Commit b8a9feb3fd5a2f98687764bf2c71391cd54affe4 - gtools

+43

-0

ChangeLog less more

	0	2015-04-09 warnes
	1
	2	* [r1920] DESCRIPTION, NAMESPACE, R/loadedPackages.R,
	3	R/na.replace.R, inst/ChangeLog, inst/NEWS, man/loadedPackages.Rd,
	4	man/na.replace.Rd: Move first()/last()/left()/right() to gdata.
	5	Add new functions na.replace() and loadedPackages().
	6	Add more text to package description.
	7
	8	2015-04-08 warnes
	9
	10	* [r1919] NAMESPACE, R/first.R, man/first.Rd, man/left.Rd: Move
	11	first/last/left/right to from gtools to gdata
	12
	13	2015-04-06 warnes
	14
	15	* [r1918] man/dirichlet.Rd: Correct URL
	16	* [r1917] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
	17	gtools 3.5.0
	18	* [r1916] inst/ChangeLog: Add ChangeLog files to repository
	19	* [r1915] R/keywords.R: Implement fix to keywords() needed for
	20	R-3.4.1, as suggested by Kurt
	21	Hornik.
	22	* [r1914] NAMESPACE, R/first.R: - Export S3 methods for first(),
	23	last(), left() and right().
	24	- Ensure code matches man page for first(), last(), left(), and
	25	right().
	26
	27	2014-10-09 warnes
	28
	29	* [r1897] DESCRIPTION, inst/NEWS: Update for 3.5.0 release of
	30	gtools
	31	* [r1896] R/first.R: Make right() and left() S3 methods for classes
	32	data.frame and matrix
	33
	34	2014-08-27 warnes
	35
	36	* [r1872] man/first.Rd: Fix man page
	37	* [r1871] DESCRIPTION, NAMESPACE, R/first.R, man/first.Rd,
	38	man/left.Rd: Finish adding first(), last(), left(), and right().
	39	* [r1870] R/first.R: Add functions first(), last(), left(), and
	40	right().
	41
0	42	2014-05-28 warnes
1	43
	44	* [r1816] DESCRIPTION, inst/NEWS: Update for gtools 3.4.1
2	45	* [r1815] tests/smartbind_Dates.R: Add test to ensure smartbind()
3	46	properly handles Date columns.
4	47	* [r1814] R/smartbind.R: smartbind: Convert non-native type columns

+26

-6

DESCRIPTION less more

0	0	Package: gtools
1		Title: Various R programming tools
2		Description: Various R programming tools
3		Version: 3.4.1
4		Date: 2014-05-27
	1	Title: Various R Programming Tools
	2	Description: Functions to assist in R programming, including:
	3	- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
	4	'getDependencies', 'keywords', 'scat'),
	5	- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
	6	- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
	7	- manipulate R's .Last function ('addLast'),
	8	- define macros ('defmacro'),
	9	- detect odd and even integers ('odd', 'even'),
	10	- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
	11	- perform a binary search ('binseach'),
	12	- sort strings containing both numeric and character components ('mixedsort'),
	13	- create a factor variable from the quantiles of a continuous variable ('quantcut'),
	14	- enumerate permutations and combinations ('combinations', 'permutation'),
	15	- calculate and convert between fold-change and log-ratio ('foldchange',
	16	'logratio2foldchange', 'foldchange2logratio'),
	17	- calculate probabilities and generate random numbers from Dirichlet distributions
	18	('rdirichlet', 'ddirichlet'),
	19	- apply a function over adjacent subsets of a vector ('running'),
	20	- Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
	21	- Efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
	22	- Generate significance stars from p-values ('stars.pval').
	23	Version: 3.4.2
	24	Date: 2015-04-06
5	25	Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
6	26	Maintainer: Gregory R. Warnes <greg@warnes.net>
7	27	License: LGPL-2.1
8		Packaged: 2014-05-28 00:24:58 UTC; warnes
	28	Packaged: 2015-04-10 12:37:28 UTC; gwarnes1
9	29	NeedsCompilation: yes
10	30	Repository: CRAN
11		Date/Publication: 2014-05-28 09:52:04
	31	Date/Publication: 2015-04-10 14:48:31

+12

-8

MD5 less more

0		d9acafea0ae89a962d136c4714fa6e88 *ChangeLog
1		3339377e32f1c247e472340e800d09dc *DESCRIPTION
2		eaba4455ced37627eb4ad325c2038794 *NAMESPACE
3		a8644a8081da8428987ac599a8287f32 *NEWS
	0	8ce65e8748f62a15a845d463ef9dc4ce *ChangeLog
	1	799ef0349c13933fc12a76ecb5f602c8 *DESCRIPTION
	2	f8ec272fd1610ad963b6fc8fb5469b64 *NAMESPACE
	3	4b56bef437760c3635aaf7a0b28b33c7 *NEWS
4	4	40be776640196133aebff67618b08dec *R/ASCIIfy.R
5	5	9eb418fd95aa09ba85aed159545dea61 *R/RSCompat.S
6	6	a86a74ba04089ad58ea22e3a994a9b14 *R/addLast.R

16	16	1da2198e1d194c705ca89381159b7b63 *R/foldchange.R
17	17	e759eb4772cb9ce930a0c570279155b3 *R/getDependencies.R
18	18	71212f4c14003458fc3e30638f339629 *R/invalid.R
19		11fc8cb8e4bd7c93cd8edefe54b9c64c *R/keywords.R
	19	3f3921bb8ada00eb6fbf7332d689e108 *R/keywords.R
20	20	f00dfc3263a5854151f244493b3f04d0 *R/lastAdd.R
	21	66f7bacaa290264693ee1b4cbe4cadc8 *R/loadedPackages.R
21	22	2bb525e1930ec3ba2afefa2ff43d74e0 *R/logit.R
22	23	a3ec77919e3a6792f88a0aa39fae4841 *R/mixedsort.R
	24	429ab819b15f97c8dd6e62db278336d9 *R/na.replace.R
23	25	93a46a6ef5937bdd112468daceac00a6 *R/newVersionAvailable.R
24	26	07cd779ab7e64f697604b8b4fa4c9d70 *R/oddeven.R
25	27	1d016a924dd59daa78ea62d986da2929 *R/permute.R

31	33	ef22fb4007dec9fb62eb5ed947292fa3 *R/stars.pval.R
32	34	e8f510e73bd2cd820c384c00d75b0080 *R/strmacro.R
33	35	d2d2d0444a049d74694203974624835c *data/ELISA.rda
34		d9acafea0ae89a962d136c4714fa6e88 *inst/ChangeLog
35		a8644a8081da8428987ac599a8287f32 *inst/NEWS
	36	8ce65e8748f62a15a845d463ef9dc4ce *inst/ChangeLog
	37	4b56bef437760c3635aaf7a0b28b33c7 *inst/NEWS
36	38	05087d9c7f92db0ac048dec226e7bc3a *man/ASCIIfy.Rd
37	39	904304f52b08ec847904ac2aa5be9aef *man/ELISA.Rd
38	40	c5b7124f5fdbcc83f2e283314df95858 *man/ask.Rd

40	42	e1a3f01f01db3e883397eaa49037af6f *man/checkRVersion.Rd
41	43	0b2fba4b1456254689640add6afec843 *man/combinations.Rd
42	44	1c240ef01582dd99e3a2e432e7dfb2ba *man/defmacro.Rd
43		22b71a514ea7acc360552527394ce9c1 *man/dirichlet.Rd
	45	3ac18878a63f7ca4913f66d5ecb72a4a *man/dirichlet.Rd
44	46	74868a3948263db0fbc2519b792acba2 *man/foldchange.Rd
45	47	c208ca0a5e9c38fcb903cfd7656d5375 *man/getDependencies.Rd
46	48	aa98190531ff93721b715e61000f76a4 *man/gtools-defunct.Rd

48	50	01c743eee2dbb9dc14d02035fa05063c *man/invalid.Rd
49	51	8d8b5429047edd4ed52f8f8f6b11f807 *man/keywords.Rd
50	52	67b9c146bd8470b1dd5ddcac782c2071 *man/lastAdd.Rd
	53	8ab31f5f313c145e05601fd8afc7b59b *man/loadedPackages.Rd
51	54	3c207d731ad8ead62af138afe2e20c5f *man/logit.Rd
52	55	422c16f570c15590fa83e1a71506757f *man/mixedsort.Rd
	56	8d5842217510c21d95fb697caee3e6c6 *man/na.replace.Rd
53	57	f4d6f8222b9448ef039d9cbf582ee29e *man/oddeven.Rd
54	58	f911c6c34412df66c1ff0d6376f46c3f *man/permute.Rd
55	59	30ac79ee93340f4174ddf91022154c0c *man/quantcut.Rd

+2

-0

NAMESPACE less more

18	18	invalid,
19	19	keywords,
20	20	lastAdd,
	21	loadedPackages,
21	22	logit,
22	23	logratio2foldchange,
23	24	mixedorder,
24	25	mixedsort,
	26	na.replace,
25	27	odd,
26	28	permutations,
27	29	permute,

+16

-0

NEWS less more

	0	gtools 3.4.2 - 2015-04-06
	1	-------------------------
	2
	3	New features:
	4
	5	- New function loadedPackages() to display name, version, and path of
	6	loaded packages (package namespaces).
	7
	8	- New function: na.replace() to replace missing values within a
	9	vector with a specified value.`
	10
	11	Bug fixes:
	12
	13	- Modify keywords() to work properly in R 3.4.X and later.
	14
	15
0	16	gtools 3.4.1 - 2014-05-27
1	17	-------------------------
2	18

+5

-1

R/keywords.R less more

31	31
32	32	item <- paste("^",topic,"$", sep="")
33	33
34		topics <- function(k) help.search(keyword=k)$matches[,"topic"]
	34	topics <- function(k)
	35	{
	36	matches <- help.search(keyword=k)$matches
	37	matches[ , match("topic", tolower(colnames(matches)))]
	38	}
35	39	matches <- lapply(kw, topics)
36	40	names(matches) <- kw
37	41

+12

-0

R/loadedPackages.R less more

	0	loadedPackages <- function(silent=FALSE)
	1	{
	2	packageNames <- loadedNamespaces()
	3	packageVersions <- sapply(packageNames, function(package) paste(packageVersion(package), sep=".") )
	4	packagePaths <- find.package(packageNames)
	5	inSearchPath <- match(packageNames, gsub('^package:', '', grep('^package:', search(), value=TRUE)))
	6	retval <- data.frame(Name=packageNames, Version=packageVersions, Path=packagePaths, SearchPath=inSearchPath)
	7	retval$SearchPath <- na.replace(retval$SearchPath, '-')
	8	retval <- retval[order(inSearchPath),]
	9	if(!silent) print(retval)
	10	retval
	11	}

+5

-0

R/na.replace.R less more

	0	na.replace <- function(x, replace)
	1	{
	2	x[is.na(x)] <- replace
	3	x
	4	}

+43

-0

inst/ChangeLog less more

	0	2015-04-09 warnes
	1
	2	* [r1920] DESCRIPTION, NAMESPACE, R/loadedPackages.R,
	3	R/na.replace.R, inst/ChangeLog, inst/NEWS, man/loadedPackages.Rd,
	4	man/na.replace.Rd: Move first()/last()/left()/right() to gdata.
	5	Add new functions na.replace() and loadedPackages().
	6	Add more text to package description.
	7
	8	2015-04-08 warnes
	9
	10	* [r1919] NAMESPACE, R/first.R, man/first.Rd, man/left.Rd: Move
	11	first/last/left/right to from gtools to gdata
	12
	13	2015-04-06 warnes
	14
	15	* [r1918] man/dirichlet.Rd: Correct URL
	16	* [r1917] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
	17	gtools 3.5.0
	18	* [r1916] inst/ChangeLog: Add ChangeLog files to repository
	19	* [r1915] R/keywords.R: Implement fix to keywords() needed for
	20	R-3.4.1, as suggested by Kurt
	21	Hornik.
	22	* [r1914] NAMESPACE, R/first.R: - Export S3 methods for first(),
	23	last(), left() and right().
	24	- Ensure code matches man page for first(), last(), left(), and
	25	right().
	26
	27	2014-10-09 warnes
	28
	29	* [r1897] DESCRIPTION, inst/NEWS: Update for 3.5.0 release of
	30	gtools
	31	* [r1896] R/first.R: Make right() and left() S3 methods for classes
	32	data.frame and matrix
	33
	34	2014-08-27 warnes
	35
	36	* [r1872] man/first.Rd: Fix man page
	37	* [r1871] DESCRIPTION, NAMESPACE, R/first.R, man/first.Rd,
	38	man/left.Rd: Finish adding first(), last(), left(), and right().
	39	* [r1870] R/first.R: Add functions first(), last(), left(), and
	40	right().
	41
0	42	2014-05-28 warnes
1	43
	44	* [r1816] DESCRIPTION, inst/NEWS: Update for gtools 3.4.1
2	45	* [r1815] tests/smartbind_Dates.R: Add test to ensure smartbind()
3	46	properly handles Date columns.
4	47	* [r1814] R/smartbind.R: smartbind: Convert non-native type columns

+16

-0

inst/NEWS less more

	0	gtools 3.4.2 - 2015-04-06
	1	-------------------------
	2
	3	New features:
	4
	5	- New function loadedPackages() to display name, version, and path of
	6	loaded packages (package namespaces).
	7
	8	- New function: na.replace() to replace missing values within a
	9	vector with a specified value.`
	10
	11	Bug fixes:
	12
	13	- Modify keywords() to work properly in R 3.4.X and later.
	14
	15
0	16	gtools 3.4.1 - 2014-05-27
1	17	-------------------------
2	18

+3

-3

man/dirichlet.Rd less more

0		% $Id: dirichlet.Rd 1433 2010-05-01 22:03:03Z warnes $
	0	% $Id: dirichlet.Rd 1918 2015-04-06 22:09:54Z warnes $
1	1	%
2	2	\name{rdirichlet}
3	3	\alias{rdirichlet}

32	32	}
33	33	\author{
34	34	Code original posted by Ben Bolker to R-News on Fri Dec 15 2000. See
35		\url{http://www.r-project.org/nocvs/mail/r-help/2000/3865.html}. Ben
36		attributed the code to Ian Wilson \email{i.wilson@maths.abdn.ac.uk}.
	35	\url{https://stat.ethz.ch/pipermail/r-help/2000-December/009561.html}.
	36	Ben attributed the code to Ian Wilson \email{i.wilson@maths.abdn.ac.uk}.
37	37	Subsequent modifications by Gregory R. Warnes
38	38	\email{greg@warnes.net}.
39	39	}

+37

-0

man/loadedPackages.Rd less more

	0	\name{loadedPackages}
	1	\alias{loadedPackages}
	2	\title{
	3	Provide Name, Version, and Path of Loaded Package Namespaces
	4	}
	5	\description{
	6	Provide name, version, and path of loaded package namespaces
	7	}
	8	\usage{
	9	loadedPackages(silent = FALSE)
	10	}
	11	\arguments{
	12	\item{silent}{Logical indicating whether the results should be printed}
	13	}
	14	\value{
	15	Data frame containing one row per loaded package namespace, with columns:
	16	\item{Package}{Package name}
	17	\item{Version}{Version string}
	18	\item{Path}{Path to package files}
	19	\item{SearchPath}{Either the index of the package namespace in the current
	20	search path, or '-' if the package namespace is not in the search
	21	path. '1' corresponds to the top of the search path (the first namespace
	22	searched for values). }
	23	}
	24	\author{
	25	Gregory R. Warnes \email{greg@warnes.net}
	26	}
	27	\seealso{
	28	\code{\link[base]{loadedNamespaces}},
	29	\code{\link[utils]{packageVersion}},
	30	\code{\link[base]{search}},
	31	\code{\link[base]{find.package}}
	32	}
	33	\examples{
	34	loadedPackages()
	35	}
	36	\keyword{package}

+34

-0

man/na.replace.Rd less more

	0	\name{na.replace}
	1	\alias{na.replace}
	2	\title{
	3	Replace Missing Values
	4	}
	5	\description{
	6	Replace missing values
	7	}
	8	\usage{
	9	na.replace(x, replace)
	10	}
	11	\arguments{
	12	\item{x}{vector possibly contining missing (\code{NA}) values.}
	13	\item{replace}{scalar replacement value}
	14	}
	15	\details{
	16	This is a convenience function that is the same as
	17	x[is.na(x)] <- replace
	18	}
	19	\value{
	20	Vector with missing values (\code{NA}) replaced by the
	21	value of \code{replace}.
	22	}
	23	\author{
	24	Gregory R. Warnes \email{greg@warnes.net}
	25	}
	26	\seealso{
	27	\code{\link[base]{is.na}}, \code{\link[stats]{na.omit}}
	28	}
	29	\examples{
	30	x <- c(1,2,3,NA,6,7,8,NA,NA)
	31	na.replace(x, '999')
	32	}
	33	\keyword{ manip }