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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1920] trunk/gtools
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From: <wa...@us...> - 2015-04-09 19:45:29
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Revision: 1920
http://sourceforge.net/p/r-gregmisc/code/1920
Author: warnes
Date: 2015-04-09 19:45:21 +0000 (Thu, 09 Apr 2015)
Log Message:
-----------
Move first()/last()/left()/right() to gdata.
Add new functions na.replace() and loadedPackages().
Add more text to package description.
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/NAMESPACE
trunk/gtools/inst/ChangeLog
trunk/gtools/inst/NEWS
Added Paths:
-----------
trunk/gtools/R/loadedPackages.R
trunk/gtools/R/na.replace.R
trunk/gtools/man/loadedPackages.Rd
trunk/gtools/man/na.replace.Rd
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/DESCRIPTION 2015-04-09 19:45:21 UTC (rev 1920)
@@ -1,8 +1,25 @@
Package: gtools
-Title: Various R programming tools
-Description: Various R programming tools
-Version: 3.5.0
-Date: 2014-10-09
+Title: Various R Programming Tools
+Description: Functions to assist in R programming, including:
+ - assist in developing, updating, and maintaning R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'),
+ - calculate the logit and inverse logit transformations ('logit', 'inv.logit')
+ - test if a value is missing, empty or contains only NA and NULL values ('invalid')
+ - manipulate R's .Last function ('addLast')
+ - define macros ('defmacro'),
+ - detect odd and even integers ('odd', 'even')
+ - convert strings containig non-ascii characters (like single quotes) to plain ASCII ('ASCIIfy'),
+ - perform a binary search ('binseach')
+ - sort strings containing both numeric and character components ('mixedsort')
+ - create a factor variable from the quantiles of a continuous variable ('quantcut')
+ - enumerate permutations and combinations ('combinations', 'permutation'),
+ - calculate and convert betwen fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'),
+ - calculate probablities and generate random numbers from dirichlet distributions ('rdirichlet', 'ddirichlet')
+ - apply a function over adjacent subsets of a vector ('running')
+ - Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects
+ - Efficient rbind of data frames, even if the column names don't match ('smartbind')
+ - Generate significance stars from p-values ('stars.pval')
+Version: 3.4.2
+Date: 2015-04-06
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 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/NAMESPACE 2015-04-09 19:45:21 UTC (rev 1920)
@@ -19,10 +19,12 @@
invalid,
keywords,
lastAdd,
+ loadedPackages,
logit,
logratio2foldchange,
mixedorder,
mixedsort,
+ na.replace,
odd,
permutations,
permute,
Added: trunk/gtools/R/loadedPackages.R
===================================================================
--- trunk/gtools/R/loadedPackages.R (rev 0)
+++ trunk/gtools/R/loadedPackages.R 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,12 @@
+loadedPackages <- function(silent=FALSE)
+{
+ packageNames <- loadedNamespaces()
+ packageVersions <- sapply(packageNames, function(package) paste(packageVersion(package), sep=".") )
+ packagePaths <- find.package(packageNames)
+ inSearchPath <- match(packageNames, gsub('^package:', '', grep('^package:', search(), value=TRUE)))
+ retval <- data.frame(Name=packageNames, Version=packageVersions, Path=packagePaths, SearchPath=inSearchPath)
+ retval$SearchPath <- na.replace(retval$SearchPath, '-')
+ retval <- retval[order(inSearchPath),]
+ if(!silent) print(retval)
+ retval
+}
Added: trunk/gtools/R/na.replace.R
===================================================================
--- trunk/gtools/R/na.replace.R (rev 0)
+++ trunk/gtools/R/na.replace.R 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,5 @@
+na.replace <- function(x, replace)
+{
+ x[is.na(x)] <- replace
+ x
+}
Modified: trunk/gtools/inst/ChangeLog
===================================================================
--- trunk/gtools/inst/ChangeLog 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/inst/ChangeLog 2015-04-09 19:45:21 UTC (rev 1920)
@@ -1,5 +1,8 @@
2015-04-06 warnes
+ * [r1918] man/dirichlet.Rd: Correct URL
+ * [r1917] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
+ gtools 3.5.0
* [r1916] inst/ChangeLog: Add ChangeLog files to repository
* [r1915] R/keywords.R: Implement fix to keywords() needed for
R-3.4.1, as suggested by Kurt
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/inst/NEWS 2015-04-09 19:45:21 UTC (rev 1920)
@@ -1,13 +1,13 @@
-gtools 3.5.0 - 2015-04-06
+gtools 3.4.2 - 2015-04-06
-------------------------
New features:
-- New functions first() and last() to retrun the first or last
- element of a vector or list.
+- New function loadedPackages() to display name, version, and path of
+ loaded packages (package namespaces).
-- New functions left() and right() to return the leftmost or
- rightmost n (default to 6) columns of a matrix or dataframe.
+- New function: na.replace() to replace missing values within a
+ vector with a specified value.`
Bug fixes:
Added: trunk/gtools/man/loadedPackages.Rd
===================================================================
--- trunk/gtools/man/loadedPackages.Rd (rev 0)
+++ trunk/gtools/man/loadedPackages.Rd 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,37 @@
+\name{loadedPackages}
+\alias{loadedPackages}
+\title{
+ Provide Name, Version, and Path of Loaded Package Namespaces
+}
+\description{
+ Provide name, version, and path of loaded package namespaces
+}
+\usage{
+loadedPackages(silent = FALSE)
+}
+\arguments{
+ \item{silent}{Logical indicating whether the results should be printed}
+}
+\value{
+ Data frame containing one row per loaded package namespace, with columns:
+ \item{Package}{Package name}
+ \item{Version}{Version string}
+ \item{Path}{Path to package files}
+ \item{SearchPath}{Either the index of the package namespace in the current
+ search path, or '-' if the package namespace is not in the search
+ path. '1' corresponds to the top of the search path (the first namespace
+ searched for values). }
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link[base]{loadedNamespaces}},
+ \code{\link[utils]{packageVersion}},
+ \code{\link[base]{search}},
+ \code{\link[base]{find.package}}
+}
+\examples{
+ loadedPackages()
+}
+\keyword{package}
Added: trunk/gtools/man/na.replace.Rd
===================================================================
--- trunk/gtools/man/na.replace.Rd (rev 0)
+++ trunk/gtools/man/na.replace.Rd 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,34 @@
+\name{na.replace}
+\alias{na.replace}
+\title{
+ Replace Missing Values
+}
+\description{
+ Replace missing values
+}
+\usage{
+na.replace(x, replace)
+}
+\arguments{
+ \item{x}{vector possibly contining missing (\code{NA}) values.}
+ \item{replace}{scalar replacement value}
+}
+\details{
+ This is a convenience function that is the same as
+ x[is.na(x)] <- replace
+}
+\value{
+ Vector with missing values (\code{NA}) replaced by the
+ value of \code{replace}.
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link[base]{is.na}}, \code{\link[stats]{na.omit}}
+}
+\examples{
+ x <- c(1,2,3,NA,6,7,8,NA,NA)
+ na.replace(x, '999')
+}
+\keyword{ manip }
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