)$info[[2]]
+ topicStrings <- lapply( topicStrings, strsplit, split=" ")
+ topicStrings <- sapply( topicStrings, function(x) x[[1]][1])
+ topicStrings <- topicStrings[topicStrings > " "]
+ topics <- topicStrings
+ }
+
+ for(topic in topics)
+ {
+ if(!is.character(topic))
+ topic <- deparse(substitute(topic))
+
+ callObj <- call("help", topic=topic, package=package)
+
+ ## Get the file path
+ help.file<- as.character(eval(callObj))
+
+ ## Get R to translate it to latex and display it
+ tools::Rd2latex(utils:::.getHelpFile(help.file))
+
+ ## new page
+ cat("\n")
+ cat("\\clearpage")
+ cat("\n")
+ }
+ }
+
+
+tmp <- function (x, ...)
+{
+}
+
+latexhelp(package="SII")
+
+@
+
+\clearpage
+
+\section{Interpolation}
+
+Do some experimentation to determine how to best perform
+interpolation/extrapolation from the small set of frequencies where
+hearing sensitivity was measured to the set of frequencies necessary
+for the calculation of SII:
+<<splineFit>>=
+
+THDI=c(25,25,30,35,45,45,55,60)
+freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+
+data(sii.constants)
+sii.freqs <- sii.constants[,1]
+
+xlist <- sort(c(sii.constants[, 1], freq))
+ylist <- rep(NA, length=length(xlist))
+names(ylist) <- xlist
+ylist[ as.character(freq) ] <- THDI
+@
+
+<<interSpline>>=
+library(splines)
+ispl <- interpSpline( THDI ~ freq )
+ispl <- predict(ispl, sii.freqs)$y
+
+ispl.l <- interpSpline( THDI ~ log(freq) )
+ispl.l <- predict(ispl.l, log(sii.freqs) )$y
+
+approx.l <- function(x,y,xout,...)
+ {
+ retval <- approx(log(x), y, log(xout), ...)
+ retval$x <- xout
+ retval
+ }
+
+@
+
+<<Spline_comparison_function, echo=FALSE>>=
+doplot <- function(logx=FALSE, separate=FALSE)
+ {
+ if(separate)
+ layout( cbind( c(1,2,3,7), c(4,5,6,7) ))
+ tmp <- function() {
+ plot(x=freq, y=THDI, col="black", cex=2, log=if(logx) "x" else "",
+ xlab="Frequency (Herz)", ylab="Threshhold of Detection (dB)",
+ xlim=range(sii.freqs), ylim=c(20,60) )
+ lines(sii.constants[, 1], sii.constants[, "Ti'.THDN"], col="red", lwd=3)
+ abline(v=sii.freqs,lty=3)
+ }
+
+ tmp()
+ lines( x=sii.constants[, 1], y=ispl, col="blue", lwd=2)
+
+ if(separate) tmp()
+ lines( x=sii.constants[, 1], y=ispl.l, col="cyan", lwd=2)
+
+ if(separate) tmp()
+ lines( spline (x=freq, y=THDI), col="green", lwd=2)
+
+ if(separate) tmp()
+ lines( spline (x=freq, y=THDI, method="natural", xout=sii.freqs), col="orange", lwd=2)
+
+ if(separate) tmp()
+ lines( approx (x=freq, y=THDI, method="linear", xout=sii.freqs, rule=2), col="magenta", lwd=2)
+
+ if(separate) tmp()
+ lines( approx.l(x=freq, y=THDI, method="linear", xout=sii.freqs, rule=2), col="brown", lwd=3)
+
+ if(separate) plot.new()
+ legend(if(separate) "center" else { if(logx) "topleft" else "bottomright" },
+ legend=c(
+ "Measured data",
+ "Matlab INTERP1(X, Y, XI, 'spline', 'extrap')",
+ "R's predict( interSpline(X,Y), XI )",
+ "R's predict( interSpline(log(X),Y), log(XI) )",
+ "R's spline(x, y)",
+ "R's spline(x, y, method='natural')",
+ "R's approx(x, y, method='linear')",
+ "R's approx(x, y, method='linear') (on log scale)",
+ "Frequencies used for SII calculation"
+ ),
+ col=c("black", "red", "blue","cyan","green","orange","magenta","brown", "black"),
+ pch=c( 1, NA, NA, NA, NA, NA, NA, NA, NA),
+ lty=c( NA, 1, 1, 1, 1, 1, 1, 1, 3),
+ lwd=c( NA, 3, 2, 2, 2, 2, 2, 2, 1),
+ bg="white",
+ cex=if(separate) 1.25 else 0.75,
+ ncol=if(separate) 2 else 1
+ )
+ if(separate)
+ layout( 1 )
+ title(paste("Spline method comparison\n", if(logx)"(log scale)"else"(natural scale)", "\n"))
+
+ }
+@
+
+<<natural_scale_one_plot, fig=TRUE, width=8, height=8>>=
+doplot(FALSE, FALSE)
+@
+
+<<natural_scale_separate_plots, fig=TRUE, width=8, height=11>>=
+doplot(FALSE, TRUE)
+@
+
+<<log_scale_one_plot, fig=TRUE, width=8, height=8>>=
+doplot(TRUE, FALSE)
+@
+
+
+<<log_scale_separate_plots, fig=TRUE, width=8, height=11>>=
+doplot(TRUE, TRUE)
+@
+
+
+
+\section{SII function definition}
+
+\subsection{Excel to R translation}
+
+First, I have defined an R function that simply translates the Excel
+code into R:
+
+<<SII:::sii.excel>>=
+args(SII:::sii.excel)
+@
+
+\subsection{R code written from the ANSI S3.5-1997}
+
+
+Second, I implemented the SII calculation following the text of the
+standard. This code is more general and quite a bit more complex.
+
+<<sii>>=
+args(sii)
+@
+
+\subsection{Utility functions}
+
+I also defined a utility function to nicely print the output.
+
+<<sii.print>>=
+
+@
+
+In order to make it easy to maintain the SII contants. A single
+Microsoft Excel file, \verb+\data\SII_Constants.xls+ is included in the
+SII \verb+data+ directory containing the complete set of SII contants,
+where each tab corresponds to one Table from the standard.
+
+<<show.reload.constants>>=
+SII:::reload.constants
+@
+
+The package mainainer may use it as :
+<<run.reload.constants, eval=FALSE>>=
+SII:::reload.constants(xls.path="./SII/extdata")
+@
+
+The SII package must then be rebuilt and reinstalled for the updated
+contants to become available.
+
+
+\section{Tests}
+
+
+\subsection{Compare interpolation details for example data}
+
+
+\subsubsection{Left Ear}
+
+<<ComparisonTable1>>=
+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",
+ interpolate=TRUE
+ )
+
+
+## comparison of our interpolation and matlab's
+tab <- cbind(
+ matlab=sii.constants[,"Ti'.THDN"],
+ R =sii.left$table[,"T'i"],
+ delta =NA
+ )
+tab[,3] <- tab[,1] - tab[,2]
+rownames(tab) <- sii.constants[,".NFreqLin"]
+t(round(tab,2))
+@
+
+<<<plot.sii, show=FALSE>>=
+compare.plot <- function(x, matlab, title)
+ {
+ plot(x)
+ lines(sii.constants[,".NFreqLin"],
+ matlab,
+ type="l", col="red", lwd=3)
+
+ legend("topleft",
+ legend=c(
+ "Measured data",
+ "Matlab INTERP1(X, Y, XI, 'spline', 'extrap')",
+ "R's approx(X,Y, XI, xout=XI,\n method='linear', rule=2)"
+ ),
+ col=c("black", "red","blue","green","orange","magenta"),
+ pch=c( 1, NA, 2, NA, NA, NA),
+ lty=c( NA, 1, 1, 1, 1, 1),
+ lwd=c( NA, 3, 2, 2, 2, 2),
+ bg="white"
+ )
+ title(title)
+ }
+@
+
+<<ComparisonFigure1,fig=TRUE>>=
+
+compare.plot(sii.left, matlab=sii.constants[, "Ti'.THDN"], title="Spline method comparison, Left Ear")
+
+@
+
+\subsubsection{Right Ear}
+
+<<ComparisonTable2>>=
+# comparison of our interpolation and matlab's
+
+matlab <- c(15.00, 15.00, 13.34, 14.27, 16.06, 17.82, 19.18, 20.00,
+ 20.26, 20.54, 21.44, 23.36, 26.93, 31.38, 34.63, 35.13,
+ 35.00, 38.29, 43.98, 48.80, 49.58)
+
+sii.right <- sii(
+ speech="raised",
+ threshold=c(15,15,20,25,35,35,45,50),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="NU6",
+ interpolate=TRUE
+ )
+
+tab <- cbind(
+ matlab=matlab,
+ R =sii.right$table [,"T'i"],
+ delta =NA
+ )
+tab[,3] <- tab[,1] - tab[,2]
+rownames(tab) <- sii.constants[,".NFreqLin"]
+t(round(tab,2))
+@
+
+<<<ComparisonFigure2,fig=TRUE>>=
+compare.plot(sii.right, matlab=matlab, title="Spline method comparison, Right Ear")
+@
+
+
+\subsection{Comparison with Excel implementation}
+
+Test the SII function using the example data from the Excel worksheet:
+
+\begin{itemize}
+ \item Left ear example
+
+ Excel code: $0.43$.
+
+ ``Translated'' R code:
+<<<sii.left.old>>=
+SII:::sii.excel(
+ c(25,25,30,35,45,45,55,60),
+ c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+ )
+@
+
+
+ New R code:
+<<sii.left>>=
+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",
+ interpolate=TRUE
+ )
+sii.left
+@
+
+
+ \item Right ear example
+
+ Excel worksheet: $0.72$.
+
+ ``Translated'' R code:
+<<<sii.right.old>>=
+SII:::sii.excel(
+ c(15,15,20,25,35,35,45,50),
+ c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+ )
+@
+
+ New R code:
+<<sii.right>>=
+sii.right <- sii(
+ speech="raised",
+ threshold=c(15,15,20,25,35,35,45,50),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="NU6",
+ interpolate=TRUE
+ )
+sii.right
+@
+
+ \item Best possible score (No detectible threshold)
+
+ Excel Spreadsheet: $0.9887$
+
+ ``Translated'' R code:
+<<<sii.best.old>>=
+SII:::sii.excel(
+ rep(0,8),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+ )
+@
+
+
+ New R code:
+<<sii.best>>=
+sii.best <- sii(
+ threshold=rep(0,8),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ interpolate=TRUE
+ )
+sii.best
+@
+
+ \item Worst possible score (No detectible threshold)
+
+ Excel Spreadsheet: $0.00$
+
+ ``Translated'' R code:
+<<<sii.worst.old>>=
+SII:::sii.excel(
+ rep(100,8),
+ c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000)
+ )
+@
+
+
+ New R code:
+<<sii.worst>>=
+sii.worst <- sii(
+ threshold=rep(100,8),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ interpolate=TRUE
+ )
+sii.worst
+@
+
+
+\end{itemize}
+
+\subsection{Test handling of missing values}
+
+<<sii.missing>>=
+sii.worst <- sii(
+ threshold=c(NA, rep(100,7)),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ interpolate=TRUE
+ )
+sii.worst
+@
+
+<<sii.missing>>=
+sii.right <- sii(
+ speech="raised",
+ threshold=c(0,15,15,20,25,35,35,45,50),
+ freq=c(NA, 250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="NU6",
+ interpolate=TRUE
+ )
+sii.right
+@
+
+<<sii.all.missing>>=
+## This should fail, because there is no data!
+sii.NONE <- try(
+ sii(
+ threshold=rep(NA,8),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ interpolate=TRUE
+ )
+ )
+sii.NONE
+@
+
+
+
+<<sii.missing>>=
+sii.right <- sii(
+ speech="raised",
+ threshold=c(15,15,20,NA,35,35,45,50),
+ freq=c(250, 500, 1000, 2000, 3000, 4000, 6000, 8000),
+ importance="NU6",
+ interpolate=TRUE
+ )
+sii.right
+@
+
+<<missing.C.1>>=
+sii.C1.NA <- sii(
+ speech = c(50.0, 40.0, 40.0, NA, 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, NA, 0.0),
+ freq = c( 250, 500, 1000, 2000, 4000, 8000),
+ method="octave",
+ importance="CST",
+ interpolate=TRUE
+ )
+sii.C1
+sii.C1.NA
+@
+
+
+
+\section{Final cleanup}
+
+Save the data we created here for debugging purposes:
+<<save data>>=
+save.image("SII-Code.Rda")
+@
+
+%\printindex{}
+
+\end{document}
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|
From: <wa...@us...> - 2013-12-06 22:03:20
|
Revision: 1752
http://sourceforge.net/p/r-gregmisc/code/1752
Author: warnes
Date: 2013-12-06 22:03:18 +0000 (Fri, 06 Dec 2013)
Log Message:
-----------
Add comment
Modified Paths:
--------------
trunk/SII/R/sii.excel.R
Modified: trunk/SII/R/sii.excel.R
===================================================================
--- trunk/SII/R/sii.excel.R 2013-12-06 21:40:11 UTC (rev 1751)
+++ trunk/SII/R/sii.excel.R 2013-12-06 22:03:18 UTC (rev 1752)
@@ -10,6 +10,7 @@
if(length(THDI) != length(freq))
stop("THDI must have the same length as freq")
+ ## Load constants into *this* environment
data(sii.constants, package="SII", envir=parent.frame())
# Interpolate unobserved frequencies
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