Commit f0b6969e6411513c907501f2708ef9cf253f3487 - gtools

Import Upstream version 3.5.0 Dirk Eddelbuettel 5 years ago

27 changed file(s) with 1729 addition(s) and 1216 deletion(s). Raw diff Collapse all Expand all

+513

-543

ChangeLog less more

	0	2015-05-27 warnes
	1
	2	* [r2039] R/mixedsort.R, man/mixedsort.Rd: Add roman numeral
	3	support to mixedorder() and mixedsort().
	4	* [r2037] man/asc.Rd: Add asc() and chr() functions for converting
	5	between characters and ASCII codes
	6	* [r2036] R/roman2int.R: roman2int() now returns NA for invalid
	7	roman numeral strings instead of generating an error.
	8	* [r2035] NAMESPACE: Add asc(), chr(), assignEdgewise(),
	9	unByteCode(), and
	10	unByteCodeAssign() to package NAMESPACE.
	11	* [r2034] R/asc.R: Add asc() and chr() functions for converting
	12	between characters and ASCII codes
	13
	14	2015-05-26 warnes
	15
	16	* [r2030] inst/ChangeLog: Add changelog to svn repository
	17
	18	2015-05-25 warnes
	19
	20	* [r2029] tests/test_ddirichlet.R: Add library call.
	21	* [r2028] man/unByteCode.Rd: Fix typo and add documentation for
	22	argument 'name'.
	23	* [r2027] man/mixedsort.Rd: Fix typo.
	24	* [r2026] man/mixedsort.Rd: Add description of blanklast argument,
	25	fix typo.
	26	* [r2025] man/quantcut.Rd: Change usage to match actual definition.
	27	* [r2024] man/mixedsort.Rd: Note characters sorting ignores case.
	28	* [r2023] man/mixedsort.Rd: Remove '...' from arglist to match
	29	source code.
	30	* [r2022] man/mixedsort.Rd: Replace unicode quotes with \code{..}.
	31
	32	2015-05-23 warnes
	33
	34	* [r2021] tests/test_ddirichlet.R: Add regression test ddirichlet()
	35	bug for x[i]=0, alpha[i]=1:
	36	ddirichlet(x, alpha) was returning NA rather than 0.
	37	* [r2020] R/dirichlet.R: ddirichlet() was incorrectly returning NA
	38	when x[i]=0 and
	39	alpha[i]=1. In this case, the one calculation became (-Inf * 0),
	40	which R evaluates to NaN. The correction is to detect this case
	41	and
	42	substitute -Inf instead of NaN.
	43
	44	2015-05-08 warnes
	45
	46	* [r2019] R/mixedsort.R: Summary: Speed up mixedorder by moving
	47	suppressWarnings outside of
	48	lapply loops. (Suggestion by Henrik Bengtsson.)
	49
	50	2015-05-02 warnes
	51
	52	* [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge
	53	* [r2017] Minor layout change.
	54	* [r2016] Remove stray 'svn' that was inserted into the code.
	55	* [r2015] Add man page for unByteCode(), assignEdgeWise(), and
	56	unByteCodeAssign()
	57
	58	2015-04-28 warnes
	59
	60	* [r1976] Changes to mixedsort():
	61	- Hands off objects that are not character vectors to the default
	62	sort.
	63	- Add 'decreasing', 'na.last', and 'blank.last' arguments.
	64	* [r1975] Add private function 'checkReverseDependencies'.
	65
	66	2015-04-23 warnes
	67
	68	* [r1950] Update NEWS and ChangeLog
	69	* [r1949] - The 'q' argument to quantcut()'s 'q' now accept an
	70	integer
	71	indicating the number of equally spaced quantile groups to
	72	create. (Suggestion and patch submitted by Ryan C. Thompson.)
	73	* [r1946] Revers accidental text deletion:
	74	* [r1945] Update for gtools 3.4.3
	75	* [r1944] Remove debugging code and stray browser() call
	76
	77	2015-04-14 warnes
	78
	79	* [r1923] Fix typo
	80
0	81	2015-04-09 warnes
1	82
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.
	83	* [r1921] Update gtools ChangeLog
	84	* [r1920] Move first()/last()/left()/right() to gdata.
5	85	Add new functions na.replace() and loadedPackages().
6	86	Add more text to package description.
7	87
8	88	2015-04-08 warnes
9	89
10		* [r1919] NAMESPACE, R/first.R, man/first.Rd, man/left.Rd: Move
11		first/last/left/right to from gtools to gdata
	90	* [r1919] Move first/last/left/right to from gtools to gdata
12	91
13	92	2015-04-06 warnes
14	93
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
	94	* [r1918] Correct URL
	95	* [r1917] Update NEWS and ChangeLog for gtools 3.5.0
	96	* [r1916] Add ChangeLog files to repository
	97	* [r1915] Implement fix to keywords() needed for R-3.4.1, as
	98	suggested by Kurt
21	99	Hornik.
22		* [r1914] NAMESPACE, R/first.R: - Export S3 methods for first(),
23		last(), left() and right().
	100	* [r1914] - Export S3 methods for first(), last(), left() and
	101	right().
24	102	- Ensure code matches man page for first(), last(), left(), and
25	103	right().
26	104
27	105	2014-10-09 warnes
28	106
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
	107	* [r1897] Update for 3.5.0 release of gtools
	108	* [r1896] Make right() and left() S3 methods for classes data.frame
	109	and matrix
33	110
34	111	2014-08-27 warnes
35	112
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().
	113	* [r1872] Fix man page
	114	* [r1871] Finish adding first(), last(), left(), and right().
	115	* [r1870] Add functions first(), last(), left(), and right().
41	116
42	117	2014-05-28 warnes
43	118
44		* [r1816] DESCRIPTION, inst/NEWS: Update for gtools 3.4.1
45		* [r1815] tests/smartbind_Dates.R: Add test to ensure smartbind()
46		properly handles Date columns.
47		* [r1814] R/smartbind.R: smartbind: Convert non-native type columns
48		(except factor) to character.
	119	* [r1816] Update for gtools 3.4.1
	120	* [r1815] Add test to ensure smartbind() properly handles Date
	121	columns.
	122	* [r1814] smartbind: Convert non-native type columns (except
	123	factor) to character.
49	124
50	125	2014-04-18 arnima
51	126
52		* [r1813] R/ASCIIfy.R, man/ASCIIfy.Rd: Main arg is 'x' like
53		showNonASCII(x), preformatted notes instead of verb
	127	* [r1813] Main arg is 'x' like showNonASCII(x), preformatted notes
	128	instead of verb
54	129
55	130	2014-04-17 warnes
56	131
57		* [r1810] man/ASCIIfy.Rd: Update ASCIIfy man page to match source
58		code and add keywords
59		* [r1809] inst/NEWS: Update NEWS for gtools 3.4.0
60		* [r1808] DESCRIPTION, NAMESPACE, R/ASCIIfy.R, man/ASCIIfy.Rd: Add
61		ASCIIfy function posted to RDevel by Arni Magnusson
	132	* [r1810] Update ASCIIfy man page to match source code and add
	133	keywords
	134	* [r1809] Update NEWS for gtools 3.4.0
	135	* [r1808] Add ASCIIfy function posted to RDevel by Arni Magnusson
62	136
63	137	2014-03-01 warnes
64	138
65		* [r1776] tests/test_mixedorder.R: Fix cut-and-paste error.
66		* [r1775] DESCRIPTION, inst/NEWS: Update files for gtools 3.3.1
67		release
68		* [r1774] R/mixedsort.R, tests/test_mixedorder.R: Fix bug in
69		gtools::mixedorder regular expression for regognizing numbers.
70		(Periods weren't escaped).
	139	* [r1776] Fix cut-and-paste error.
	140	* [r1775] Update files for gtools 3.3.1 release
	141	* [r1774] Fix bug in gtools::mixedorder regular expression for
	142	regognizing numbers. (Periods weren't escaped).
71	143
72	144	2014-02-11 warnes
73	145
74		* [r1773] R/clean_up_dependencies2.R: Create and use locate copy of
75		tools:::.split_op_version.
76		* [r1772] inst/NEWS: Update for gtools 3.3.0.
77		* [r1771] man/getDependencies.Rd: Fix arguments
78		* [r1770] man/getDependencies.Rd: Update arguments to match code.
79		* [r1769] DESCRIPTION, NAMESPACE, R/clean_up_dependencies2.R,
80		R/getDependencies.R, man/getDependencies.Rd: Add
81		getDependencies() function to return a list of package
82		dependencies.
	146	* [r1773] Create and use locate copy of tools:::.split_op_version.
	147	* [r1772] Update for gtools 3.3.0.
	148	* [r1771] Fix arguments
	149	* [r1770] Update arguments to match code.
	150	* [r1769] Add getDependencies() function to return a list of
	151	package dependencies.
83	152
84	153	2014-01-14 warnes
85	154
86		* [r1768] DESCRIPTION, inst/NEWS: Update for bug-fix release
87		* [r1767] tests, tests/test_binsearch.R: Add test file for
88		binsearch() function.
89		* [r1766] R/binsearch.R: Fixed bug where binsearch() returned the
90		wrong endpoint & value when the found value was at the upper
91		endpoint.
	155	* [r1768] Update for bug-fix release
	156	* [r1767] Add test file for binsearch() function.
	157	* [r1766] Fixed bug where binsearch() returned the wrong endpoint &
	158	value when the found value was at the upper endpoint.
92	159
93	160	2014-01-13 warnes
94	161
95		* [r1765] man/smartbind.Rd: Fix typo
	162	* [r1765] Fix typo
96	163
97	164	2014-01-11 warnes
98	165
99		* [r1764] inst/NEWS: Update for gtools release 3.2.0
100		* [r1763] man/gtools-defunct.Rd: fixes for R CMD check
101		* [r1762] DESCRIPTION, NAMESPACE, R/capture.R, R/defunct.R,
102		R/keywords.R, man/capture.Rd, man/gtools-defunct.Rd,
103		man/stars.pval.Rd: Fixes for gtools release 3.2.0
	166	* [r1764] Update for gtools release 3.2.0
	167	* [r1763] fixes for R CMD check
	168	* [r1762] Fixes for gtools release 3.2.0
104	169
105	170	2013-12-23 warnes
106	171
107		* [r1761] R/keywords.R, man/keywords.Rd: Extend the keywords()
108		function to return keywords associated with a specified topic via
109		'keywords(topic)'.
110		* [r1760] man/stars.pval.Rd: Add keyword.
111		* [r1759] NAMESPACE, R/stars.pval.R, man/stars.pval.Rd: Add
112		stars.pval() function to convert p-values into significance
113		symbols.
	172	* [r1761] Extend the keywords() function to return keywords
	173	associated with a specified topic via 'keywords(topic)'.
	174	* [r1760] Add keyword.
	175	* [r1759] Add stars.pval() function to convert p-values into
	176	significance symbols.
114	177
115	178	2013-11-26 warnes
116	179
117		* [r1748] R/mixedsort.R: mixedorder() was failing to correctly
118		handle numbers including
	180	* [r1748] mixedorder() was failing to correctly handle numbers
	181	including
119	182	decimals due to a faulty regular expression. Prior to the fix:
120	183
121	184	> drr

136	199
137	200	2013-11-18 warnes
138	201
139		* [r1747] R/capture.R: Use ".Deprecated" instead of warning.
	202	* [r1747] Use ".Deprecated" instead of warning.
140	203
141	204	2013-11-06 warnes
142	205
143		* [r1746] DESCRIPTION, inst/NEWS: Update files for gtools 3.1.1
144		* [r1745] R/mixedsort.R: Fix problem with mixedorder/mixedsort when
145		there is only zero or one elements in the vector.
	206	* [r1746] Update files for gtools 3.1.1
	207	* [r1745] Fix problem with mixedorder/mixedsort when there is only
	208	zero or one elements in the vector.
146	209
147	210	2013-09-23 warnes
148	211
149		* [r1716] man/gtools-deprecated.Rd: Comment out empty sections in
150		gtools-deprecated.Rd
151		* [r1715] DESCRIPTION, inst/NEWS: Update files for gtools 3.1.0
	212	* [r1716] Comment out empty sections in gtools-deprecated.Rd
	213	* [r1715] Update files for gtools 3.1.0 release
	214	* [r1714] Make 'addLast()' defunct.
	215	* [r1713] Mark 'addLast()' as defunct and move 'lastAdd()' function
	216	to a separate file.
	217	* [r1712] Update for gtools 3.0.1 release
	218	* [r1711] Use 'suppressWarnings() instead of 'options(warn=-1)' in
	219	'mixedorder()'.
	220
	221	2013-07-07 warnes
	222
	223	* [r1705] Fix typo.
	224
	225	2013-07-06 warnes
	226
	227	* [r1704] Fix Rd warning.
	228	* [r1703] Include lastAdd in NAMESPACE
	229	* [r1702] Change assert from deprecated to defunct.
	230	* [r1701] Improve deprecation message
	231	* [r1700] Update for gtools 3.0.0
	232	* [r1699] Create new function lastAdd to replace addLast and mark
	233	addLast as deprecated.
	234
	235	2013-07-05 warnes
	236
	237	* [r1698] Point out that addLast() modifies the value of .Last in
	238	the global environment.
	239	* [r1697] Point out that addLast() modifies the value of .Last in
	240	the global environment.
	241	* [r1696] Update for gtools 2.7.2 mark 2
	242	* [r1695] Remove cross-reference to (obsolete?) moc package
	243	* [r1694] Update for gtools 2.7.2
	244	* [r1693] Update for R version 3.0.0 and later
	245
	246	2013-03-17 warnes
	247
	248	* [r1640] Fix error in smartbind: factor levels were not being
	249	handled if the factor column was not present in the first data
	250	frame.
	251
	252	2012-06-19 warnes
	253
	254	* [r1570] Update for gtools 2.7.0.
	255	* [r1569] Document new 'verbose' argument to smartbind().
	256	* [r1568] Clean up R CMD check warnings.
	257
	258	2012-05-04 warnes
	259
	260	* [r1529] smartbind(): Improve handling of factors and ordered
	261	factors.
	262
	263	2011-10-05 warnes
	264
	265	* [r1518] Update version number for release
	266	* [r1517] Add 'sep' argument to smartbind() to allow specification
	267	of character used to separate components of constructed names
	268
	269	2011-09-28 warnes
	270
	271	* [r1513] smartbind(): Prevent coersion to data frame from mangling
	272	column names.
	273	* [r1512] Add 'fill' argument to smartbind() to specify a value to
	274	use for
	275	missing entries.
	276	* [r1511] Add 'fill' argument to smartbind() to specify a value to
	277	use for
	278	missing entries.
	279
	280	2010-08-14 warnes
	281
	282	* [r1451] Modify mixedorder()/mixedsort() to better handle strings
	283	containing multiple periods, like version numbers (e.g 1.1.2,
	284	1.2.1. 1.1.1.1).
	285
	286	2010-05-01 warnes
	287
	288	* [r1434] Update version number for new release
	289	* [r1433] Change Greg's email address to greg@warnes.net
	290	* [r1432] Fix error in checkRVersion()
	291
	292	2010-04-28 ggrothendieck2
	293
	294	* [r1431] fixed problems with R CMD CHECK
	295
	296	2009-05-09 warnes
	297
	298	* [r1328] Escape $ in .Rd file to avoid latex issues
	299	* [r1327] Update NEWS and create softlinks for NEWS and ChangeLog
	300	in top level directory
	301	* [r1326] Move actual NEWS file into inst.
	302	* [r1325] Update Greg's email address and fix Rd syntax errors
	303
	304	2009-02-16 warnes
	305
	306	* [r1313] Correct windows make flags as suggested by Brian Ripley.
	307
	308	2008-08-15 warnes
	309
	310	* [r1303] Add keywords() function to show /doc/KEYWORDS file
	311
	312	2008-05-29 warnes
	313
	314	* [r1285] Add newVersionAvailable() function to compare running and
	315	latest available R versions
	316
	317	2008-05-26 warnes
	318
	319	* [r1284] Update license specification
	320	* [r1283] Remove 'assert' man page
	321
	322	2008-05-22 warnes
	323
	324	* [r1282] Finish rename of assert.R to assert-depricated.Rd
	325	* [r1281] Add checkRVersion.R file
	326	* [r1280] Rename again to get correct extension!
	327	* [r1279] Update NEWS for 2.5.0
	328	* [r1278] Add man page for checkRVersion
	329	* [r1277] Rename assert-deprecated.R to assert.R to meet R file
	330	name requirements.
	331	* [r1276] Add checkRVersion to NAMESPACE, and increment version in
	332	DESCRIPTION.
	333	* [r1275] Remove broken SEE LSO reference
	334
	335	2008-04-12 warnes
	336
	337	* [r1259] Improve text explanation of how defmacro() and strmacro()
	338	differ from
	339	function().
	340	* [r1258] assert() is now deprecated in favor of base::stopifnot()
	341	* [r1257] Rename 'assert.R' to 'deprecated.R'.
	342	* [r1256] Assert is now deprecated in favor of base::stopifnot(),
	343	so add call to
	344	.Deprecated() to inform the user.
	345
	346	2007-11-30 warnes
	347
	348	* [r1228] Update defnitions of odd() and even() to use modulus
	349	operator instead of division. Prettier, I think, :-D
	350
	351	2007-08-08 warnes
	352
	353	* [r1121] Fix bug identified by R-2.6's check routings in
	354	binsearch()
	355	* [r1120] Add the binsearch(), previously in the genetics package.
	356
	357	2007-07-18 ggorjan
	358
	359	* [r1100] typo fixed
	360
	361	2007-04-12 warnes
	362
	363	* [r1088] Add ask() function to prompt the user and collect a
	364	single response.
	365
	366	2007-04-07 warnes
	367
	368	* [r1087] Fix improper escapes in regexp detected by R 2.5.0
	369	package check.
	370
	371	2007-03-23 warnes
	372
	373	* [r1083] Allow permutations for r>n provided repeats.allowed=TRUE
	374
	375	2006-11-28 warnes
	376
	377	* [r1023] Replace F with FALSE in smartbind example.
	378
	379	2006-11-27 warnes
	380
	381	* [r1022] Replace T with TRUE in smartbind example
	382	* [r1021] Temprary remove to reset binary flag
	383	* [r1020] Temprary remove to reset binary flag
	384	* [r1019] Add smartbind() to list of exported functions, and add
	385	corresponding
	386	documentation file.
	387	* [r1018] Update my email address
	388
	389	2006-11-14 ggorjan
	390
	391	* [r1012] Removed executable property
	392
	393	2006-08-02 warnes
	394
	395	* [r977] Update my email address
	396
	397	2006-05-05 nj7w
	398
	399	* [r958] Fixed minor typo - in {value} - n was replaced by r
	400	* [r957] Fixed minor typos
	401
	402	2006-03-01 warnes
	403
	404	* [r903] Add smartbind function
	405
	406	2006-01-18 warnes
	407
	408	* [r845] Add concept tags to make mixedsort easier to locate.
	409
	410	2005-12-21 warnes
	411
	412	* [r837] Update version number and date
	413	* [r836] Note changes for 2.2.3
	414	* [r835] Should now work on Windows
	415
	416	2005-12-20 warnes
	417
	418	* [r834] Temporary fix to allow setTCPNoDelay.c to compile on
	419	Windows. If compiled on windows calling setTCPNoDelay will just
	420	raise an error.
	421
	422	2005-12-14 warnes
	423
	424	* [r813] Change C++ comment to standard comment
	425
	426	2005-12-13 nj7w
	427
	428	* [r810] * empty log message *
	429	* [r809] Updated NEWS and removed ChangeLog
	430
	431	2005-12-12 nj7w
	432
	433	* [r800] Updated version for CRAN release
	434
	435	2005-12-08 warnes
	436
	437	* [r790] Add C source code for setTCPNoDelay.
	438
	439	2005-12-01 nj7w
	440
	441	* [r776] Updated Greg's email address
	442
	443	2005-11-29 warnes
	444
	445	* [r769] Add UseDynLib to NAMESPACE so the shared library gets
	446	properly loaded.
	447	* [r768] - Remove debugging comments
	448	- Change return value on success to "Success".
	449
	450	2005-11-22 warnes
	451
	452	* [r758] NAMESPACE
	453	* [r757] Update news for 2.2.1 release.
	454	* [r756] Fixes for R CMD check
	455	* [r755] Add setTCPNoDelay() function and documentation
	456	* [r745] New function 'addLast' that adds functions to R's .Last()
	457	so that
	458	they will be executed when R is terminating.
	459
	460	2005-09-22 warnes
	461
	462	* [r678] More changes for strmacro(), also changes for 2.1.1
152	463	release
153		* [r1714] man/addLast-deprecated.Rd, man/gtools-defunct.Rd,
154		man/gtools-deprecated.Rd, man/lastAdd.Rd: Make 'addLast()'
155		defunct.
156		* [r1713] R/addLast.R, R/lastAdd.R: Mark 'addLast()' as defunct and
157		move 'lastAdd()' function to a separate file.
158		* [r1712] DESCRIPTION, inst/NEWS: Update for gtools 3.0.1 release
159		* [r1711] R/mixedsort.R: Use 'suppressWarnings() instead of
160		'options(warn=-1)' in 'mixedorder()'.
161
162		2013-07-07 warnes
163
164		* [r1705] man/lastAdd.Rd: Fix typo.
165
166		2013-07-06 warnes
167
168		* [r1704] man/lastAdd.Rd: Fix Rd warning.
169		* [r1703] NAMESPACE: Include lastAdd in NAMESPACE
170		* [r1702] R/deprecated.R: Change assert from deprecated to defunct.
171		* [r1701] R/addLast.R: Improve deprecation message
172		* [r1700] DESCRIPTION, inst/NEWS: Update for gtools 3.0.0
173		* [r1699] R/addLast.R, man/addLast-deprecated.Rd, man/addLast.Rd,
174		man/gtools-defunct.Rd, man/gtools-deprecated.Rd, man/lastAdd.Rd:
175		Create new function lastAdd to replace addLast and mark addLast
176		as deprecated.
177
178		2013-07-05 warnes
179
180		* [r1698] inst/NEWS: Point out that addLast() modifies the value of
181		.Last in the global environment.
182		* [r1697] man/addLast.Rd: Point out that addLast() modifies the
183		value of .Last in the global environment.
184		* [r1696] DESCRIPTION, inst/NEWS: Update for gtools 2.7.2 mark 2
185		* [r1695] man/logit.Rd: Remove cross-reference to (obsolete?) moc
186		package
187		* [r1694] DESCRIPTION, inst/NEWS: Update for gtools 2.7.2
188		* [r1693] R/checkRVersion.R: Update for R version 3.0.0 and later
189
190		2013-03-17 warnes
191
192		* [r1640] R/smartbind.R: Fix error in smartbind: factor levels were
193		not being handled if the factor column was not present in the
194		first data frame.
195
196		2012-06-19 warnes
197
198		* [r1570] DESCRIPTION, inst/NEWS: Update for gtools 2.7.0.
199		* [r1569] man/smartbind.Rd: Document new 'verbose' argument to
200		smartbind().
201		* [r1568] R/addLast.R, R/running.R: Clean up R CMD check warnings.
202
203		2012-05-04 warnes
204
205		* [r1529] R/smartbind.R: smartbind(): Improve handling of factors
206		and ordered factors.
207
208		2011-10-05 warnes
209
210		* [r1518] DESCRIPTION: Update version number for release
211		* [r1517] R/smartbind.R, man/smartbind.Rd: Add 'sep' argument to
212		smartbind() to allow specification of character used to separate
213		components of constructed names
214
215		2011-09-28 warnes
216
217		* [r1513] R/smartbind.R: smartbind(): Prevent coersion to data
218		frame from mangling column names.
219		* [r1512] R/smartbind.R, inst/NEWS: Add 'fill' argument to
220		smartbind() to specify a value to use for
221		missing entries.
222		* [r1511] DESCRIPTION, man/smartbind.Rd: Add 'fill' argument to
223		smartbind() to specify a value to use for
224		missing entries.
225
226		2010-08-14 warnes
227
228		* [r1451] R/mixedsort.R: Modify mixedorder()/mixedsort() to better
229		handle strings containing multiple periods, like version numbers
230		(e.g 1.1.2, 1.2.1. 1.1.1.1).
231
232		2010-05-01 warnes
233
234		* [r1434] DESCRIPTION: Update version number for new release
235		* [r1433] DESCRIPTION, man/addLast.Rd, man/ask.Rd,
236		man/binsearch.Rd, man/capture.Rd, man/combinations.Rd,
237		man/defmacro.Rd, man/dirichlet.Rd, man/foldchange.Rd,
238		man/invalid.Rd, man/keywords.Rd, man/logit.Rd, man/mixedsort.Rd,
239		man/oddeven.Rd, man/permute.Rd, man/quantcut.Rd, man/running.Rd,
240		man/scat.Rd, man/setTCPNoDelay.Rd, man/smartbind.Rd: Change
241		Greg's email address to greg@warnes.net
242		* [r1432] R/checkRVersion.R: Fix error in checkRVersion()
243
244		2010-04-28 ggrothendieck2
245
246		* [r1431] R/quantcut.R, R/strmacro.R, man/binsearch.Rd,
247		man/capture.Rd, man/setTCPNoDelay.Rd: fixed problems with R CMD
248		CHECK
249
250		2009-05-09 warnes
251
252		* [r1328] man/keywords.Rd: Escape $ in .Rd file to avoid latex
253		issues
254		* [r1327] ChangeLog, NEWS, inst/NEWS: Update NEWS and create
255		softlinks for NEWS and ChangeLog in top level directory
256		* [r1326] NEWS, inst, inst/NEWS: Move actual NEWS file into inst.
257		* [r1325] DESCRIPTION, man/addLast.Rd, man/binsearch.Rd,
258		man/capture.Rd, man/combinations.Rd, man/defmacro.Rd,
259		man/dirichlet.Rd, man/foldchange.Rd, man/gtools-deprecated.Rd,
260		man/invalid.Rd, man/logit.Rd, man/mixedsort.Rd, man/oddeven.Rd,
261		man/permute.Rd, man/quantcut.Rd, man/running.Rd, man/scat.Rd,
262		man/setTCPNoDelay.Rd, man/smartbind.Rd: Update Greg's email
263		address and fix Rd syntax errors
264
265		2009-02-16 warnes
266
267		* [r1313] src/Makevars.win: Correct windows make flags as suggested
268		by Brian Ripley.
269
270		2008-08-15 warnes
271
272		* [r1303] DESCRIPTION, NAMESPACE, R/keywords.R, man/keywords.Rd:
273		Add keywords() function to show /doc/KEYWORDS file
274
275		2008-05-29 warnes
276
277		* [r1285] R/newVersionAvailable.R: Add newVersionAvailable()
278		function to compare running and latest available R versions
279
280		2008-05-26 warnes
281
282		* [r1284] DESCRIPTION: Update license specification
283		* [r1283] man/assert-deprecated.Rd: Remove 'assert' man page
284
285		2008-05-22 warnes
286
287		* [r1282] man/assert.R: Finish rename of assert.R to
288		assert-depricated.Rd
289		* [r1281] R/checkRVersion.R: Add checkRVersion.R file
290		* [r1280] man/assert-deprecated.Rd: Rename again to get correct
291		extension!
292		* [r1279] NEWS: Update NEWS for 2.5.0
293		* [r1278] man/checkRVersion.Rd: Add man page for checkRVersion
294		* [r1277] man/assert-deprecated.R, man/assert.R: Rename
295		assert-deprecated.R to assert.R to meet R file name requirements.
296		* [r1276] DESCRIPTION, NAMESPACE: Add checkRVersion to NAMESPACE,
297		and increment version in DESCRIPTION.
298		* [r1275] man/gtools-deprecated.Rd: Remove broken SEE LSO reference
299
300		2008-04-12 warnes
301
302		* [r1259] man/defmacro.Rd: Improve text explanation of how
303		defmacro() and strmacro() differ from
304		function().
305		* [r1258] NEWS, man/assert-deprecated.R, man/assert.Rd,
306		man/gtools-deprecated.Rd: assert() is now deprecated in favor of
307		base::stopifnot()
308		* [r1257] R/assert.R, R/deprecated.R: Rename 'assert.R' to
309		'deprecated.R'.
310		* [r1256] R/assert.R: Assert is now deprecated in favor of
311		base::stopifnot(), so add call to
312		.Deprecated() to inform the user.
313
314		2007-11-30 warnes
315
316		* [r1228] R/oddeven.R: Update defnitions of odd() and even() to use
317		modulus operator instead of division. Prettier, I think, :-D
318
319		2007-08-08 warnes
320
321		* [r1121] DESCRIPTION, R/binsearch.R: Fix bug identified by R-2.6's
322		check routings in binsearch()
323		* [r1120] DESCRIPTION, NAMESPACE, NEWS, R/binsearch.R,
324		man/binsearch.Rd: Add the binsearch(), previously in the genetics
325		package.
326
327		2007-07-18 ggorjan
328
329		* [r1100] man/combinations.Rd: typo fixed
330
331		2007-04-12 warnes
332
333		* [r1088] NAMESPACE, NEWS, R/ask.R, man/ask.Rd: Add ask() function
334		to prompt the user and collect a single response.
335
336		2007-04-07 warnes
337
338		* [r1087] DESCRIPTION, R/mixedsort.R: Fix improper escapes in
339		regexp detected by R 2.5.0 package check.
340
341		2007-03-23 warnes
342
343		* [r1083] R/combinations.R: Allow permutations for r>n provided
344		repeats.allowed=TRUE
345
346		2006-11-28 warnes
347
348		* [r1023] man/smartbind.Rd: Replace F with FALSE in smartbind
349		example.
350
351		2006-11-27 warnes
352
353		* [r1022] man/smartbind.Rd: Replace T with TRUE in smartbind
354		example
355		* [r1021] data/ELISA.rda: Temprary remove to reset binary flag
356		* [r1020] data/ELISA.rda: Temprary remove to reset binary flag
357		* [r1019] DESCRIPTION, NAMESPACE, NEWS, R/smartbind.R,
358		man/smartbind.Rd: Add smartbind() to list of exported functions,
359		and add corresponding
360		documentation file.
361		* [r1018] DESCRIPTION: Update my email address
362
363		2006-11-14 ggorjan
364
365		* [r1012] R/combinations.R, R/running.R, man/ELISA.Rd,
366		man/combinations.Rd: Removed executable property
367
368		2006-08-02 warnes
369
370		* [r977] man/addLast.Rd, man/assert.Rd, man/capture.Rd,
371		man/combinations.Rd, man/defmacro.Rd, man/dirichlet.Rd,
372		man/foldchange.Rd, man/invalid.Rd, man/logit.Rd,
373		man/mixedsort.Rd, man/oddeven.Rd, man/permute.Rd,
374		man/quantcut.Rd, man/running.Rd, man/scat.Rd,
375		man/setTCPNoDelay.Rd: Update my email address
376
377		2006-05-05 nj7w
378
379		* [r958] man/combinations.Rd: Fixed minor typo - in {value} - n was
380		replaced by r
381		* [r957] NAMESPACE, man/capture.Rd: Fixed minor typos
382
383		2006-03-01 warnes
384
385		* [r903] R/smartbind.R: Add smartbind function
386
387		2006-01-18 warnes
388
389		* [r845] man/mixedsort.Rd: Add concept tags to make mixedsort
390		easier to locate.
391
392		2005-12-21 warnes
393
394		* [r837] DESCRIPTION: Update version number and date
395		* [r836] NEWS: Note changes for 2.2.3
396		* [r835] src/Makevars.win, src/setTCPNoDelay.c: Should now work on
397		Windows
398
399		2005-12-20 warnes
400
401		* [r834] src/setTCPNoDelay.c: Temporary fix to allow
402		setTCPNoDelay.c to compile on Windows. If compiled on windows
403		calling setTCPNoDelay will just raise an error.
404
405		2005-12-14 warnes
406
407		* [r813] src/setTCPNoDelay.c: Change C++ comment to standard
408		comment
409
410		2005-12-13 nj7w
411
412		* [r810] ChangeLog: * empty log message *
413		* [r809] NEWS: Updated NEWS and removed ChangeLog
414
415		2005-12-12 nj7w
416
417		* [r800] DESCRIPTION: Updated version for CRAN release
418
419		2005-12-08 warnes
420
421		* [r790] src, src/setTCPNoDelay.c: Add C source code for
422		setTCPNoDelay.
423
424		2005-12-01 nj7w
425
426		* [r776] man/combinations.Rd, man/foldchange.Rd, man/invalid.Rd,
427		man/logit.Rd, man/mixedsort.Rd, man/oddeven.Rd, man/quantcut.Rd,
428		man/running.Rd: Updated Greg's email address
429
430		2005-11-29 warnes
431
432		* [r769] NAMESPACE: Add UseDynLib to NAMESPACE so the shared
433		library gets properly loaded.
434		* [r768] R/setTCPNoDelay.R: - Remove debugging comments
435		- Change return value on success to "Success".
436
437		2005-11-22 warnes
438
439		* [r758] NAMESPACE: NAMESPACE
440		* [r757] NEWS: Update news for 2.2.1 release.
441		* [r756] man/addLast.Rd, man/setTCPNoDelay.Rd: Fixes for R CMD
442		check
443		* [r755] DESCRIPTION, NAMESPACE, R/setTCPNoDelay.R,
444		man/setTCPNoDelay.Rd: Add setTCPNoDelay() function and
445		documentation
446		* [r745] R/addLast.R, man/addLast.Rd: New function 'addLast' that
447		adds functions to R's .Last() so that
448		they will be executed when R is terminating.
449
450		2005-09-22 warnes
451
452		* [r678] DESCRIPTION, NAMESPACE, man/defmacro.Rd: More changes for
453		strmacro(), also changes for 2.1.1 release
454		* [r677] R/defmacro.R, R/strmacro.R, man/defmacro.Rd: Add strmaco()
455		which defines functions that use strings for macro definition
	464	* [r677] Add strmaco() which defines functions that use strings for
	465	macro definition
456	466
457	467	2005-09-21 warnes
458	468
459		* [r676] DESCRIPTION, R/defmacro.R, man/defmacro.Rd: Add support
460		for DOTS/... arguments to defmacro
	469	* [r676] Add support for DOTS/... arguments to defmacro
461	470
462	471	2005-09-12 nj7w
463	472
464		* [r671] man/assert.Rd, man/dirichlet.Rd, man/permute.Rd,
465		man/scat.Rd: Updated Greg's email
	473	* [r671] Updated Greg's email
466	474
467	475	2005-09-02 nj7w
468	476
469		* [r653] NAMESPACE: Exported assert
470		* [r652] DESCRIPTION: Updated the version number
471		* [r651] NEWS: Added NEWS
472		* [r650] ChangeLog: Added ChangeLog
473		* [r649] man/assert.Rd: Fixed syntax errors
	477	* [r653] Exported assert
	478	* [r652] Updated the version number
	479	* [r651] Added NEWS
	480	* [r650] Added ChangeLog
	481	* [r649] Fixed syntax errors
474	482
475	483	2005-09-02 warnes
476	484
477		* [r648] R/assert.R, man/assert.Rd: Add assert() and documentation
478		* [r647] man/defmacro.Rd: Fix problem in defmacro.Rd file: don't
479		use \code{} in the example section.
	485	* [r648] Add assert() and documentation
	486	* [r647] Fix problem in defmacro.Rd file: don't use \code{} in the
	487	example section.
480	488
481	489	2005-08-31 warnes
482	490
483		* [r645] DESCRIPTION, NAMESPACE, R/defmacro.R, man/defmacro.Rd:
484		Adding the defmacro() function, extracted from
	491	* [r645] Adding the defmacro() function, extracted from
485	492
486	493	Lumley T. "Programmer's Niche: Macros in {R}", R News, 2001, Vol
487	494	1,
488	495	No. 3, pp 11--13, \url{http://CRAN.R-project.org/doc/Rnews/}
489		* [r642] DESCRIPTION, DESCRIPTION.in: Add stand-alone DESCRIPTION
490		file and remove old DESCRIPTION.in file.
	496	* [r642] Add stand-alone DESCRIPTION file and remove old
	497	DESCRIPTION.in file.
491	498
492	499	2005-06-13 nj7w
493	500
494		* [r626] R/mixedsort.R: Fixed a bug in mixedsort - check if
495		"which.na" and "which.blank" is numeric(0) before subsetting the
496		datasets.
	501	* [r626] Fixed a bug in mixedsort - check if "which.na" and
	502	"which.blank" is numeric(0) before subsetting the datasets.
497	503
498	504	2005-06-09 nj7w
499	505
500		* [r625] R/RSCompat.S, R/combinations.R, R/dirichlet.R,
501		R/foldchange.R, R/invalid.R, R/logit.R, R/mixedsort.R,
502		R/oddeven.R, R/permute.R, R/quantcut.R, R/running.R, R/scat.R,
503		man/ELISA.Rd, man/combinations.Rd, man/dirichlet.Rd,
504		man/foldchange.Rd, man/invalid.Rd, man/logit.Rd,
505		man/mixedsort.Rd, man/oddeven.Rd, man/permute.Rd,
506		man/quantcut.Rd, man/running.Rd, man/scat.Rd: Updating the
507		version number, and various help files to synchronize splitting
508		of gregmisc bundle in 4 individual components.
	506	* [r625] Updating the version number, and various help files to
	507	synchronize splitting of gregmisc bundle in 4 individual
	508	components.
509	509
510	510	2005-05-10 warnes
511	511
512		* [r619] R/mixedsort.R: Fix handling of NA's in mixedorder. We were
513		using a high UTF character to try
	512	* [r619] Fix handling of NA's in mixedorder. We were using a high
	513	UTF character to try
514	514	to put NA's at the end of the sort order, but R 2.1.0 checks if
515	515	characters
516	516	are in the correct range. Instead, we explicitly force NA's to

518	518
519	519	2005-04-07 warnes
520	520
521		* [r606] NAMESPACE, R/scat.R, man/scat.Rd: - Add scat() function
522		which writes its arguments to stderr and
	521	* [r606] - Add scat() function which writes its arguments to stderr
	522	and
523	523	flushes so that output is immediately displayed, but only if
524	524	'getOption("DEBUG")' is true.
525	525
526	526	2005-04-02 warnes
527	527
528		* [r600] NAMESPACE, R/drop.levels.R, man/drop.levels.Rd: Move
529		drop.levels() from gtools to gdata.
530		* [r599] R/mixedsort.R: Minor reordering of functions in file
531		* [r598] NAMESPACE, R/frameApply.R, man/frameApply.Rd: Move
532		frameApply() to gdata package.
533		* [r597] R/mixedsort.R: Fix error if only one value passed to
534		mixedorder.
535		* [r596] R/quantcut.R, man/quantcut.Rd: Add proper handling where
536		more than one quantile obtains the same value
	528	* [r600] Move drop.levels() from gtools to gdata.
	529	* [r599] Minor reordering of functions in file
	530	* [r598] Move frameApply() to gdata package.
	531	* [r597] Fix error if only one value passed to mixedorder.
	532	* [r596] Add proper handling where more than one quantile obtains
	533	the same value
537	534
538	535	2005-04-01 warnes
539	536
540		* [r595] man/ELISA.Rd, man/combinations.Rd, man/dirichlet.Rd,
541		man/drop.levels.Rd, man/foldchange.Rd, man/invalid.Rd,
542		man/logit.Rd, man/mixedsort.Rd, man/oddeven.Rd, man/permute.Rd,
543		man/quantcut.Rd, man/running.Rd: Add CVS ID tag to file headers.
544		* [r594] R/frameApply.R, man/frameApply.Rd: Fixes from Jim Rogers
545		for R CMD check problems in frameApply
	537	* [r595] Add CVS ID tag to file headers.
	538	* [r594] Fixes from Jim Rogers for R CMD check problems in
	539	frameApply
546	540
547	541	2005-03-31 warnes
548	542
549		* [r591] R/drop.levels.R, R/frameApply.R, man/drop.levels.Rd,
550		man/frameApply.Rd: Updates to drop.levels() and frameApply() from
551		Jim Rogers
552		* [r590] data, data/ELISA.rda, man/ELISA.Rd: Add ELISA data set
553		used by frameApply and drop.levels examples
	543	* [r591] Updates to drop.levels() and frameApply() from Jim Rogers
	544	* [r590] Add ELISA data set used by frameApply and drop.levels
	545	examples
554	546
555	547	2005-02-25 warnes
556	548
557		* [r562] man/frameApply.Rd: Replace 'T' with TRUE.
558		* [r561] man/frameApply.Rd: Remove dependency on ELISA data set for
559		the example.
560		* [r558] NAMESPACE: Add drop.levels, frameApply to namespace
561		export.
	549	* [r562] Replace 'T' with TRUE.
	550	* [r561] Remove dependency on ELISA data set for the example.
	551	* [r558] Add drop.levels, frameApply to namespace export.
562	552
563	553	2005-02-15 warnes
564	554
565		* [r542] R/drop.levels.R, R/frameApply.R, man/drop.levels.Rd,
566		man/frameApply.Rd: Add frameApply and drop.levels contributed by
567		Jim Rogers.
	555	* [r542] Add frameApply and drop.levels contributed by Jim Rogers.
568	556
569	557	2005-01-12 warnes
570	558
571		* [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
572		poeple from installing on old
	559	* [r515] Add dependency on R 1.9.0+ to prevent poeple from
	560	installing on old
573	561	versions of R which don't support namespaces.
574	562
575	563	2004-09-27 warneg
576	564
577		* [r461] DESCRIPTION, DESCRIPTION.in, man/running.Rd: Updated to
578		pass R CMD check.
	565	* [r461] Updated to pass R CMD check.
579	566
580	567	2004-09-03 warneg
581	568
582		* [r446] DESCRIPTION, NAMESPACE, R/dirichlet.R, R/foldchange.R,
583		R/invalid.R, R/mixedsort.R, R/oddeven.R, R/permute.R,
584		R/quantcut.R, R/running.R, man/running.Rd: initial bundle checkin
	569	* [r446] initial bundle checkin
585	570
586	571	2004-09-02 warneg
587	572
588		* [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision
	573	* [r442] Initial revision
589	574
590	575	2004-08-27 warnes
591	576
592		* [r441] R/mixedsort.R, man/mixedsort.Rd: Fixed bug in mixedsort,
593		and modified reorder.factor to use mixedsort.
	577	* [r441] Fixed bug in mixedsort, and modified reorder.factor to use
	578	mixedsort.
594	579
595	580	2004-08-26 warnes
596	581
597		* [r440] R/mixedsort.R: - Fix bug pointed out by Jim Rogers.
	582	* [r440] - Fix bug pointed out by Jim Rogers.
598	583	- Use a more distictive internal separator: $@$ instead of just $
599	584	- Capitalization is now irrelevent for search order (unlike
600	585	ASCII).
601	586
602	587	2004-06-08 warnes
603	588
604		* [r372] R/running.R, man/running.Rd: Nitin Jain added by=
605		parameter to allow specifying separation between groups.
	589	* [r372] Nitin Jain added by= parameter to allow specifying
	590	separation between groups.
606	591
607	592	2004-05-26 warnes
608	593
609		* [r345] man/combinations.Rd: Escape underscores in email addresses
610		so Latex is happy.
611		* [r343] R/combinations.R: Replace 'T' with 'TRUE' to pass R CMD
612		check.
	594	* [r345] Escape underscores in email addresses so Latex is happy.
	595	* [r343] Replace 'T' with 'TRUE' to pass R CMD check.
613	596
614	597	2004-05-25 warnes
615	598
616		* [r334] R/combinations.R: Remove extraneous comments.
617		* [r333] R/combinations.R: Fix an error in the code when using
618		repeats.allow=T and r>2. Bug
	599	* [r334] Remove extraneous comments.
	600	* [r333] Fix an error in the code when using repeats.allow=T and
	601	r>2. Bug
619	602	report and fix both due to Elizabeth Purdom
620	603	<epurdom@stanford.edu>.
621	604
622	605	2004-05-24 warnes
623	606
624		* [r323] R/invalid.R: Check if argument is a vector before doing
625		is.na to avoid generating a warning.
626		* [r322] R/invalid.R, man/invalid.Rd: Add invalid() function for
627		testing if a parameter value is non-missing, non-NA,
	607	* [r323] Check if argument is a vector before doing is.na to avoid
	608	generating a warning.
	609	* [r322] Add invalid() function for testing if a parameter value is
	610	non-missing, non-NA,
628	611	non-NULL.
629	612
630	613	2004-04-27 warnes
631	614
632		* [r321] R/running.R, man/running.Rd: Replaced argument `as.list'
633		with `simplify'. Updated documentation,
	615	* [r321] Replaced argument `as.list' with `simplify'. Updated
	616	documentation,
634	617	and updated examples appropriately.
635	618
636	619	2004-04-26 warnes
637	620
638		* [r320] R/running.R, man/running.Rd: Added as.list argument to
639		return one list element per evaluation.
	621	* [r320] Added as.list argument to return one list element per
	622	evaluation.
640	623
641	624	2004-03-26 warnes
642	625
643		* [r303] man/combinations.Rd: Uncomment and fix large 'n' example.
644		* [r301] man/running.Rd: - Update to match changes in running()
	626	* [r303] Uncomment and fix large 'n' example.
	627	* [r301] - Update to match changes in running()
645	628	- Add examples to illustrate new arguments.
646	629	- Modify running correlation plot example to be more clear.
647		* [r299] R/running.R: More of the same.
648		* [r297] R/running.R: Fix bug discovered by Sean Davis
649		<sdavis2@mail.nih.gov>. The running
	630	* [r299] More of the same.
	631	* [r297] Fix bug discovered by Sean Davis <sdavis2@mail.nih.gov>.
	632	The running
650	633	function took an improper shortcut. When allow.fewer=FALSE it was
651	634	still passing shorter lists of elements to the called function,
652	635	and

657	640
658	641	2004-01-21 warnes
659	642
660		* [r277] R/capture.R: - Mark sprint() as depreciated.
	643	* [r277] - Mark sprint() as depreciated.
661	644	- Replace references to sprint with capture.output()
662	645	- Use match.arg for halign and valign arguments to
663	646	textplot.default.

669	652
670	653	2003-12-03 warnes
671	654
672		* [r253] man/foldchange.Rd: - match function argument defaults with
673		'usage'
	655	* [r253] - match function argument defaults with 'usage'
674	656
675	657	2003-11-21 warnes
676	658
677		* [r237] man/foldchange.Rd: Removed 'deqn' call that was confusing
678		things.
679		* [r234] man/logit.Rd: Add email address to author field
680		* [r233] R/foldchange.R, man/foldchange.Rd: - new files
681		* [r232] R/mixedsort.R, man/mixedsort.Rd: - Change 'T' to 'TRUE' in
682		mixedsort.R
	659	* [r237] Removed 'deqn' call that was confusing things.
	660	* [r234] Add email address to author field
	661	* [r233] - new files
	662	* [r232] - Change 'T' to 'TRUE' in mixedsort.R
683	663	- Add missing brace in mixedsort.Rd
684	664
685	665	2003-11-20 warnes
686	666
687		* [r230] R/oddeven.R, man/oddeven.Rd: - Move 'odd' and 'even'
688		functions to a separate file & provide documentation
	667	* [r230] - Move 'odd' and 'even' functions to a separate file &
	668	provide documentation
689	669
690	670	2003-11-18 warnes
691	671
692		* [r227] R/mixedsort.R, man/mixedsort.Rd: - Renamed smartsort to
693		mixedsort and added documentation.
	672	* [r227] - Renamed smartsort to mixedsort and added documentation.
694	673
695	674	2003-11-10 warnes
696	675
697		* [r220] R/capture.R, man/capture.Rd: - Add files contributed by
698		Arni Magnusson
	676	* [r220] - Add files contributed by Arni Magnusson
699	677	<arnima@u.washington.edu>. As well as some of my own.
700	678
701	679	2003-05-23 warnes
702	680
703		* [r196] R/logit.R, man/logit.Rd: - library() backported from
704		1.7-devel. This version of the function
	681	* [r196] - library() backported from 1.7-devel. This version of the
	682	function
705	683	adds the "pos=" argument to specify where in the search path the
706	684	library should be placed.
707	685

715	693
716	694	2003-04-22 warnes
717	695
718		* [r189] man/combinations.Rd: - Fixed tpyo in example that allowed
719		combinations(500,2) to run when
	696	* [r189] - Fixed tpyo in example that allowed combinations(500,2)
	697	to run when
720	698	it should have been ignred for testing..
721	699
722	700	2003-04-10 warnes
723	701
724		* [r186] man/combinations.Rd: - Added note about the need to
725		increase options("expressions") to use
	702	* [r186] - Added note about the need to increase
	703	options("expressions") to use
726	704	large values for 'n'. Prompted by bug report from Huan Huang
727	705	<huan.huang@bnpparibas.com
728	706
729	707	2003-04-04 warnes
730	708
731		* [r183] R/RSCompat.S: - Replace 'T' with 'TRUE'
732		* [r182] R/dirichlet.R: - Change occurences of 'T' to 'TRUE'
733		* [r181] man/capture.Rd: - Allow optional arguments to sprint to be
734		passed to print
	709	* [r183] - Replace 'T' with 'TRUE'
	710	* [r182] - Change occurences of 'T' to 'TRUE'
	711	* [r181] - Allow optional arguments to sprint to be passed to print
735	712	- Fix R CMD check errors
736		* [r180] R/capture.R: - Allow optional arguments to sprint to be
737		passed to print
	713	* [r180] - Allow optional arguments to sprint to be passed to print
738	714
739	715	2003-04-03 warnes
740	716
741		* [r177] man/capture.Rd: - Had mistyped 'sprint' as 'sprintf'.
742		* [r176] man/capture.Rd: - Add help file for capture and sprintf.
	717	* [r177] - Had mistyped 'sprint' as 'sprintf'.
	718	* [r176] - Add help file for capture and sprintf.
743	719
744	720	2003-04-02 warnes
745	721
746		* [r174] R/capture.R: - Added file 'capture.R' containing capture()
747		and sprint().
	722	* [r174] - Added file 'capture.R' containing capture() and
	723	sprint().
748	724
749	725	2003-03-07 warnes
750	726
751		* [r168] R/RSCompat.S: - Minor changes to code to allow the package
752		to be provided as an
	727	* [r168] - Minor changes to code to allow the package to be
	728	provided as an
753	729	S-Plus chapter.
754	730
755	731	2003-01-30 warnes
756	732
757		* [r161] man/running.Rd: - Fixed typo in email address.
	733	* [r161] - Fixed typo in email address.
758	734
759	735	2003-01-02 warnes
760	736
761		* [r148] R/RSCompat.S: - Add nlevels function.
	737	* [r148] - Add nlevels function.
762	738
763	739	2002-10-11 warnes
764	740
765		* [r133] R/permute.R, man/permute.Rd: - Add permute() function
766		(wraper for sample) and man page
767		* [r132] man/dirichlet.Rd: - Escaped underscores in my email
768		address that was causing a parse
	741	* [r133] - Add permute() function (wraper for sample) and man page
	742	* [r132] - Escaped underscores in my email address that was causing
	743	a parse
769	744	error in the {r,p}dirichlet man page.
770	745
771	746	2002-09-30 warnes
772	747
773		* [r128] R/dirichlet.R, man/dirichlet.Rd: - Added rdirichlet() and
774		ddirichlet() with accompaning help page and tests.
	748	* [r128] - Added rdirichlet() and ddirichlet() with accompaning
	749	help page and tests.
775	750
776	751	2002-09-24 warnes
777	752
778		* [r122] R/running.R: - Fixed error where running was always
779		calling running2 with
	753	* [r122] - Fixed error where running was always calling running2
	754	with
780	755	'fun=mean', ignoring the specified funtion.
781	756
782	757	2002-09-23 warnes
783	758
784		* [r117] man/combinations.Rd, man/quantcut.Rd: - Modified all files
785		to include CVS Id and Log tags.
786		* [r116] R/combinations.R: - Added CrossTable() and barplot2() code
787		and docs contributed by Marc Schwartz.
	759	* [r117] - Modified all files to include CVS Id and Log tags.
	760	* [r116] - Added CrossTable() and barplot2() code and docs
	761	contributed by Marc Schwartz.
788	762	- Permit combinations() to be used when r>n provided
789	763	repeat.allowed=TRUE
790	764	- Bumped up version number
791	765
792	766	2002-08-01 warnes
793	767
794		* [r114] R/running.R: - Corrected documentation mismatch for ci,
795		ci.default.
	768	* [r114] - Corrected documentation mismatch for ci, ci.default.
796	769
797	770	- Replaced all occurences of '_' for assignment with '<-'.
798	771

804	777
805	778	2002-04-09 warneg
806	779
807		* [r109] R/combinations.R, man/combinations.Rd, man/running.Rd:
808		Checkin for version 0.5.3
	780	* [r109] Checkin for version 0.5.3
809	781
810	782	2002-03-26 warneg
811	783
812		* [r97] man/quantcut.Rd: Initial Checkin
813		* [r96] R/quantcut.R: Initial checkin.
	784	* [r97] Initial Checkin
	785	* [r96] Initial checkin.
814	786
815	787	2002-03-20 warneg
816	788
817		* [r91] R/RSCompat.S: - Added definition of is.R function.
	789	* [r91] - Added definition of is.R function.
818	790
819	791	- Added boxplot.formula
820	792
821	793	2002-03-07 warneg
822	794
823		* [r90] man/running.Rd: - Added documentation and example for
824		running2
825		* [r89] R/running.R: - Added "running2", which handles both
826		univariate and bivariate cases
	795	* [r90] - Added documentation and example for running2
	796	* [r89] - Added "running2", which handles both univariate and
	797	bivariate cases
827	798	- Modified "running" to call "running2"
828	799
829	800	2002-02-05 warneg
830	801
831		* [r75] R/RSCompat.S: - Fix typo that caused code meant to run only
832		under S-Plus to run
	802	* [r75] - Fix typo that caused code meant to run only under S-Plus
	803	to run
833	804	under R, causing problems.
834	805
835	806	2001-12-19 warneg
836	807
837		* [r67] R/RSCompat.S: - Added code for %in%.
	808	* [r67] - Added code for %in%.
838	809
839	810	2001-09-18 warneg
840	811
841		* [r18] R/RSCompat.S: Release 0.3.2
	812	* [r18] Release 0.3.2
842	813
843	814	2001-09-01 warneg
844	815
845		* [r17] R/RSCompat.S: Initial checkin.
846		* [r16] R/running.R, man/running.Rd: Release 0.3.0
	816	* [r17] Initial checkin.
	817	* [r16] Release 0.3.0
847	818
848	819	2001-08-25 warneg
849	820
850		* [r13] R/running.R: Initial CVS checkin.
851		* [r11] man/combinations.Rd: Fixed a typo and a syntax error.
852		* [r7] man/running.Rd: Initial Checkin
	821	* [r13] Initial CVS checkin.
	822	* [r11] Fixed a typo and a syntax error.
	823	* [r7] Initial Checkin
853	824
854	825	2001-06-29 warneg
855	826
856		* [r6] ., R, R/combinations.R, man, man/combinations.Rd: Initial
857		revision.
858
	827	* [r6] Initial revision.
	828

+20

-15

DESCRIPTION less more

0	0	Package: gtools
1	1	Title: Various R Programming Tools
2	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'),
	3	- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
	4	'getDependencies', 'keywords', 'scat'),
5	5	- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
6	6	- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
7	7	- manipulate R's .Last function ('addLast'),
8	8	- define macros ('defmacro'),
9	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'),
	10	- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
	11	- perform a binary search ('binsearch'),
12	12	- sort strings containing both numeric and character components ('mixedsort'),
13	13	- create a factor variable from the quantiles of a continuous variable ('quantcut'),
14	14	- enumerate permutations and combinations ('combinations', 'permutation'),
15		- calculate and convert between fold-change and log-ratio ('foldchange',
	15	- calculate and convert between fold-change and log-ratio ('foldchange',
16	16	'logratio2foldchange', 'foldchange2logratio'),
17		- calculate probabilities and generate random numbers from Dirichlet distributions
	17	- calculate probabilities and generate random numbers from Dirichlet distributions
18	18	('rdirichlet', 'ddirichlet'),
19	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
	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	- convert characters to/from ASCII codes.
	24	Version: 3.5.0
	25	Date: 2015-05-26
25	26	Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
26	27	Maintainer: Gregory R. Warnes <greg@warnes.net>
27		License: LGPL-2.1
28		Packaged: 2015-04-10 12:37:28 UTC; gwarnes1
	28	License: GPL-2
	29	Repository: CRAN
	30	Repository/R-Forge/Project: r-gregmisc
	31	Repository/R-Forge/Revision: 2048
	32	Repository/R-Forge/DateTimeStamp: 2015-05-27 16:38:37
	33	Date/Publication: 2015-05-29 10:36:40
29	34	NeedsCompilation: yes
30		Repository: CRAN
31		Date/Publication: 2015-04-10 14:48:31
	35	Packaged: 2015-05-27 16:45:10 UTC; rforge
	36	Depends: R (>= 2.10)

+26

-16

MD5 less more

0		8ce65e8748f62a15a845d463ef9dc4ce *ChangeLog
1		799ef0349c13933fc12a76ecb5f602c8 *DESCRIPTION
2		f8ec272fd1610ad963b6fc8fb5469b64 *NAMESPACE
3		4b56bef437760c3635aaf7a0b28b33c7 *NEWS
	0	4b0aeb3913d411a5e1e6127d40dd770d *ChangeLog
	1	bc9c4bf090a979e97a42a514cced2b0b *DESCRIPTION
	2	d4beab1e34afb8dc3c154213bdbd7fe7 *NAMESPACE
	3	b92b360a7ff045e56efb600e1b5d3932 *NEWS
4	4	40be776640196133aebff67618b08dec *R/ASCIIfy.R
5	5	9eb418fd95aa09ba85aed159545dea61 *R/RSCompat.S
6	6	a86a74ba04089ad58ea22e3a994a9b14 *R/addLast.R
	7	c6b3619410daf7b88dfc6e852fe1c322 *R/asc.R
7	8	c4ae0d6b5867f6751981e9f93cd2f619 *R/ask.R
8	9	7e3c03026275ec8e336c73314cb73a69 *R/binsearch.R
9	10	c70220a92fd3c5781638e3779cbd55ff *R/checkRVersion.R
	11	b1dfaaaf624c59b2ee5eeb680a412be7 *R/checkReverseDependencies.R
10	12	421b9d08ece06f33c20d21ad62ad768b *R/clean_up_dependencies2.R
11	13	529f69b81b6b734a4f637d250b5b71f9 *R/combinations.R
12	14	1c333b16a59dcaf7ccf20151962b6375 *R/defmacro.R
13	15	28d70252e7e25f8e3743fc07434acba9 *R/defunct.R
14	16	344b58e1976792a3295238c17df7e917 *R/deprecated.R
15		c089bb5f542501dc1e3ba07f032c84ed *R/dirichlet.R
	17	e5149cd525adc83044c3a3eed1d432bf *R/dirichlet.R
16	18	1da2198e1d194c705ca89381159b7b63 *R/foldchange.R
17	19	e759eb4772cb9ce930a0c570279155b3 *R/getDependencies.R
18	20	71212f4c14003458fc3e30638f339629 *R/invalid.R
19		3f3921bb8ada00eb6fbf7332d689e108 *R/keywords.R
	21	d7058406d6e00cdae229c8ee030df465 *R/keywords.R
20	22	f00dfc3263a5854151f244493b3f04d0 *R/lastAdd.R
21	23	66f7bacaa290264693ee1b4cbe4cadc8 *R/loadedPackages.R
22	24	2bb525e1930ec3ba2afefa2ff43d74e0 *R/logit.R
23		a3ec77919e3a6792f88a0aa39fae4841 *R/mixedsort.R
	25	a93b94a3690a900de1eb5145194a34f2 *R/mixedsort.R
24	26	429ab819b15f97c8dd6e62db278336d9 *R/na.replace.R
25	27	93a46a6ef5937bdd112468daceac00a6 *R/newVersionAvailable.R
26	28	07cd779ab7e64f697604b8b4fa4c9d70 *R/oddeven.R
27	29	1d016a924dd59daa78ea62d986da2929 *R/permute.R
28		576dc3d2738e3eeedbce8e9f5d5765a1 *R/quantcut.R
	30	d01a487fce38a8d7ecd8949767c56f81 *R/quantcut.R
	31	5a3ee0e3dfa4eb4cae1737af02cf8c6f *R/roman2int.R
29	32	02390191f23321a34fcfc41719d66dc6 *R/running.R
30	33	a5ea32bab219fd7c634f034dddada96b *R/scat.R
31	34	e5ddc84d8a502feed32f7f6b1b5e25ab *R/setTCPNoDelay.R
32		f6c7ff23b703889d580383ea3e7205d8 *R/smartbind.R
	35	9633d96613b34ba3539dc2f9cb038af3 *R/smartbind.R
33	36	ef22fb4007dec9fb62eb5ed947292fa3 *R/stars.pval.R
34		e8f510e73bd2cd820c384c00d75b0080 *R/strmacro.R
35		d2d2d0444a049d74694203974624835c *data/ELISA.rda
36		8ce65e8748f62a15a845d463ef9dc4ce *inst/ChangeLog
37		4b56bef437760c3635aaf7a0b28b33c7 *inst/NEWS
38		05087d9c7f92db0ac048dec226e7bc3a *man/ASCIIfy.Rd
	37	bbc04a8581924855fb4107a90811fa52 *R/strmacro.R
	38	e302b31547caf90872346ee1f0867e1f *R/trimws.R
	39	8e36d638d9b5c0c03d6f78235d07df96 *R/unByteCode.R
	40	acc7c743e7b54a541d54b8c7af52043e *data/ELISA.rda
	41	4b0aeb3913d411a5e1e6127d40dd770d *inst/ChangeLog
	42	b92b360a7ff045e56efb600e1b5d3932 *inst/NEWS
	43	e45b4855b4a81e953876cbec7cd1b588 *man/ASCIIfy.Rd
39	44	904304f52b08ec847904ac2aa5be9aef *man/ELISA.Rd
	45	b2eac3f299f642616aa71dc03f1352f0 *man/asc.Rd
40	46	c5b7124f5fdbcc83f2e283314df95858 *man/ask.Rd
41	47	ecbe8481bdcff0d8abd1a47cc64ca7b2 *man/binsearch.Rd
42	48	e1a3f01f01db3e883397eaa49037af6f *man/checkRVersion.Rd

52	58	67b9c146bd8470b1dd5ddcac782c2071 *man/lastAdd.Rd
53	59	8ab31f5f313c145e05601fd8afc7b59b *man/loadedPackages.Rd
54	60	3c207d731ad8ead62af138afe2e20c5f *man/logit.Rd
55		422c16f570c15590fa83e1a71506757f *man/mixedsort.Rd
	61	74e953706b708ad96dfde10268feaafa *man/mixedsort.Rd
56	62	8d5842217510c21d95fb697caee3e6c6 *man/na.replace.Rd
57	63	f4d6f8222b9448ef039d9cbf582ee29e *man/oddeven.Rd
58	64	f911c6c34412df66c1ff0d6376f46c3f *man/permute.Rd
59		30ac79ee93340f4174ddf91022154c0c *man/quantcut.Rd
	65	f417491b0b09a309c23f27f97af4dd5f *man/quantcut.Rd
	66	90873b9cb32a59aaaf62cbc5b302e82b *man/roman2int.Rd
60	67	20033253beddc01faf5829cdf43f01fb *man/running.Rd
61	68	f781e22f646cf803a7f24129525521fc *man/scat.Rd
62	69	5dae46a9758c2a81d25d87881f7b42ee *man/setTCPNoDelay.Rd
63	70	ece07b78ccb279ab1f88a836c6a0378d *man/smartbind.Rd
64	71	7ba286fa2b1bc994de1c6ec78883cdc8 *man/stars.pval.Rd
	72	b726be2eb3bedb0e2f6a4d4e878eef8d *man/unByteCode.Rd
65	73	8d4158b8eb92153e2d3f581682b2a3c1 *src/Makevars.win
	74	ca5f00b573fc8591602b6378746e2eee *src/roman2int.c
66	75	bb28a3858ac5a6152565d3b8cef8c70c *src/setTCPNoDelay.c
67	76	6c36d5eac8884ab13c200c1113cf9236 *tests/smartbind_Dates.R
68	77	b859dff6a12425f4ba692dc7706e99ed *tests/test_binsearch.R
	78	b4b7e4ed52ac89a56e2125620e524c4a *tests/test_ddirichlet.R
69	79	33c5986481c62f046106b02abc4d0c74 *tests/test_mixedorder.R

-2

NAMESPACE less more

1	1
2	2	export(
3	3	addLast,
	4	asc,
	5	ASCIIfy,
4	6	ask,
5	7	assert,
6		ASCIIfy,
	8	assignEdgewise,
7	9	binsearch,
8	10	capture,
	11	chr,
9	12	checkRVersion,
10	13	combinations,
11	14	ddirichlet,

29	32	permute,
30	33	quantcut,
31	34	rdirichlet,
	35	roman2int,
32	36	running,
33	37	scat,
34	38	setTCPNoDelay,
35	39	smartbind,
36	40	sprint,
37	41	stars.pval,
38		strmacro
	42	strmacro,
	43	unByteCode,
	44	unByteCodeAssign
39	45	)

+47

-0

NEWS less more

	0	gtools 3.5.0 - 2015-04-28
	1	-------------------------
	2
	3	New Functions:
	4
	5	- New roman2int() functon to convert roman numerals to integers
	6	without the range restriction of utils::as.roman().
	7
	8	- New asc() and chr() functions to convert between ASCII codes and
	9	characters. (Based on the 'Data Debrief' blog entry for 2011-03-09
	10	at http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html).
	11
	12	- New unByteCode() and unByteCodeAssign() functions to convert a
	13	byte-code functon to an interpeted code function.
	14
	15	- New assignEdgewise() function for making assignments into locked
	16	environments. (Used by unByteCodeAssign().)
	17
	18	Enhacements:
	19
	20	- mixedsort() and mixedorder() now have arguments 'decreasing',
	21	'na.last', and 'blank.last' arguments to control sort ordering.
	22
	23	- mixedsort() and mixedirdeR() now support Roman numerals via the
	24	arguments 'numeric.type', and 'roman.case'. (Request by David
	25	Winsemius, suggested code changes by Henrik Bengtsson.)
	26
	27	- speed up mixedorder() (and hence mixedsort()) by moving
	28	suppressWarnings() outside of lapply loops. (Suggestion by Henrik
	29	Bengtsson.)
	30
	31	- The 'q' argument to quantcut() now accept an integer
	32	indicating the number of equally spaced quantile groups to
	33	create. (Suggestion and patch submitted by Ryan C. Thompson.)
	34
	35	Bug fixes:
	36
	37	- Removed stray browser() call in smartbind().
	38
	39	- ddirichlet(x, alpha) was incorrectly returning NA when for any i,
	40	x[i]=0 and alpha[i]=1. (Bug report by John Nolan.)
	41
	42	Other changes:
	43
	44	- Correct typographical errors in package description.
	45
	46
0	47	gtools 3.4.2 - 2015-04-06
1	48	-------------------------
2	49

-0

R/asc.R less more

	0	asc <- function(char, simplify=TRUE)
	1	sapply(char, function(x) strtoi(charToRaw(x),16L), simplify=simplify )
	2
	3	chr <- function(ascii) sapply(ascii, function(x) rawToChar(as.raw(x)) )

+22

-0

R/checkReverseDependencies.R less more

	0	packagefile="gdata_2.16.0.tar.gz"
	1	destdir=tempdir()
	2
	3	checkReverseDependencies <- function(packagefile, destdir=tempdir(), cleanup=FALSE )
	4	{
	5	if(!file.exists(packagefile))
	6	stop(packagefile, " does not exist!")
	7
	8	cat("Using directory '", destdir, "'. Remember to delete it when done.\n", sep='')
	9
	10	file.copy(packagefile, destdir)
	11
	12	package <- gsub("_.*$", "", packagefile)
	13
	14	rdeps <- tools::package_dependencies(package, db=available.packages(), reverse = TRUE)[[1]]
	15	cat( length(rdeps), "reverse dependencies:\n")
	16	print(rdeps)
	17
	18	tools::check_packages_in_dir(destdir, reverse=list(), Ncpus=6)
	19
	20	if(cleanup) unlink(destdir, recursive=TRUE, force=TRUE)
	21	}

-3

R/dirichlet.R less more

0		# $Id: dirichlet.R 625 2005-06-09 14:20:30Z nj7w $
	0	# $Id: dirichlet.R 2020 2015-05-23 22:12:57Z warnes $
1	1
2	2	# Posted by Ben Bolker to R-News on Fri Dec 15 2000
3	3	# http://www.r-project.org/nocvs/mail/r-help/2000/3865.html

28	28	dirichlet1 <- function(x, alpha)
29	29	{
30	30	logD <- sum(lgamma(alpha)) - lgamma(sum(alpha))
31		s<-sum((alpha-1)*log(x))
	31	s <-(alpha-1)*log(x)
	32	s <- ifelse(alpha==1 & x==0, -Inf, s)
32	33	exp(sum(s)-logD)
33
34	34	}
35	35
36	36	# make sure x is a matrix

-10

R/keywords.R less more

7	7	}
8	8	else
9	9	{
10
11		## Local copy of trim.character to avoid cyclic dependency with gdata ##
12		trim <- function(s)
13		{
14		s <- sub(pattern="^[[:blank:]]+", replacement="", x=s)
15		s <- sub(pattern="[[:blank:]]+$", replacement="", x=s)
16		s
17		}
18
19	10	kw <- scan(file=file, what=character(), sep="\n", quiet=TRUE)
20	11	kw <- grep("&", kw, value=TRUE)
21	12	kw <- gsub("&[^&]*$","", kw)
22	13	kw <- gsub("&+"," ", kw)
23		kw <- na.omit(trim(kw))
	14	kw <- na.omit(trimws(kw))
24	15
25	16	ischar <- tryCatch(is.character(topic) && length(topic) ==
26	17	1L, error = identity)

+71

-25

R/mixedsort.R less more

0		# $Id: mixedsort.R 1774 2014-03-01 20:02:08Z warnes $
	0	mixedsort <- function(x,
	1	decreasing=FALSE,
	2	na.last=TRUE,
	3	blank.last=FALSE,
	4	numeric.type=c("decimal", "roman"),
	5	roman.case=c("upper","lower","both")
	6	)
	7	{
	8	ord <- mixedorder(x,
	9	decreasing=decreasing,
	10	na.last=na.last,
	11	blank.last=blank.last,
	12	numeric.type=numeric.type,
	13	roman.case=roman.case
	14	)
	15	x[ord]
	16	}
1	17
2		mixedsort <- function(x) x[mixedorder(x)]
3
4		mixedorder <- function(x)
	18	mixedorder <- function(x,
	19	decreasing=FALSE,
	20	na.last=TRUE,
	21	blank.last=FALSE,
	22	numeric.type=c("decimal", "roman"),
	23	roman.case=c("upper","lower","both")
	24	)
5	25	{
6	26	# - Split each each character string into an vector of strings and
7	27	# numbers
8	28	# - Separately rank numbers and strings
9	29	# - Combine orders so that strings follow numbers
10	30
	31	numeric.type <- match.arg(numeric.type)
	32	roman.case <- match.arg(roman.case)
	33
11	34	if(length(x)<1)
12	35	return(NULL)
13	36	else if(length(x)==1)
14	37	return(1)
15	38
16		if( is.numeric(x) )
17		return( order(x) )
18
	39	if( !is.character(x) )
	40	return( order(x, decreasing=decreasing, na.last=na.last) )
19	41
20	42	delim="\\$\\@\\$"
21	43
22		numeric <- function(x)
	44	if(numeric.type=="decimal")
23	45	{
24		suppressWarnings( as.numeric(x) )
	46	regex <- "((?:(?i)(?:[-+]?)(?:(?=[.]?[0123456789])(?:[0123456789]*)(?:(?:[.])(?:[0123456789]{0,}))?)(?:(?:[eE])(?:(?:[-+]?)(?:[0123456789]+))\|)))" # uses PERL syntax
	47	numeric <- function(x) as.numeric(x)
25	48	}
	49	else if (numeric.type=="roman")
	50	{
	51	regex <- switch(roman.case,
	52	"both" = "([IVXCLDMivxcldm]+)",
	53	"upper" = "([IVXCLDM]+)",
	54	"lower" = "([ivxcldm]+)"
	55	)
	56	numeric <- function(x) roman2int(x)
	57	}
	58	else
	59	stop("Unknown value for numeric.type: ", numeric.type)
26	60
27	61	nonnumeric <- function(x)
28	62	{
29		suppressWarnings( ifelse(is.na(as.numeric(x)), toupper(x), NA) )
	63	ifelse(is.na(numeric(x)), toupper(x), NA)
30	64	}
31	65
32	66	x <- as.character(x)

34	68	which.nas <- which(is.na(x))
35	69	which.blanks <- which(x=="")
36	70
37		if(length(which.blanks) >0)
38		x[ which.blanks ] <- -Inf
39
40		if(length(which.nas) >0)
41		x[ which.nas ] <- Inf
42
43	71	####
44	72	# - Convert each character string into an vector containing single
45	73	# character and numeric values.
46	74	####
47	75
48	76	# find and mark numbers in the form of +1.23e+45.67
49		delimited <- gsub("([+-]{0,1}[0-9]+\\.{0,1}[0-9]([eE][\\+\\-]{0,1}[0-9]+\\.{0,1}[0-9]){0,1})",
50		paste(delim,"\\1",delim,sep=""), x)
	77	delimited <- gsub(regex,
	78	paste(delim,"\\1",delim,sep=""),
	79	x,
	80	perl=TRUE)
51	81
52	82	# separate out numbers
53	83	step1 <- strsplit(delimited, delim)

56	86	step1 <- lapply( step1, function(x) x[x>""] )
57	87
58	88	# create numeric version of data
59		step1.numeric <- lapply( step1, numeric )
	89	suppressWarnings( step1.numeric <- lapply( step1, numeric ) )
60	90
61	91	# create non-numeric version of data
62		step1.character <- lapply( step1, nonnumeric )
	92	suppressWarnings( step1.character <- lapply( step1, nonnumeric ) )
63	93
64	94	# now transpose so that 1st vector contains 1st element from each
65	95	# original string

78	108	)
79	109
80	110	# now order them
81		rank.numeric <- sapply(step1.numeric.t,rank)
	111	rank.numeric <- sapply(step1.numeric.t, rank)
82	112	rank.character <- sapply(step1.character.t,
83	113	function(x) as.numeric(factor(x)))
84	114

94	124
95	125	order.frame <- as.data.frame(rank.overall)
96	126	if(length(which.nas) > 0)
97		order.frame[which.nas,] <- Inf
98		retval <- do.call("order",order.frame)
	127	if(is.na(na.last))
	128	order.frame[which.nas,] <- NA
	129	else if(na.last)
	130	order.frame[which.nas,] <- Inf
	131	else
	132	order.frame[which.nas,] <- -Inf
	133
	134	if(length(which.blanks) > 0)
	135	if(is.na(blank.last))
	136	order.frame[which.blanks,] <- NA
	137	else if(blank.last)
	138	order.frame[which.blanks,] <- 1e99
	139	else
	140	order.frame[which.blanks,] <- -1e99
	141
	142	order.frame <- as.list(order.frame)
	143	order.frame$decreasing <- decreasing
	144	order.frame$na.last <- NA
	145
	146	retval <- do.call("order", order.frame)
99	147
100	148	return(retval)
101	149	}
102
103

-2

R/quantcut.R less more

0		# $Id: quantcut.R 1431 2010-04-28 17:23:08Z ggrothendieck2 $
	0	# $Id: quantcut.R 1949 2015-04-23 21:47:48Z warnes $
1	1
2		quantcut <- function(x, q=seq(0,1,by=0.25), na.rm=TRUE, ... )
	2	quantcut <- function(x, q=4, na.rm=TRUE, ... )
3	3	{
	4	if(length(q)==1)
	5	q <- seq(0,1, length.out=q+1)
	6
4	7	quant <- quantile(x, q, na.rm=na.rm)
5	8	dups <- duplicated(quant)
6	9	if(any(dups))

+48

-0

R/roman2int.R less more

	0	testConvert <- function()
	1	{
	2	roman <- 'IVXLCDM'
	3	retval <- romandigit.convert(roman)
	4	stopifnot(retval==c(1,5,10,50,100,500,1000))
	5	return(TRUE)
	6	}
	7
	8	romandigit.convert <- function(roman)
	9	{
	10	retval <- .C('convert',
	11	roman=as.character(roman),
	12	nchar=as.integer(nchar(roman)),
	13	values=integer(nchar(roman))
	14	)
	15	retval$values
	16	}
	17
	18	roman2int.inner <- function(roman)
	19	{
	20	results <- .C("roman2int",
	21	roman = as.character(roman),
	22	nchar = as.integer(nchar(roman)),
	23	value = integer(1),
	24
	25	PACKAGE="gtools")
	26
	27	return(results$value)
	28	}
	29
	30	roman2int <- function(roman)
	31	{
	32	roman <- trimws(toupper(as.character(roman)))
	33
	34	tryIt <- function(x)
	35	{
	36	retval <- try(roman2int.inner(x), silent=TRUE)
	37	if(is.numeric(retval))
	38	retval
	39	else
	40	NA
	41	}
	42
	43	retval <- sapply(roman, tryIt)
	44
	45	retval
	46	}
	47

-1

R/smartbind.R less more

166	166
167	167	if(length(colClass)>1) # not just plain factor
168	168	{
169		browser()
170	169	warning( "column '", col, "' of class ",
171	170	paste("'", colClass, "'", collapse=":",
172	171	sep="'"),

-23

R/strmacro.R less more

21	21	{
22	22	a[[i]] <- a[[i]]
23	23	}
24		#if (nn[i] == "DOTS")
25		# {
26		# nn[i] <- "..."
27		# a[[i]] <- formals(function(...){})[[1]]
28		# }
29	24	}
30	25	names(a) <- nn
31	26	a <- as.list(a)

37	32	## build replacement list
38	33	reptab <- a # copy defaults first
39	34	reptab$"..." <- NULL
40		#reptab$DOTS <- ""
41	35
42	36	args <- match.call(expand.dots=TRUE)[-1]
43		#print(args)
44	37
45	38	for(item in names(args))
46		##if(item %in% names(reptab))
47	39	reptab[[item]] <- args[[item]]
48		##else
49		## {
50		## browser()
51		## oldval <- reptab[["DOTS"]]
52		## addval <- paste(item, "=", args[[item]])
53		## if(oldval>"")
54		## newval <- paste(c(oldval, addval), collapse=", ")
55		## else
56		## newval <- addval
57		## reptab[["DOTS"]] <- newval
58		## }
59
60		#print(reptab)
61	40
62	41	## do the replacements
63	42	body <- strexpr

76	55	body)
77	56	}
78	57
79		#print(body)
80
81	58	fun <- parse(text=body)
82	59	eval(fun, parent.frame())
83	60

+11

-0

R/trimws.R less more

	0	## trimws was added in R 2.3.0. If we're using a previous version of
	1	## R we need to define it.
	2	if(!exists('trimws', mode='function'))
	3	trimws <- function(s)
	4	{
	5	s <- sub(pattern="^[[:blank:]]+", replacement="", x=s)
	6	s <- sub(pattern="[[:blank:]]+$", replacement="", x=s)
	7	s
	8	}
	9
	10

+29

-0

R/unByteCode.R less more

	0	## Convert a byte-compiled function to an interpreted-code function
	1	unByteCode <- function(fun)
	2	{
	3	FUN <- eval(parse(text=deparse(fun)))
	4	environment(FUN) <- environment(fun)
	5	FUN
	6	}
	7
	8	## Replace function definition inside of a locked environment HACK
	9	assignEdgewise <- function(name, env, value)
	10	{
	11	unlockBinding(name, env=env)
	12	assign( name, envir=env, value=value)
	13	lockBinding(name, env=env)
	14	invisible(value)
	15	}
	16
	17	## Replace byte-compiled function in a locked environment with an
	18	## interpreted-code function
	19	unByteCodeAssign <- function(fun)
	20	{
	21	name <- gsub('^.*::+','', deparse(substitute(fun)))
	22	FUN <- unByteCode(fun)
	23	retval <- assignEdgewise(name=name,
	24	env=environment(FUN),
	25	value=FUN
	26	)
	27	invisible(retval)
	28	}

data/ELISA.rda less more

Binary diff not shown

+513

-543

inst/ChangeLog less more

	0	2015-05-27 warnes
	1
	2	* [r2039] R/mixedsort.R, man/mixedsort.Rd: Add roman numeral
	3	support to mixedorder() and mixedsort().
	4	* [r2037] man/asc.Rd: Add asc() and chr() functions for converting
	5	between characters and ASCII codes
	6	* [r2036] R/roman2int.R: roman2int() now returns NA for invalid
	7	roman numeral strings instead of generating an error.
	8	* [r2035] NAMESPACE: Add asc(), chr(), assignEdgewise(),
	9	unByteCode(), and
	10	unByteCodeAssign() to package NAMESPACE.
	11	* [r2034] R/asc.R: Add asc() and chr() functions for converting
	12	between characters and ASCII codes
	13
	14	2015-05-26 warnes
	15
	16	* [r2030] inst/ChangeLog: Add changelog to svn repository
	17
	18	2015-05-25 warnes
	19
	20	* [r2029] tests/test_ddirichlet.R: Add library call.
	21	* [r2028] man/unByteCode.Rd: Fix typo and add documentation for
	22	argument 'name'.
	23	* [r2027] man/mixedsort.Rd: Fix typo.
	24	* [r2026] man/mixedsort.Rd: Add description of blanklast argument,
	25	fix typo.
	26	* [r2025] man/quantcut.Rd: Change usage to match actual definition.
	27	* [r2024] man/mixedsort.Rd: Note characters sorting ignores case.
	28	* [r2023] man/mixedsort.Rd: Remove '...' from arglist to match
	29	source code.
	30	* [r2022] man/mixedsort.Rd: Replace unicode quotes with \code{..}.
	31
	32	2015-05-23 warnes
	33
	34	* [r2021] tests/test_ddirichlet.R: Add regression test ddirichlet()
	35	bug for x[i]=0, alpha[i]=1:
	36	ddirichlet(x, alpha) was returning NA rather than 0.
	37	* [r2020] R/dirichlet.R: ddirichlet() was incorrectly returning NA
	38	when x[i]=0 and
	39	alpha[i]=1. In this case, the one calculation became (-Inf * 0),
	40	which R evaluates to NaN. The correction is to detect this case
	41	and
	42	substitute -Inf instead of NaN.
	43
	44	2015-05-08 warnes
	45
	46	* [r2019] R/mixedsort.R: Summary: Speed up mixedorder by moving
	47	suppressWarnings outside of
	48	lapply loops. (Suggestion by Henrik Bengtsson.)
	49
	50	2015-05-02 warnes
	51
	52	* [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge
	53	* [r2017] Minor layout change.
	54	* [r2016] Remove stray 'svn' that was inserted into the code.
	55	* [r2015] Add man page for unByteCode(), assignEdgeWise(), and
	56	unByteCodeAssign()
	57
	58	2015-04-28 warnes
	59
	60	* [r1976] Changes to mixedsort():
	61	- Hands off objects that are not character vectors to the default
	62	sort.
	63	- Add 'decreasing', 'na.last', and 'blank.last' arguments.
	64	* [r1975] Add private function 'checkReverseDependencies'.
	65
	66	2015-04-23 warnes
	67
	68	* [r1950] Update NEWS and ChangeLog
	69	* [r1949] - The 'q' argument to quantcut()'s 'q' now accept an
	70	integer
	71	indicating the number of equally spaced quantile groups to
	72	create. (Suggestion and patch submitted by Ryan C. Thompson.)
	73	* [r1946] Revers accidental text deletion:
	74	* [r1945] Update for gtools 3.4.3
	75	* [r1944] Remove debugging code and stray browser() call
	76
	77	2015-04-14 warnes
	78
	79	* [r1923] Fix typo
	80
0	81	2015-04-09 warnes
1	82
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.
	83	* [r1921] Update gtools ChangeLog
	84	* [r1920] Move first()/last()/left()/right() to gdata.
5	85	Add new functions na.replace() and loadedPackages().
6	86	Add more text to package description.
7	87
8	88	2015-04-08 warnes
9	89
10		* [r1919] NAMESPACE, R/first.R, man/first.Rd, man/left.Rd: Move
11		first/last/left/right to from gtools to gdata
	90	* [r1919] Move first/last/left/right to from gtools to gdata
12	91
13	92	2015-04-06 warnes
14	93
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
	94	* [r1918] Correct URL
	95	* [r1917] Update NEWS and ChangeLog for gtools 3.5.0
	96	* [r1916] Add ChangeLog files to repository
	97	* [r1915] Implement fix to keywords() needed for R-3.4.1, as
	98	suggested by Kurt
21	99	Hornik.
22		* [r1914] NAMESPACE, R/first.R: - Export S3 methods for first(),
23		last(), left() and right().
	100	* [r1914] - Export S3 methods for first(), last(), left() and
	101	right().
24	102	- Ensure code matches man page for first(), last(), left(), and
25	103	right().
26	104
27	105	2014-10-09 warnes
28	106
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
	107	* [r1897] Update for 3.5.0 release of gtools
	108	* [r1896] Make right() and left() S3 methods for classes data.frame
	109	and matrix
33	110
34	111	2014-08-27 warnes
35	112
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().
	113	* [r1872] Fix man page
	114	* [r1871] Finish adding first(), last(), left(), and right().
	115	* [r1870] Add functions first(), last(), left(), and right().
41	116
42	117	2014-05-28 warnes
43	118
44		* [r1816] DESCRIPTION, inst/NEWS: Update for gtools 3.4.1
45		* [r1815] tests/smartbind_Dates.R: Add test to ensure smartbind()
46		properly handles Date columns.
47		* [r1814] R/smartbind.R: smartbind: Convert non-native type columns
48		(except factor) to character.
	119	* [r1816] Update for gtools 3.4.1
	120	* [r1815] Add test to ensure smartbind() properly handles Date
	121	columns.
	122	* [r1814] smartbind: Convert non-native type columns (except
	123	factor) to character.
49	124
50	125	2014-04-18 arnima
51	126
52		* [r1813] R/ASCIIfy.R, man/ASCIIfy.Rd: Main arg is 'x' like
53		showNonASCII(x), preformatted notes instead of verb
	127	* [r1813] Main arg is 'x' like showNonASCII(x), preformatted notes
	128	instead of verb
54	129
55	130	2014-04-17 warnes
56	131
57		* [r1810] man/ASCIIfy.Rd: Update ASCIIfy man page to match source
58		code and add keywords
59		* [r1809] inst/NEWS: Update NEWS for gtools 3.4.0
60		* [r1808] DESCRIPTION, NAMESPACE, R/ASCIIfy.R, man/ASCIIfy.Rd: Add
61		ASCIIfy function posted to RDevel by Arni Magnusson
	132	* [r1810] Update ASCIIfy man page to match source code and add
	133	keywords
	134	* [r1809] Update NEWS for gtools 3.4.0
	135	* [r1808] Add ASCIIfy function posted to RDevel by Arni Magnusson
62	136
63	137	2014-03-01 warnes
64	138
65		* [r1776] tests/test_mixedorder.R: Fix cut-and-paste error.
66		* [r1775] DESCRIPTION, inst/NEWS: Update files for gtools 3.3.1
67		release
68		* [r1774] R/mixedsort.R, tests/test_mixedorder.R: Fix bug in
69		gtools::mixedorder regular expression for regognizing numbers.
70		(Periods weren't escaped).
	139	* [r1776] Fix cut-and-paste error.
	140	* [r1775] Update files for gtools 3.3.1 release
	141	* [r1774] Fix bug in gtools::mixedorder regular expression for
	142	regognizing numbers. (Periods weren't escaped).
71	143
72	144	2014-02-11 warnes
73	145
74		* [r1773] R/clean_up_dependencies2.R: Create and use locate copy of
75		tools:::.split_op_version.
76		* [r1772] inst/NEWS: Update for gtools 3.3.0.
77		* [r1771] man/getDependencies.Rd: Fix arguments
78		* [r1770] man/getDependencies.Rd: Update arguments to match code.
79		* [r1769] DESCRIPTION, NAMESPACE, R/clean_up_dependencies2.R,
80		R/getDependencies.R, man/getDependencies.Rd: Add
81		getDependencies() function to return a list of package
82		dependencies.
	146	* [r1773] Create and use locate copy of tools:::.split_op_version.
	147	* [r1772] Update for gtools 3.3.0.
	148	* [r1771] Fix arguments
	149	* [r1770] Update arguments to match code.
	150	* [r1769] Add getDependencies() function to return a list of
	151	package dependencies.
83	152
84	153	2014-01-14 warnes
85	154
86		* [r1768] DESCRIPTION, inst/NEWS: Update for bug-fix release
87		* [r1767] tests, tests/test_binsearch.R: Add test file for
88		binsearch() function.
89		* [r1766] R/binsearch.R: Fixed bug where binsearch() returned the
90		wrong endpoint & value when the found value was at the upper
91		endpoint.
	155	* [r1768] Update for bug-fix release
	156	* [r1767] Add test file for binsearch() function.
	157	* [r1766] Fixed bug where binsearch() returned the wrong endpoint &
	158	value when the found value was at the upper endpoint.
92	159
93	160	2014-01-13 warnes
94	161
95		* [r1765] man/smartbind.Rd: Fix typo
	162	* [r1765] Fix typo
96	163
97	164	2014-01-11 warnes
98	165
99		* [r1764] inst/NEWS: Update for gtools release 3.2.0
100		* [r1763] man/gtools-defunct.Rd: fixes for R CMD check
101		* [r1762] DESCRIPTION, NAMESPACE, R/capture.R, R/defunct.R,
102		R/keywords.R, man/capture.Rd, man/gtools-defunct.Rd,
103		man/stars.pval.Rd: Fixes for gtools release 3.2.0
	166	* [r1764] Update for gtools release 3.2.0
	167	* [r1763] fixes for R CMD check
	168	* [r1762] Fixes for gtools release 3.2.0
104	169
105	170	2013-12-23 warnes
106	171
107		* [r1761] R/keywords.R, man/keywords.Rd: Extend the keywords()
108		function to return keywords associated with a specified topic via
109		'keywords(topic)'.
110		* [r1760] man/stars.pval.Rd: Add keyword.
111		* [r1759] NAMESPACE, R/stars.pval.R, man/stars.pval.Rd: Add
112		stars.pval() function to convert p-values into significance
113		symbols.
	172	* [r1761] Extend the keywords() function to return keywords
	173	associated with a specified topic via 'keywords(topic)'.
	174	* [r1760] Add keyword.
	175	* [r1759] Add stars.pval() function to convert p-values into
	176	significance symbols.
114	177
115	178	2013-11-26 warnes
116	179
117		* [r1748] R/mixedsort.R: mixedorder() was failing to correctly
118		handle numbers including
	180	* [r1748] mixedorder() was failing to correctly handle numbers
	181	including
119	182	decimals due to a faulty regular expression. Prior to the fix:
120	183
121	184	> drr

136	199
137	200	2013-11-18 warnes
138	201
139		* [r1747] R/capture.R: Use ".Deprecated" instead of warning.
	202	* [r1747] Use ".Deprecated" instead of warning.
140	203
141	204	2013-11-06 warnes
142	205
143		* [r1746] DESCRIPTION, inst/NEWS: Update files for gtools 3.1.1
144		* [r1745] R/mixedsort.R: Fix problem with mixedorder/mixedsort when
145		there is only zero or one elements in the vector.
	206	* [r1746] Update files for gtools 3.1.1
	207	* [r1745] Fix problem with mixedorder/mixedsort when there is only
	208	zero or one elements in the vector.
146	209
147	210	2013-09-23 warnes
148	211
149		* [r1716] man/gtools-deprecated.Rd: Comment out empty sections in
150		gtools-deprecated.Rd
151		* [r1715] DESCRIPTION, inst/NEWS: Update files for gtools 3.1.0
	212	* [r1716] Comment out empty sections in gtools-deprecated.Rd
	213	* [r1715] Update files for gtools 3.1.0 release
	214	* [r1714] Make 'addLast()' defunct.
	215	* [r1713] Mark 'addLast()' as defunct and move 'lastAdd()' function
	216	to a separate file.
	217	* [r1712] Update for gtools 3.0.1 release
	218	* [r1711] Use 'suppressWarnings() instead of 'options(warn=-1)' in
	219	'mixedorder()'.
	220
	221	2013-07-07 warnes
	222
	223	* [r1705] Fix typo.
	224
	225	2013-07-06 warnes
	226
	227	* [r1704] Fix Rd warning.
	228	* [r1703] Include lastAdd in NAMESPACE
	229	* [r1702] Change assert from deprecated to defunct.
	230	* [r1701] Improve deprecation message
	231	* [r1700] Update for gtools 3.0.0
	232	* [r1699] Create new function lastAdd to replace addLast and mark
	233	addLast as deprecated.
	234
	235	2013-07-05 warnes
	236
	237	* [r1698] Point out that addLast() modifies the value of .Last in
	238	the global environment.
	239	* [r1697] Point out that addLast() modifies the value of .Last in
	240	the global environment.
	241	* [r1696] Update for gtools 2.7.2 mark 2
	242	* [r1695] Remove cross-reference to (obsolete?) moc package
	243	* [r1694] Update for gtools 2.7.2
	244	* [r1693] Update for R version 3.0.0 and later
	245
	246	2013-03-17 warnes
	247
	248	* [r1640] Fix error in smartbind: factor levels were not being
	249	handled if the factor column was not present in the first data
	250	frame.
	251
	252	2012-06-19 warnes
	253
	254	* [r1570] Update for gtools 2.7.0.
	255	* [r1569] Document new 'verbose' argument to smartbind().
	256	* [r1568] Clean up R CMD check warnings.
	257
	258	2012-05-04 warnes
	259
	260	* [r1529] smartbind(): Improve handling of factors and ordered
	261	factors.
	262
	263	2011-10-05 warnes
	264
	265	* [r1518] Update version number for release
	266	* [r1517] Add 'sep' argument to smartbind() to allow specification
	267	of character used to separate components of constructed names
	268
	269	2011-09-28 warnes
	270
	271	* [r1513] smartbind(): Prevent coersion to data frame from mangling
	272	column names.
	273	* [r1512] Add 'fill' argument to smartbind() to specify a value to
	274	use for
	275	missing entries.
	276	* [r1511] Add 'fill' argument to smartbind() to specify a value to
	277	use for
	278	missing entries.
	279
	280	2010-08-14 warnes
	281
	282	* [r1451] Modify mixedorder()/mixedsort() to better handle strings
	283	containing multiple periods, like version numbers (e.g 1.1.2,
	284	1.2.1. 1.1.1.1).
	285
	286	2010-05-01 warnes
	287
	288	* [r1434] Update version number for new release
	289	* [r1433] Change Greg's email address to greg@warnes.net
	290	* [r1432] Fix error in checkRVersion()
	291
	292	2010-04-28 ggrothendieck2
	293
	294	* [r1431] fixed problems with R CMD CHECK
	295
	296	2009-05-09 warnes
	297
	298	* [r1328] Escape $ in .Rd file to avoid latex issues
	299	* [r1327] Update NEWS and create softlinks for NEWS and ChangeLog
	300	in top level directory
	301	* [r1326] Move actual NEWS file into inst.
	302	* [r1325] Update Greg's email address and fix Rd syntax errors
	303
	304	2009-02-16 warnes
	305
	306	* [r1313] Correct windows make flags as suggested by Brian Ripley.
	307
	308	2008-08-15 warnes
	309
	310	* [r1303] Add keywords() function to show /doc/KEYWORDS file
	311
	312	2008-05-29 warnes
	313
	314	* [r1285] Add newVersionAvailable() function to compare running and
	315	latest available R versions
	316
	317	2008-05-26 warnes
	318
	319	* [r1284] Update license specification
	320	* [r1283] Remove 'assert' man page
	321
	322	2008-05-22 warnes
	323
	324	* [r1282] Finish rename of assert.R to assert-depricated.Rd
	325	* [r1281] Add checkRVersion.R file
	326	* [r1280] Rename again to get correct extension!
	327	* [r1279] Update NEWS for 2.5.0
	328	* [r1278] Add man page for checkRVersion
	329	* [r1277] Rename assert-deprecated.R to assert.R to meet R file
	330	name requirements.
	331	* [r1276] Add checkRVersion to NAMESPACE, and increment version in
	332	DESCRIPTION.
	333	* [r1275] Remove broken SEE LSO reference
	334
	335	2008-04-12 warnes
	336
	337	* [r1259] Improve text explanation of how defmacro() and strmacro()
	338	differ from
	339	function().
	340	* [r1258] assert() is now deprecated in favor of base::stopifnot()
	341	* [r1257] Rename 'assert.R' to 'deprecated.R'.
	342	* [r1256] Assert is now deprecated in favor of base::stopifnot(),
	343	so add call to
	344	.Deprecated() to inform the user.
	345
	346	2007-11-30 warnes
	347
	348	* [r1228] Update defnitions of odd() and even() to use modulus
	349	operator instead of division. Prettier, I think, :-D
	350
	351	2007-08-08 warnes
	352
	353	* [r1121] Fix bug identified by R-2.6's check routings in
	354	binsearch()
	355	* [r1120] Add the binsearch(), previously in the genetics package.
	356
	357	2007-07-18 ggorjan
	358
	359	* [r1100] typo fixed
	360
	361	2007-04-12 warnes
	362
	363	* [r1088] Add ask() function to prompt the user and collect a
	364	single response.
	365
	366	2007-04-07 warnes
	367
	368	* [r1087] Fix improper escapes in regexp detected by R 2.5.0
	369	package check.
	370
	371	2007-03-23 warnes
	372
	373	* [r1083] Allow permutations for r>n provided repeats.allowed=TRUE
	374
	375	2006-11-28 warnes
	376
	377	* [r1023] Replace F with FALSE in smartbind example.
	378
	379	2006-11-27 warnes
	380
	381	* [r1022] Replace T with TRUE in smartbind example
	382	* [r1021] Temprary remove to reset binary flag
	383	* [r1020] Temprary remove to reset binary flag
	384	* [r1019] Add smartbind() to list of exported functions, and add
	385	corresponding
	386	documentation file.
	387	* [r1018] Update my email address
	388
	389	2006-11-14 ggorjan
	390
	391	* [r1012] Removed executable property
	392
	393	2006-08-02 warnes
	394
	395	* [r977] Update my email address
	396
	397	2006-05-05 nj7w
	398
	399	* [r958] Fixed minor typo - in {value} - n was replaced by r
	400	* [r957] Fixed minor typos
	401
	402	2006-03-01 warnes
	403
	404	* [r903] Add smartbind function
	405
	406	2006-01-18 warnes
	407
	408	* [r845] Add concept tags to make mixedsort easier to locate.
	409
	410	2005-12-21 warnes
	411
	412	* [r837] Update version number and date
	413	* [r836] Note changes for 2.2.3
	414	* [r835] Should now work on Windows
	415
	416	2005-12-20 warnes
	417
	418	* [r834] Temporary fix to allow setTCPNoDelay.c to compile on
	419	Windows. If compiled on windows calling setTCPNoDelay will just
	420	raise an error.
	421
	422	2005-12-14 warnes
	423
	424	* [r813] Change C++ comment to standard comment
	425
	426	2005-12-13 nj7w
	427
	428	* [r810] * empty log message *
	429	* [r809] Updated NEWS and removed ChangeLog
	430
	431	2005-12-12 nj7w
	432
	433	* [r800] Updated version for CRAN release
	434
	435	2005-12-08 warnes
	436
	437	* [r790] Add C source code for setTCPNoDelay.
	438
	439	2005-12-01 nj7w
	440
	441	* [r776] Updated Greg's email address
	442
	443	2005-11-29 warnes
	444
	445	* [r769] Add UseDynLib to NAMESPACE so the shared library gets
	446	properly loaded.
	447	* [r768] - Remove debugging comments
	448	- Change return value on success to "Success".
	449
	450	2005-11-22 warnes
	451
	452	* [r758] NAMESPACE
	453	* [r757] Update news for 2.2.1 release.
	454	* [r756] Fixes for R CMD check
	455	* [r755] Add setTCPNoDelay() function and documentation
	456	* [r745] New function 'addLast' that adds functions to R's .Last()
	457	so that
	458	they will be executed when R is terminating.
	459
	460	2005-09-22 warnes
	461
	462	* [r678] More changes for strmacro(), also changes for 2.1.1
152	463	release
153		* [r1714] man/addLast-deprecated.Rd, man/gtools-defunct.Rd,
154		man/gtools-deprecated.Rd, man/lastAdd.Rd: Make 'addLast()'
155		defunct.
156		* [r1713] R/addLast.R, R/lastAdd.R: Mark 'addLast()' as defunct and
157		move 'lastAdd()' function to a separate file.
158		* [r1712] DESCRIPTION, inst/NEWS: Update for gtools 3.0.1 release
159		* [r1711] R/mixedsort.R: Use 'suppressWarnings() instead of
160		'options(warn=-1)' in 'mixedorder()'.
161
162		2013-07-07 warnes
163
164		* [r1705] man/lastAdd.Rd: Fix typo.
165
166		2013-07-06 warnes
167
168		* [r1704] man/lastAdd.Rd: Fix Rd warning.
169		* [r1703] NAMESPACE: Include lastAdd in NAMESPACE
170		* [r1702] R/deprecated.R: Change assert from deprecated to defunct.
171		* [r1701] R/addLast.R: Improve deprecation message
172		* [r1700] DESCRIPTION, inst/NEWS: Update for gtools 3.0.0
173		* [r1699] R/addLast.R, man/addLast-deprecated.Rd, man/addLast.Rd,
174		man/gtools-defunct.Rd, man/gtools-deprecated.Rd, man/lastAdd.Rd:
175		Create new function lastAdd to replace addLast and mark addLast
176		as deprecated.
177
178		2013-07-05 warnes
179
180		* [r1698] inst/NEWS: Point out that addLast() modifies the value of
181		.Last in the global environment.
182		* [r1697] man/addLast.Rd: Point out that addLast() modifies the
183		value of .Last in the global environment.
184		* [r1696] DESCRIPTION, inst/NEWS: Update for gtools 2.7.2 mark 2
185		* [r1695] man/logit.Rd: Remove cross-reference to (obsolete?) moc
186		package
187		* [r1694] DESCRIPTION, inst/NEWS: Update for gtools 2.7.2
188		* [r1693] R/checkRVersion.R: Update for R version 3.0.0 and later
189
190		2013-03-17 warnes
191
192		* [r1640] R/smartbind.R: Fix error in smartbind: factor levels were
193		not being handled if the factor column was not present in the
194		first data frame.
195
196		2012-06-19 warnes
197
198		* [r1570] DESCRIPTION, inst/NEWS: Update for gtools 2.7.0.
199		* [r1569] man/smartbind.Rd: Document new 'verbose' argument to
200		smartbind().
201		* [r1568] R/addLast.R, R/running.R: Clean up R CMD check warnings.
202
203		2012-05-04 warnes
204
205		* [r1529] R/smartbind.R: smartbind(): Improve handling of factors
206		and ordered factors.
207
208		2011-10-05 warnes
209
210		* [r1518] DESCRIPTION: Update version number for release
211		* [r1517] R/smartbind.R, man/smartbind.Rd: Add 'sep' argument to
212		smartbind() to allow specification of character used to separate
213		components of constructed names
214
215		2011-09-28 warnes
216
217		* [r1513] R/smartbind.R: smartbind(): Prevent coersion to data
218		frame from mangling column names.
219		* [r1512] R/smartbind.R, inst/NEWS: Add 'fill' argument to
220		smartbind() to specify a value to use for
221		missing entries.
222		* [r1511] DESCRIPTION, man/smartbind.Rd: Add 'fill' argument to
223		smartbind() to specify a value to use for
224		missing entries.
225
226		2010-08-14 warnes
227
228		* [r1451] R/mixedsort.R: Modify mixedorder()/mixedsort() to better
229		handle strings containing multiple periods, like version numbers
230		(e.g 1.1.2, 1.2.1. 1.1.1.1).
231
232		2010-05-01 warnes
233
234		* [r1434] DESCRIPTION: Update version number for new release
235		* [r1433] DESCRIPTION, man/addLast.Rd, man/ask.Rd,
236		man/binsearch.Rd, man/capture.Rd, man/combinations.Rd,
237		man/defmacro.Rd, man/dirichlet.Rd, man/foldchange.Rd,
238		man/invalid.Rd, man/keywords.Rd, man/logit.Rd, man/mixedsort.Rd,
239		man/oddeven.Rd, man/permute.Rd, man/quantcut.Rd, man/running.Rd,
240		man/scat.Rd, man/setTCPNoDelay.Rd, man/smartbind.Rd: Change
241		Greg's email address to greg@warnes.net
242		* [r1432] R/checkRVersion.R: Fix error in checkRVersion()
243
244		2010-04-28 ggrothendieck2
245
246		* [r1431] R/quantcut.R, R/strmacro.R, man/binsearch.Rd,
247		man/capture.Rd, man/setTCPNoDelay.Rd: fixed problems with R CMD
248		CHECK
249
250		2009-05-09 warnes
251
252		* [r1328] man/keywords.Rd: Escape $ in .Rd file to avoid latex
253		issues
254		* [r1327] ChangeLog, NEWS, inst/NEWS: Update NEWS and create
255		softlinks for NEWS and ChangeLog in top level directory
256		* [r1326] NEWS, inst, inst/NEWS: Move actual NEWS file into inst.
257		* [r1325] DESCRIPTION, man/addLast.Rd, man/binsearch.Rd,
258		man/capture.Rd, man/combinations.Rd, man/defmacro.Rd,
259		man/dirichlet.Rd, man/foldchange.Rd, man/gtools-deprecated.Rd,
260		man/invalid.Rd, man/logit.Rd, man/mixedsort.Rd, man/oddeven.Rd,
261		man/permute.Rd, man/quantcut.Rd, man/running.Rd, man/scat.Rd,
262		man/setTCPNoDelay.Rd, man/smartbind.Rd: Update Greg's email
263		address and fix Rd syntax errors
264
265		2009-02-16 warnes
266
267		* [r1313] src/Makevars.win: Correct windows make flags as suggested
268		by Brian Ripley.
269
270		2008-08-15 warnes
271
272		* [r1303] DESCRIPTION, NAMESPACE, R/keywords.R, man/keywords.Rd:
273		Add keywords() function to show /doc/KEYWORDS file
274
275		2008-05-29 warnes
276
277		* [r1285] R/newVersionAvailable.R: Add newVersionAvailable()
278		function to compare running and latest available R versions
279
280		2008-05-26 warnes
281
282		* [r1284] DESCRIPTION: Update license specification
283		* [r1283] man/assert-deprecated.Rd: Remove 'assert' man page
284
285		2008-05-22 warnes
286
287		* [r1282] man/assert.R: Finish rename of assert.R to
288		assert-depricated.Rd
289		* [r1281] R/checkRVersion.R: Add checkRVersion.R file
290		* [r1280] man/assert-deprecated.Rd: Rename again to get correct
291		extension!
292		* [r1279] NEWS: Update NEWS for 2.5.0
293		* [r1278] man/checkRVersion.Rd: Add man page for checkRVersion
294		* [r1277] man/assert-deprecated.R, man/assert.R: Rename
295		assert-deprecated.R to assert.R to meet R file name requirements.
296		* [r1276] DESCRIPTION, NAMESPACE: Add checkRVersion to NAMESPACE,
297		and increment version in DESCRIPTION.
298		* [r1275] man/gtools-deprecated.Rd: Remove broken SEE LSO reference
299
300		2008-04-12 warnes
301
302		* [r1259] man/defmacro.Rd: Improve text explanation of how
303		defmacro() and strmacro() differ from
304		function().
305		* [r1258] NEWS, man/assert-deprecated.R, man/assert.Rd,
306		man/gtools-deprecated.Rd: assert() is now deprecated in favor of
307		base::stopifnot()
308		* [r1257] R/assert.R, R/deprecated.R: Rename 'assert.R' to
309		'deprecated.R'.
310		* [r1256] R/assert.R: Assert is now deprecated in favor of
311		base::stopifnot(), so add call to
312		.Deprecated() to inform the user.
313
314		2007-11-30 warnes
315
316		* [r1228] R/oddeven.R: Update defnitions of odd() and even() to use
317		modulus operator instead of division. Prettier, I think, :-D
318
319		2007-08-08 warnes
320
321		* [r1121] DESCRIPTION, R/binsearch.R: Fix bug identified by R-2.6's
322		check routings in binsearch()
323		* [r1120] DESCRIPTION, NAMESPACE, NEWS, R/binsearch.R,
324		man/binsearch.Rd: Add the binsearch(), previously in the genetics
325		package.
326
327		2007-07-18 ggorjan
328
329		* [r1100] man/combinations.Rd: typo fixed
330
331		2007-04-12 warnes
332
333		* [r1088] NAMESPACE, NEWS, R/ask.R, man/ask.Rd: Add ask() function
334		to prompt the user and collect a single response.
335
336		2007-04-07 warnes
337
338		* [r1087] DESCRIPTION, R/mixedsort.R: Fix improper escapes in
339		regexp detected by R 2.5.0 package check.
340
341		2007-03-23 warnes
342
343		* [r1083] R/combinations.R: Allow permutations for r>n provided
344		repeats.allowed=TRUE
345
346		2006-11-28 warnes
347
348		* [r1023] man/smartbind.Rd: Replace F with FALSE in smartbind
349		example.
350
351		2006-11-27 warnes
352
353		* [r1022] man/smartbind.Rd: Replace T with TRUE in smartbind
354		example
355		* [r1021] data/ELISA.rda: Temprary remove to reset binary flag
356		* [r1020] data/ELISA.rda: Temprary remove to reset binary flag
357		* [r1019] DESCRIPTION, NAMESPACE, NEWS, R/smartbind.R,
358		man/smartbind.Rd: Add smartbind() to list of exported functions,
359		and add corresponding
360		documentation file.
361		* [r1018] DESCRIPTION: Update my email address
362
363		2006-11-14 ggorjan
364
365		* [r1012] R/combinations.R, R/running.R, man/ELISA.Rd,
366		man/combinations.Rd: Removed executable property
367
368		2006-08-02 warnes
369
370		* [r977] man/addLast.Rd, man/assert.Rd, man/capture.Rd,
371		man/combinations.Rd, man/defmacro.Rd, man/dirichlet.Rd,
372		man/foldchange.Rd, man/invalid.Rd, man/logit.Rd,
373		man/mixedsort.Rd, man/oddeven.Rd, man/permute.Rd,
374		man/quantcut.Rd, man/running.Rd, man/scat.Rd,
375		man/setTCPNoDelay.Rd: Update my email address
376
377		2006-05-05 nj7w
378
379		* [r958] man/combinations.Rd: Fixed minor typo - in {value} - n was
380		replaced by r
381		* [r957] NAMESPACE, man/capture.Rd: Fixed minor typos
382
383		2006-03-01 warnes
384
385		* [r903] R/smartbind.R: Add smartbind function
386
387		2006-01-18 warnes
388
389		* [r845] man/mixedsort.Rd: Add concept tags to make mixedsort
390		easier to locate.
391
392		2005-12-21 warnes
393
394		* [r837] DESCRIPTION: Update version number and date
395		* [r836] NEWS: Note changes for 2.2.3
396		* [r835] src/Makevars.win, src/setTCPNoDelay.c: Should now work on
397		Windows
398
399		2005-12-20 warnes
400
401		* [r834] src/setTCPNoDelay.c: Temporary fix to allow
402		setTCPNoDelay.c to compile on Windows. If compiled on windows
403		calling setTCPNoDelay will just raise an error.
404
405		2005-12-14 warnes
406
407		* [r813] src/setTCPNoDelay.c: Change C++ comment to standard
408		comment
409
410		2005-12-13 nj7w
411
412		* [r810] ChangeLog: * empty log message *
413		* [r809] NEWS: Updated NEWS and removed ChangeLog
414
415		2005-12-12 nj7w
416
417		* [r800] DESCRIPTION: Updated version for CRAN release
418
419		2005-12-08 warnes
420
421		* [r790] src, src/setTCPNoDelay.c: Add C source code for
422		setTCPNoDelay.
423
424		2005-12-01 nj7w
425
426		* [r776] man/combinations.Rd, man/foldchange.Rd, man/invalid.Rd,
427		man/logit.Rd, man/mixedsort.Rd, man/oddeven.Rd, man/quantcut.Rd,
428		man/running.Rd: Updated Greg's email address
429
430		2005-11-29 warnes
431
432		* [r769] NAMESPACE: Add UseDynLib to NAMESPACE so the shared
433		library gets properly loaded.
434		* [r768] R/setTCPNoDelay.R: - Remove debugging comments
435		- Change return value on success to "Success".
436
437		2005-11-22 warnes
438
439		* [r758] NAMESPACE: NAMESPACE
440		* [r757] NEWS: Update news for 2.2.1 release.
441		* [r756] man/addLast.Rd, man/setTCPNoDelay.Rd: Fixes for R CMD
442		check
443		* [r755] DESCRIPTION, NAMESPACE, R/setTCPNoDelay.R,
444		man/setTCPNoDelay.Rd: Add setTCPNoDelay() function and
445		documentation
446		* [r745] R/addLast.R, man/addLast.Rd: New function 'addLast' that
447		adds functions to R's .Last() so that
448		they will be executed when R is terminating.
449
450		2005-09-22 warnes
451
452		* [r678] DESCRIPTION, NAMESPACE, man/defmacro.Rd: More changes for
453		strmacro(), also changes for 2.1.1 release
454		* [r677] R/defmacro.R, R/strmacro.R, man/defmacro.Rd: Add strmaco()
455		which defines functions that use strings for macro definition
	464	* [r677] Add strmaco() which defines functions that use strings for
	465	macro definition
456	466
457	467	2005-09-21 warnes
458	468
459		* [r676] DESCRIPTION, R/defmacro.R, man/defmacro.Rd: Add support
460		for DOTS/... arguments to defmacro
	469	* [r676] Add support for DOTS/... arguments to defmacro
461	470
462	471	2005-09-12 nj7w
463	472
464		* [r671] man/assert.Rd, man/dirichlet.Rd, man/permute.Rd,
465		man/scat.Rd: Updated Greg's email
	473	* [r671] Updated Greg's email
466	474
467	475	2005-09-02 nj7w
468	476
469		* [r653] NAMESPACE: Exported assert
470		* [r652] DESCRIPTION: Updated the version number
471		* [r651] NEWS: Added NEWS
472		* [r650] ChangeLog: Added ChangeLog
473		* [r649] man/assert.Rd: Fixed syntax errors
	477	* [r653] Exported assert
	478	* [r652] Updated the version number
	479	* [r651] Added NEWS
	480	* [r650] Added ChangeLog
	481	* [r649] Fixed syntax errors
474	482
475	483	2005-09-02 warnes
476	484
477		* [r648] R/assert.R, man/assert.Rd: Add assert() and documentation
478		* [r647] man/defmacro.Rd: Fix problem in defmacro.Rd file: don't
479		use \code{} in the example section.
	485	* [r648] Add assert() and documentation
	486	* [r647] Fix problem in defmacro.Rd file: don't use \code{} in the
	487	example section.
480	488
481	489	2005-08-31 warnes
482	490
483		* [r645] DESCRIPTION, NAMESPACE, R/defmacro.R, man/defmacro.Rd:
484		Adding the defmacro() function, extracted from
	491	* [r645] Adding the defmacro() function, extracted from
485	492
486	493	Lumley T. "Programmer's Niche: Macros in {R}", R News, 2001, Vol
487	494	1,
488	495	No. 3, pp 11--13, \url{http://CRAN.R-project.org/doc/Rnews/}
489		* [r642] DESCRIPTION, DESCRIPTION.in: Add stand-alone DESCRIPTION
490		file and remove old DESCRIPTION.in file.
	496	* [r642] Add stand-alone DESCRIPTION file and remove old
	497	DESCRIPTION.in file.
491	498
492	499	2005-06-13 nj7w
493	500
494		* [r626] R/mixedsort.R: Fixed a bug in mixedsort - check if
495		"which.na" and "which.blank" is numeric(0) before subsetting the
496		datasets.
	501	* [r626] Fixed a bug in mixedsort - check if "which.na" and
	502	"which.blank" is numeric(0) before subsetting the datasets.
497	503
498	504	2005-06-09 nj7w
499	505
500		* [r625] R/RSCompat.S, R/combinations.R, R/dirichlet.R,
501		R/foldchange.R, R/invalid.R, R/logit.R, R/mixedsort.R,
502		R/oddeven.R, R/permute.R, R/quantcut.R, R/running.R, R/scat.R,
503		man/ELISA.Rd, man/combinations.Rd, man/dirichlet.Rd,
504		man/foldchange.Rd, man/invalid.Rd, man/logit.Rd,
505		man/mixedsort.Rd, man/oddeven.Rd, man/permute.Rd,
506		man/quantcut.Rd, man/running.Rd, man/scat.Rd: Updating the
507		version number, and various help files to synchronize splitting
508		of gregmisc bundle in 4 individual components.
	506	* [r625] Updating the version number, and various help files to
	507	synchronize splitting of gregmisc bundle in 4 individual
	508	components.
509	509
510	510	2005-05-10 warnes
511	511
512		* [r619] R/mixedsort.R: Fix handling of NA's in mixedorder. We were
513		using a high UTF character to try
	512	* [r619] Fix handling of NA's in mixedorder. We were using a high
	513	UTF character to try
514	514	to put NA's at the end of the sort order, but R 2.1.0 checks if
515	515	characters
516	516	are in the correct range. Instead, we explicitly force NA's to

518	518
519	519	2005-04-07 warnes
520	520
521		* [r606] NAMESPACE, R/scat.R, man/scat.Rd: - Add scat() function
522		which writes its arguments to stderr and
	521	* [r606] - Add scat() function which writes its arguments to stderr
	522	and
523	523	flushes so that output is immediately displayed, but only if
524	524	'getOption("DEBUG")' is true.
525	525
526	526	2005-04-02 warnes
527	527
528		* [r600] NAMESPACE, R/drop.levels.R, man/drop.levels.Rd: Move
529		drop.levels() from gtools to gdata.
530		* [r599] R/mixedsort.R: Minor reordering of functions in file
531		* [r598] NAMESPACE, R/frameApply.R, man/frameApply.Rd: Move
532		frameApply() to gdata package.
533		* [r597] R/mixedsort.R: Fix error if only one value passed to
534		mixedorder.
535		* [r596] R/quantcut.R, man/quantcut.Rd: Add proper handling where
536		more than one quantile obtains the same value
	528	* [r600] Move drop.levels() from gtools to gdata.
	529	* [r599] Minor reordering of functions in file
	530	* [r598] Move frameApply() to gdata package.
	531	* [r597] Fix error if only one value passed to mixedorder.
	532	* [r596] Add proper handling where more than one quantile obtains
	533	the same value
537	534
538	535	2005-04-01 warnes
539	536
540		* [r595] man/ELISA.Rd, man/combinations.Rd, man/dirichlet.Rd,
541		man/drop.levels.Rd, man/foldchange.Rd, man/invalid.Rd,
542		man/logit.Rd, man/mixedsort.Rd, man/oddeven.Rd, man/permute.Rd,
543		man/quantcut.Rd, man/running.Rd: Add CVS ID tag to file headers.
544		* [r594] R/frameApply.R, man/frameApply.Rd: Fixes from Jim Rogers
545		for R CMD check problems in frameApply
	537	* [r595] Add CVS ID tag to file headers.
	538	* [r594] Fixes from Jim Rogers for R CMD check problems in
	539	frameApply
546	540
547	541	2005-03-31 warnes
548	542
549		* [r591] R/drop.levels.R, R/frameApply.R, man/drop.levels.Rd,
550		man/frameApply.Rd: Updates to drop.levels() and frameApply() from
551		Jim Rogers
552		* [r590] data, data/ELISA.rda, man/ELISA.Rd: Add ELISA data set
553		used by frameApply and drop.levels examples
	543	* [r591] Updates to drop.levels() and frameApply() from Jim Rogers
	544	* [r590] Add ELISA data set used by frameApply and drop.levels
	545	examples
554	546
555	547	2005-02-25 warnes
556	548
557		* [r562] man/frameApply.Rd: Replace 'T' with TRUE.
558		* [r561] man/frameApply.Rd: Remove dependency on ELISA data set for
559		the example.
560		* [r558] NAMESPACE: Add drop.levels, frameApply to namespace
561		export.
	549	* [r562] Replace 'T' with TRUE.
	550	* [r561] Remove dependency on ELISA data set for the example.
	551	* [r558] Add drop.levels, frameApply to namespace export.
562	552
563	553	2005-02-15 warnes
564	554
565		* [r542] R/drop.levels.R, R/frameApply.R, man/drop.levels.Rd,
566		man/frameApply.Rd: Add frameApply and drop.levels contributed by
567		Jim Rogers.
	555	* [r542] Add frameApply and drop.levels contributed by Jim Rogers.
568	556
569	557	2005-01-12 warnes
570	558
571		* [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
572		poeple from installing on old
	559	* [r515] Add dependency on R 1.9.0+ to prevent poeple from
	560	installing on old
573	561	versions of R which don't support namespaces.
574	562
575	563	2004-09-27 warneg
576	564
577		* [r461] DESCRIPTION, DESCRIPTION.in, man/running.Rd: Updated to
578		pass R CMD check.
	565	* [r461] Updated to pass R CMD check.
579	566
580	567	2004-09-03 warneg
581	568
582		* [r446] DESCRIPTION, NAMESPACE, R/dirichlet.R, R/foldchange.R,
583		R/invalid.R, R/mixedsort.R, R/oddeven.R, R/permute.R,
584		R/quantcut.R, R/running.R, man/running.Rd: initial bundle checkin
	569	* [r446] initial bundle checkin
585	570
586	571	2004-09-02 warneg
587	572
588		* [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision
	573	* [r442] Initial revision
589	574
590	575	2004-08-27 warnes
591	576
592		* [r441] R/mixedsort.R, man/mixedsort.Rd: Fixed bug in mixedsort,
593		and modified reorder.factor to use mixedsort.
	577	* [r441] Fixed bug in mixedsort, and modified reorder.factor to use
	578	mixedsort.
594	579
595	580	2004-08-26 warnes
596	581
597		* [r440] R/mixedsort.R: - Fix bug pointed out by Jim Rogers.
	582	* [r440] - Fix bug pointed out by Jim Rogers.
598	583	- Use a more distictive internal separator: $@$ instead of just $
599	584	- Capitalization is now irrelevent for search order (unlike
600	585	ASCII).
601	586
602	587	2004-06-08 warnes
603	588
604		* [r372] R/running.R, man/running.Rd: Nitin Jain added by=
605		parameter to allow specifying separation between groups.
	589	* [r372] Nitin Jain added by= parameter to allow specifying
	590	separation between groups.
606	591
607	592	2004-05-26 warnes
608	593
609		* [r345] man/combinations.Rd: Escape underscores in email addresses
610		so Latex is happy.
611		* [r343] R/combinations.R: Replace 'T' with 'TRUE' to pass R CMD
612		check.
	594	* [r345] Escape underscores in email addresses so Latex is happy.
	595	* [r343] Replace 'T' with 'TRUE' to pass R CMD check.
613	596
614	597	2004-05-25 warnes
615	598
616		* [r334] R/combinations.R: Remove extraneous comments.
617		* [r333] R/combinations.R: Fix an error in the code when using
618		repeats.allow=T and r>2. Bug
	599	* [r334] Remove extraneous comments.
	600	* [r333] Fix an error in the code when using repeats.allow=T and
	601	r>2. Bug
619	602	report and fix both due to Elizabeth Purdom
620	603	<epurdom@stanford.edu>.
621	604
622	605	2004-05-24 warnes
623	606
624		* [r323] R/invalid.R: Check if argument is a vector before doing
625		is.na to avoid generating a warning.
626		* [r322] R/invalid.R, man/invalid.Rd: Add invalid() function for
627		testing if a parameter value is non-missing, non-NA,
	607	* [r323] Check if argument is a vector before doing is.na to avoid
	608	generating a warning.
	609	* [r322] Add invalid() function for testing if a parameter value is
	610	non-missing, non-NA,
628	611	non-NULL.
629	612
630	613	2004-04-27 warnes
631	614
632		* [r321] R/running.R, man/running.Rd: Replaced argument `as.list'
633		with `simplify'. Updated documentation,
	615	* [r321] Replaced argument `as.list' with `simplify'. Updated
	616	documentation,
634	617	and updated examples appropriately.
635	618
636	619	2004-04-26 warnes
637	620
638		* [r320] R/running.R, man/running.Rd: Added as.list argument to
639		return one list element per evaluation.
	621	* [r320] Added as.list argument to return one list element per
	622	evaluation.
640	623
641	624	2004-03-26 warnes
642	625
643		* [r303] man/combinations.Rd: Uncomment and fix large 'n' example.
644		* [r301] man/running.Rd: - Update to match changes in running()
	626	* [r303] Uncomment and fix large 'n' example.
	627	* [r301] - Update to match changes in running()
645	628	- Add examples to illustrate new arguments.
646	629	- Modify running correlation plot example to be more clear.
647		* [r299] R/running.R: More of the same.
648		* [r297] R/running.R: Fix bug discovered by Sean Davis
649		<sdavis2@mail.nih.gov>. The running
	630	* [r299] More of the same.
	631	* [r297] Fix bug discovered by Sean Davis <sdavis2@mail.nih.gov>.
	632	The running
650	633	function took an improper shortcut. When allow.fewer=FALSE it was
651	634	still passing shorter lists of elements to the called function,
652	635	and

657	640
658	641	2004-01-21 warnes
659	642
660		* [r277] R/capture.R: - Mark sprint() as depreciated.
	643	* [r277] - Mark sprint() as depreciated.
661	644	- Replace references to sprint with capture.output()
662	645	- Use match.arg for halign and valign arguments to
663	646	textplot.default.

669	652
670	653	2003-12-03 warnes
671	654
672		* [r253] man/foldchange.Rd: - match function argument defaults with
673		'usage'
	655	* [r253] - match function argument defaults with 'usage'
674	656
675	657	2003-11-21 warnes
676	658
677		* [r237] man/foldchange.Rd: Removed 'deqn' call that was confusing
678		things.
679		* [r234] man/logit.Rd: Add email address to author field
680		* [r233] R/foldchange.R, man/foldchange.Rd: - new files
681		* [r232] R/mixedsort.R, man/mixedsort.Rd: - Change 'T' to 'TRUE' in
682		mixedsort.R
	659	* [r237] Removed 'deqn' call that was confusing things.
	660	* [r234] Add email address to author field
	661	* [r233] - new files
	662	* [r232] - Change 'T' to 'TRUE' in mixedsort.R
683	663	- Add missing brace in mixedsort.Rd
684	664
685	665	2003-11-20 warnes
686	666
687		* [r230] R/oddeven.R, man/oddeven.Rd: - Move 'odd' and 'even'
688		functions to a separate file & provide documentation
	667	* [r230] - Move 'odd' and 'even' functions to a separate file &
	668	provide documentation
689	669
690	670	2003-11-18 warnes
691	671
692		* [r227] R/mixedsort.R, man/mixedsort.Rd: - Renamed smartsort to
693		mixedsort and added documentation.
	672	* [r227] - Renamed smartsort to mixedsort and added documentation.
694	673
695	674	2003-11-10 warnes
696	675
697		* [r220] R/capture.R, man/capture.Rd: - Add files contributed by
698		Arni Magnusson
	676	* [r220] - Add files contributed by Arni Magnusson
699	677	<arnima@u.washington.edu>. As well as some of my own.
700	678
701	679	2003-05-23 warnes
702	680
703		* [r196] R/logit.R, man/logit.Rd: - library() backported from
704		1.7-devel. This version of the function
	681	* [r196] - library() backported from 1.7-devel. This version of the
	682	function
705	683	adds the "pos=" argument to specify where in the search path the
706	684	library should be placed.
707	685

715	693
716	694	2003-04-22 warnes
717	695
718		* [r189] man/combinations.Rd: - Fixed tpyo in example that allowed
719		combinations(500,2) to run when
	696	* [r189] - Fixed tpyo in example that allowed combinations(500,2)
	697	to run when
720	698	it should have been ignred for testing..
721	699
722	700	2003-04-10 warnes
723	701
724		* [r186] man/combinations.Rd: - Added note about the need to
725		increase options("expressions") to use
	702	* [r186] - Added note about the need to increase
	703	options("expressions") to use
726	704	large values for 'n'. Prompted by bug report from Huan Huang
727	705	<huan.huang@bnpparibas.com
728	706
729	707	2003-04-04 warnes
730	708
731		* [r183] R/RSCompat.S: - Replace 'T' with 'TRUE'
732		* [r182] R/dirichlet.R: - Change occurences of 'T' to 'TRUE'
733		* [r181] man/capture.Rd: - Allow optional arguments to sprint to be
734		passed to print
	709	* [r183] - Replace 'T' with 'TRUE'
	710	* [r182] - Change occurences of 'T' to 'TRUE'
	711	* [r181] - Allow optional arguments to sprint to be passed to print
735	712	- Fix R CMD check errors
736		* [r180] R/capture.R: - Allow optional arguments to sprint to be
737		passed to print
	713	* [r180] - Allow optional arguments to sprint to be passed to print
738	714
739	715	2003-04-03 warnes
740	716
741		* [r177] man/capture.Rd: - Had mistyped 'sprint' as 'sprintf'.
742		* [r176] man/capture.Rd: - Add help file for capture and sprintf.
	717	* [r177] - Had mistyped 'sprint' as 'sprintf'.
	718	* [r176] - Add help file for capture and sprintf.
743	719
744	720	2003-04-02 warnes
745	721
746		* [r174] R/capture.R: - Added file 'capture.R' containing capture()
747		and sprint().
	722	* [r174] - Added file 'capture.R' containing capture() and
	723	sprint().
748	724
749	725	2003-03-07 warnes
750	726
751		* [r168] R/RSCompat.S: - Minor changes to code to allow the package
752		to be provided as an
	727	* [r168] - Minor changes to code to allow the package to be
	728	provided as an
753	729	S-Plus chapter.
754	730
755	731	2003-01-30 warnes
756	732
757		* [r161] man/running.Rd: - Fixed typo in email address.
	733	* [r161] - Fixed typo in email address.
758	734
759	735	2003-01-02 warnes
760	736
761		* [r148] R/RSCompat.S: - Add nlevels function.
	737	* [r148] - Add nlevels function.
762	738
763	739	2002-10-11 warnes
764	740
765		* [r133] R/permute.R, man/permute.Rd: - Add permute() function
766		(wraper for sample) and man page
767		* [r132] man/dirichlet.Rd: - Escaped underscores in my email
768		address that was causing a parse
	741	* [r133] - Add permute() function (wraper for sample) and man page
	742	* [r132] - Escaped underscores in my email address that was causing
	743	a parse
769	744	error in the {r,p}dirichlet man page.
770	745
771	746	2002-09-30 warnes
772	747
773		* [r128] R/dirichlet.R, man/dirichlet.Rd: - Added rdirichlet() and
774		ddirichlet() with accompaning help page and tests.
	748	* [r128] - Added rdirichlet() and ddirichlet() with accompaning
	749	help page and tests.
775	750
776	751	2002-09-24 warnes
777	752
778		* [r122] R/running.R: - Fixed error where running was always
779		calling running2 with
	753	* [r122] - Fixed error where running was always calling running2
	754	with
780	755	'fun=mean', ignoring the specified funtion.
781	756
782	757	2002-09-23 warnes
783	758
784		* [r117] man/combinations.Rd, man/quantcut.Rd: - Modified all files
785		to include CVS Id and Log tags.
786		* [r116] R/combinations.R: - Added CrossTable() and barplot2() code
787		and docs contributed by Marc Schwartz.
	759	* [r117] - Modified all files to include CVS Id and Log tags.
	760	* [r116] - Added CrossTable() and barplot2() code and docs
	761	contributed by Marc Schwartz.
788	762	- Permit combinations() to be used when r>n provided
789	763	repeat.allowed=TRUE
790	764	- Bumped up version number
791	765
792	766	2002-08-01 warnes
793	767
794		* [r114] R/running.R: - Corrected documentation mismatch for ci,
795		ci.default.
	768	* [r114] - Corrected documentation mismatch for ci, ci.default.
796	769
797	770	- Replaced all occurences of '_' for assignment with '<-'.
798	771

804	777
805	778	2002-04-09 warneg
806	779
807		* [r109] R/combinations.R, man/combinations.Rd, man/running.Rd:
808		Checkin for version 0.5.3
	780	* [r109] Checkin for version 0.5.3
809	781
810	782	2002-03-26 warneg
811	783
812		* [r97] man/quantcut.Rd: Initial Checkin
813		* [r96] R/quantcut.R: Initial checkin.
	784	* [r97] Initial Checkin
	785	* [r96] Initial checkin.
814	786
815	787	2002-03-20 warneg
816	788
817		* [r91] R/RSCompat.S: - Added definition of is.R function.
	789	* [r91] - Added definition of is.R function.
818	790
819	791	- Added boxplot.formula
820	792
821	793	2002-03-07 warneg
822	794
823		* [r90] man/running.Rd: - Added documentation and example for
824		running2
825		* [r89] R/running.R: - Added "running2", which handles both
826		univariate and bivariate cases
	795	* [r90] - Added documentation and example for running2
	796	* [r89] - Added "running2", which handles both univariate and
	797	bivariate cases
827	798	- Modified "running" to call "running2"
828	799
829	800	2002-02-05 warneg
830	801
831		* [r75] R/RSCompat.S: - Fix typo that caused code meant to run only
832		under S-Plus to run
	802	* [r75] - Fix typo that caused code meant to run only under S-Plus
	803	to run
833	804	under R, causing problems.
834	805
835	806	2001-12-19 warneg
836	807
837		* [r67] R/RSCompat.S: - Added code for %in%.
	808	* [r67] - Added code for %in%.
838	809
839	810	2001-09-18 warneg
840	811
841		* [r18] R/RSCompat.S: Release 0.3.2
	812	* [r18] Release 0.3.2
842	813
843	814	2001-09-01 warneg
844	815
845		* [r17] R/RSCompat.S: Initial checkin.
846		* [r16] R/running.R, man/running.Rd: Release 0.3.0
	816	* [r17] Initial checkin.
	817	* [r16] Release 0.3.0
847	818
848	819	2001-08-25 warneg
849	820
850		* [r13] R/running.R: Initial CVS checkin.
851		* [r11] man/combinations.Rd: Fixed a typo and a syntax error.
852		* [r7] man/running.Rd: Initial Checkin
	821	* [r13] Initial CVS checkin.
	822	* [r11] Fixed a typo and a syntax error.
	823	* [r7] Initial Checkin
853	824
854	825	2001-06-29 warneg
855	826
856		* [r6] ., R, R/combinations.R, man, man/combinations.Rd: Initial
857		revision.
858
	827	* [r6] Initial revision.
	828

+47

-0

inst/NEWS less more

	0	gtools 3.5.0 - 2015-04-28
	1	-------------------------
	2
	3	New Functions:
	4
	5	- New roman2int() functon to convert roman numerals to integers
	6	without the range restriction of utils::as.roman().
	7
	8	- New asc() and chr() functions to convert between ASCII codes and
	9	characters. (Based on the 'Data Debrief' blog entry for 2011-03-09
	10	at http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html).
	11
	12	- New unByteCode() and unByteCodeAssign() functions to convert a
	13	byte-code functon to an interpeted code function.
	14
	15	- New assignEdgewise() function for making assignments into locked
	16	environments. (Used by unByteCodeAssign().)
	17
	18	Enhacements:
	19
	20	- mixedsort() and mixedorder() now have arguments 'decreasing',
	21	'na.last', and 'blank.last' arguments to control sort ordering.
	22
	23	- mixedsort() and mixedirdeR() now support Roman numerals via the
	24	arguments 'numeric.type', and 'roman.case'. (Request by David
	25	Winsemius, suggested code changes by Henrik Bengtsson.)
	26
	27	- speed up mixedorder() (and hence mixedsort()) by moving
	28	suppressWarnings() outside of lapply loops. (Suggestion by Henrik
	29	Bengtsson.)
	30
	31	- The 'q' argument to quantcut() now accept an integer
	32	indicating the number of equally spaced quantile groups to
	33	create. (Suggestion and patch submitted by Ryan C. Thompson.)
	34
	35	Bug fixes:
	36
	37	- Removed stray browser() call in smartbind().
	38
	39	- ddirichlet(x, alpha) was incorrectly returning NA when for any i,
	40	x[i]=0 and alpha[i]=1. (Bug report by John Nolan.)
	41
	42	Other changes:
	43
	44	- Correct typographical errors in package description.
	45
	46
0	47	gtools 3.4.2 - 2015-04-06
1	48	-------------------------
2	49

-2

man/ASCIIfy.Rd less more

21	21	}
22	22	\author{Arni Magnusson \email{arnima@hafro.is}}
23	23	\note{
24		To render single backslashes, use these or similar techniques:
25		\preformatted{
	24	To render single backslashes, use these or similar techniques:\preformatted{
26	25	write(ASCIIfy(x), "file.txt")
27	26	cat(paste(ASCIIfy(x), collapse="\n"), "\n", sep="")}
28	27

+67

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man/asc.Rd less more

	0	\name{asc}
	1	\alias{asc}
	2	\alias{chr}
	3	\title{Convert between characters and ASCII codes}
	4	\description{
	5	\code{asc} returns the ASCII codes for the specified characters.
	6	\code{chr} returns the characters corresponding to the specified ASCII codes.
	7	}
	8	\usage{
	9	asc(char, simplify=TRUE)
	10	chr(ascii)
	11	}
	12	\arguments{
	13	\item{char}{vector of character strings}
	14
	15	\item{simplify}{logical indicating whether to attempt to convert the
	16	result into a vector or matrix object. See \code{\link[base]{sapply}}
	17	for details.
	18	}
	19	\item{ascii}{vector or list of vectors containing integer ASCII codes}
	20	}
	21	\value{
	22	\code{asc} returns the integer ASCII values for each character
	23	in the elements of \code{char}. If \code{simplify=FALSE} the result
	24	will be a list contining one vector per element of \code{char}. If
	25	\code{simplify=TRUE}, the code will attempt to convert the result into
	26	a vector or matrix.
	27
	28	\code{asc} returns the characters corresponding to the provided ASCII
	29	values.
	30	}
	31	\author{
	32	Adapted by Gregory R. Warnes \email{greg@warnes.net} from code posted
	33	on the 'Data Debrief' blog on 2011-03-09 at
	34	\url{http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html}.
	35	}
	36	\seealso{
	37	\code{\link[base]{strtoi}},
	38	\code{\link[base]{charToRaw}},
	39	\code{\link[base]{rawToChar}},
	40	\code{\link[base]{as.raw}}
	41	}
	42	\examples{
	43	## ascii codes for lowercase letters
	44	asc(letters)
	45
	46	## uppercase letters from ascii codes
	47	chr(65:90)
	48
	49	## works on muti-character strings
	50	( tmp <- asc('hello!') )
	51	chr(tmp)
	52
	53	## Use 'simplify=FALSE' to return the result as a list
	54	( tmp <- asc('hello!', simplify=FALSE) )
	55	chr(tmp)
	56
	57	## When simplify=FALSE the results can be...
	58	asc( c('a', 'e', 'i', 'o', 'u', 'y' ) ) # a vector
	59	asc( c('ae', 'io', 'uy' ) ) # or a matrix
	60
	61	## When simplify=TRUE the results are always a list...
	62	asc( c('a', 'e', 'i', 'o', 'u', 'y' ), simplify=FALSE )
	63	asc( c('ae', 'io', 'uy' ), simplify=FALSE)
	64	}
	65	\keyword{character}
	66	\keyword{programming}

+69

-22

man/mixedsort.Rd less more

0		% $Id: mixedsort.Rd 1433 2010-05-01 22:03:03Z warnes $
1		%
2	0	\name{mixedsort}
3	1	\alias{mixedsort}
4	2	\alias{mixedorder}
5	3	\title{Order or Sort strings with embedded numbers so that the numbers
6	4	are in the correct order}
7	5	\description{
8		These functions sort or order character strings containing numbers so
9		that the numbers are numerically sorted rather than sorted by
10		character value. I.e. "Asprin 50mg" will come before "Asprin 100mg".
11		In addition, case of character strings is ignored so that "a", will
12		come before "B" and "C".
	6	These functions sort or order character strings containing embedded
	7	numbers so that the numbers are numerically sorted rather than sorted
	8	by character value. I.e. "Asprin 50mg" will come before
	9	"Asprin 100mg". In addition, case of character strings is ignored so
	10	that "a", will come before "B" and "C".
13	11	}
14	12	\usage{
15		mixedsort(x)
	13	mixedsort(x, decreasing=FALSE, na.last=TRUE, blank.last=FALSE,
	14	numeric.type=c("decimal", "roman"),
	15	roman.case=c("upper","lower","both") )
	16	mixedorder(x, decreasing=FALSE, na.last=TRUE, blank.last=FALSE,
	17	numeric.type=c("decimal", "roman"),
	18	roman.case=c("upper","lower","both") )
16	19	}
17	20	\arguments{
18		\item{x}{ Character vector to be sorted }
	21	\item{x}{Vector to be sorted.}
	22	\item{decreasing}{logical. Should the sort be increasing or
	23	decreasing? Note that \code{descending=TRUE} reverses the meanings of
	24	\code{na.last} and \code{blanks.last}.}
	25	\item{na.last}{for controlling the treatment of \code{NA} values. If \code{TRUE}, missing
	26	values in the data are put last; if \code{FALSE}, they are put
	27	first; if \code{NA}, they are removed.}
	28	\item{blank.last}{for controlling the treatment of blank values. If \code{TRUE}, blank
	29	values in the data are put last; if \code{FALSE}, they are put
	30	first; if \code{NA}, they are removed.}
	31	\item{numeric.type}{either "decimal" (default) or "roman". Are numeric values represented as
	32	decimal numbers (\code{numeric.type="decimal"}) or as Roman numerals
	33	(\code{numeric.type="roman"})? }
	34	\item{roman.case}{one of "upper", "lower", or "both". Are roman
	35	numerals represented using only capital letters ('IX') or lower-case
	36	letters ('ix') or both?}
19	37	}
20	38	\details{
21		I often have character vectors (e.g. factor labels) that contain
22		both text and numeric data, such as compound and dose. This function
	39	I often have character vectors (e.g. factor labels), such as compound
	40	and dose, that contain both text and numeric data. This function
23	41	is useful for sorting these character vectors into a logical order.
24	42
25	43	It does so by splitting each character vector into a sequence of
26	44	character and numeric sections, and then sorting along these sections,
27	45	with numbers being sorted by numeric value (e.g. "50" comes before
28	46	"100"), followed by characters strings sorted by character
29		value (e.g. "A" comes before "B").
	47	value (e.g. "A" comes before "B") \emph{ignoring case} (e.g. 'A' has
	48	the same sort order as 'a').
30	49
31		Empty strings are always sorted to the front of the list, and \code{NA}
32		values to the end.
	50	By default, sort order is ascending, empty strings are sorted to the front,
	51	and \code{NA} values to the end. Setting \code{descending=TRUE}
	52	changes the sort order to descending and reverses the meanings of
	53	\code{na.last} and \code{blank.last}.
	54
	55	Parsing looks for decimal numbers unless \code{numeric.type="roman"},
	56	in which parsing looks for roman numerals, with character case
	57	specified by \code{roman.case}.
	58
33	59	}
34	60	\value{
35	61	\code{mixedorder} returns a vector giving the sort order of the input

38	64	\author{ Gregory R. Warnes \email{greg@warnes.net} }
39	65	\seealso{ \code{\link[base]{sort}}, \code{\link[base]{order}} }
40	66	\examples{
41		# compound & dose labels
	67	## compound & dose labels
42	68	Treatment <- c("Control", "Asprin 10mg/day", "Asprin 50mg/day",
43	69	"Asprin 100mg/day", "Acetomycin 100mg/day",
44	70	"Acetomycin 1000mg/day")
45	71
46		# ordinary sort puts the dosages in the wrong order
	72	## ordinary sort puts the dosages in the wrong order
47	73	sort(Treatment)
48	74
49		# but mixedsort does the 'right' thing
	75	## but mixedsort does the 'right' thing
50	76	mixedsort(Treatment)
51	77
52		# Here is a more complex example
	78	## Here is a more complex example
53	79	x <- rev(c("AA 0.50 ml", "AA 1.5 ml", "AA 500 ml", "AA 1500 ml",
54	80	"EXP 1", "AA 1e3 ml", "A A A", "1 2 3 A", "NA", NA, "1e2",
55	81	"", "-", "1A", "1 A", "100", "100A", "Inf"))
56	82
57	83	mixedorder(x)
58	84
59		mixedsort(x)
60		# notice that plain numbers, including 'Inf' show up before strings.
	85	mixedsort(x) # Notice that plain numbers, including 'Inf' show up
	86	# before strings, NAs at the end, and blanks at the
	87	# beginning .
61	88
	89
	90	mixedsort(x, na.last=TRUE) # default
	91	mixedsort(x, na.last=FALSE) # push NAs to the front
	92
	93
	94	mixedsort(x, blank.last=FALSE) # default
	95	mixedsort(x, blank.last=TRUE) # push blanks to the end
	96
	97	mixedsort(x, decreasing=FALSE) # default
	98	mixedsort(x, decreasing=TRUE) # reverse sort order
	99
	100	## Roman numerals
	101	chapters <- c("V. Non Sequiturs", "II. More Nonsense",
	102	"I. Nonsense", "IV. Nonesensical Citations",
	103	"III. Utter Nonsense")
	104	mixedsort(chapters, numeric.type="roman" )
	105
	106	## Lower-case Roman numerals
	107	vals <- c("xix", "xii", "mcv", "iii", "iv", "dcclxxii", "cdxcii",
	108	"dcxcviii", "dcvi", "cci")
	109	(ordered <- mixedsort(vals, numeric.type="roman", roman.case="lower"))
	110	roman2int(ordered)
62	111	}
63	112	\keyword{univar}
64	113	\keyword{manip}
65
66
67	114	\concept{natural sort}
68	115	\concept{dictionary sort}
69	116

+17

-9

man/quantcut.Rd less more

0		% $Id: quantcut.Rd 1433 2010-05-01 22:03:03Z warnes $
	0	% $Id: quantcut.Rd 2025 2015-05-25 14:13:12Z warnes $
1	1	%
2	2	\name{quantcut}
3	3	\alias{quantcut}

7	7	Create a factor variable using the quantiles of a continous variable.
8	8	}
9	9	\usage{
10		quantcut(x, q=seq(0,1,by=0.25), na.rm=TRUE, ...)
	10	quantcut(x, q=4, na.rm=TRUE, ...)
11	11	}
12	12	%- maybe also `usage' for other objects documented here.
13	13	\arguments{
14	14	\item{x}{ Continous variable. }
15		\item{q}{ Vector of quantiles used for creating groups. Defaults to
16		\code{seq(0, 1, by=0.25)}. See \code{\link{quantile}} for details. }
	15	\item{q}{ Either a integer number of equally spaced quantile groups to
	16	create, or a vector of quantiles used for creating groups. Defaults to
	17	\code{q=4} which is equivalent to \code{q=seq(0, 1, by=0.25)}.
	18	See \code{\link{quantile}} for details. }
17	19	\item{na.rm}{ Boolean indicating whether missing values should be
18	20	removed when computing quantiles. Defaults to TRUE.}
19	21	\item{\dots}{ Optional arguments passed to \code{\link{cut}}. }

30	32	of quantile intervals.
31	33	}
32	34	\value{
33		Factor variable with one level for each quantile interval given by \code{q}.
	35	Factor variable with one level for each quantile interval.
34	36	}
35	37
36	38	\author{Gregory R. Warnes \email{greg@warnes.net}}

50	52	table(quartiles)
51	53
52	54	## cut into deciles
53		deciles <- quantcut( x, seq(0,1,by=0.1) )
54		table(deciles)
	55	deciles.1 <- quantcut( x, 10 )
	56	table(deciles.1)
	57	# or equivalently
	58	deciles.2 <- quantcut( x, seq(0,1,by=0.1) )
	59
	60	\testonly{
	61	stopifnot(identical(deciles.1, deciles.2))
	62	}
55	63
56	64	## show handling of 'tied' quantiles.
57	65	x <- round(x) # discretize to create ties
58	66	stem(x) # display the ties
59		deciles <- quantcut( x, seq(0,1,by=0.1) )
	67	deciles <- quantcut( x, 10 )
60	68
61		table(deciles) # note that there are only 5 groups (not 10)
	69	table(deciles) # note that there are only 5 groups (not 10)
62	70	# due to duplicates
63	71
64	72	}

+47

-0

man/roman2int.Rd less more

	0	\name{roman2int}
	1	\alias{roman2int}
	2	\title{Convert Roman Numerals to Integers}
	3	\description{
	4	Convert roman numerals to integers
	5	}
	6	\usage{
	7	roman2int(roman)
	8	}
	9	\arguments{
	10	\item{roman}{character vector containing roman numerals}
	11	}
	12	\details{
	13	This functon will convert roman numerals to integers without the upper bound
	14	imposed by R (3899), ignoring case.
	15	}
	16	\value{
	17	A integer vector with the same length as \code{roman}. Character
	18	strings which are not valid roman numerals will be converted to \code{NA}.
	19	}
	20	\author{
	21	Gregory R. Warnes \email{greg@warnes.net}
	22	}
	23	\seealso{
	24	\code{\link[utils]{as.roman}}
	25	}
	26	\examples{
	27	roman2int( c('I', 'V', 'X', 'C', 'L', 'D', 'M' ) )
	28
	29	# works regardless of case
	30	roman2int( 'MMXVI' )
	31	roman2int( 'mmxvi' )
	32
	33	# works beyond R's limit of 3899
	34	val.3899 <- 'MMMDCCCXCIX'
	35	val.3900 <- 'MMMCM'
	36	val.4000 <- 'MMMM'
	37	as.numeric(as.roman( val.3899 ))
	38	as.numeric(as.roman( val.3900 ))
	39	as.numeric(as.roman( val.4000 ))
	40
	41	roman2int(val.3899)
	42	roman2int(val.3900)
	43	roman2int(val.4000)
	44
	45	}
	46	\keyword{arith}

+83

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man/unByteCode.Rd less more

	0	\name{unByteCode}
	1	\alias{unByteCode}
	2	\alias{unByteCodeAssign}
	3	\alias{assignEdgewise}
	4	\title{
	5	Convert a Byte-Code Function to an Interpreted-Code Function
	6	}
	7	\description{
	8	Convert a byte-code function to an interpreted-code function
	9	}
	10	\usage{
	11	unByteCode(fun)
	12	assignEdgewise(name, env, value)
	13	unByteCodeAssign(fun)
	14	}
	15	\arguments{
	16	\item{fun}{function to be modified}
	17	\item{name}{object name}
	18	\item{env}{namespace}
	19	\item{value}{new function body}
	20	}
	21	\details{
	22	The purpose of these functions is to allow a byte coded function to be
	23	converted back into a fully interpreted function as a \emph{temporary}
	24	work around for issues in byte-code interpretation.
	25
	26	\code{unByteCode} returns a copy of the function that is directly interpreted
	27	from text rather than from byte-code.
	28
	29	\code{assignEdgewise} makes an assignment into a locked environemnt.
	30
	31	\code{unByteCodeAssign} changes the specified function \emph{in its source
	32	environment} to be directly interpreted from text rather than from byte-code.
	33	}
	34	\value{
	35	All three functions return a copy of the modified function or assigned value.
	36	}
	37	\references{
	38	These functions were inspired as a work-around to R bug
	39	\url{https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15215}.
	40	}
	41	\author{
	42	Gregory R. Warnes \email{greg@warnes.net}
	43	}
	44	\note{
	45	These functions are not intended as a permanent solution to issues
	46	with byte-code compilation or interpretation. Any such issues should
	47	be promtply reported to the R maintainers via the R Bug Tracking
	48	System at \url{https://bugs.r-project.org} and via the R-devel
	49	mailing list \url{https://stat.ethz.ch/mailman/listinfo/r-devel}.
	50	}
	51	\seealso{
	52	\code{\link[compiler]{disassemble}},
	53	\code{\link{assign}}
	54	}
	55	\examples{
	56	datURL <- "https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659"
	57	dat <- as.matrix(read.csv(file=datURL, row.names=1))
	58	dist2 <- function(x) as.dist(1-cor(t(x), method="pearson"))
	59	hclust1 <- function(x) hclust(x, method = "single")
	60
	61	distance <- dist2(dat)
	62	cluster <- hclust1(distance)
	63
	64	dend <- as.dendrogram(cluster)
	65
	66	\dontrun{
	67	## In R 2.3.0 and earlier crashes R: with a node stack overflow error
	68	plot(dend)
	69	## Error in xy.coords(x, y, recycle = TRUE) : node stack overflow
	70	}
	71
	72	## convert stats:::plotNode from byte-code to interpreted-code
	73	unByteCodeAssign(stats:::plotNode)
	74
	75	# increase recursion limit
	76	options("expressions"=5e4)
	77
	78	# now the function does not crash
	79	plot(dend)
	80	}
	81	\keyword{programming}
	82	\keyword{utilites}

+62

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src/roman2int.c less more

	0	#include <R.h>
	1
	2	void convert(
	3	char** letters,
	4	int* nchar,
	5	int* values
	6	)
	7	{
	8	if(*nchar<1) return;
	9
	10	for(int i=0; i<*nchar; i++)
	11	{
	12	if(letters[0][i]== 'I')
	13	values[i]=1;
	14	else if(letters[0][i]== 'V')
	15	values[i]=5;
	16	else if(letters[0][i]== 'X')
	17	values[i]=10;
	18	else if(letters[0][i]== 'L')
	19	values[i]=50;
	20	else if(letters[0][i]== 'C')
	21	values[i]=100;
	22	else if(letters[0][i]== 'D')
	23	values[i]=500;
	24	else if(letters[0][i]== 'M')
	25	values[i]=1000;
	26	else error("Invalid roman numeral '%c'", letters[0][i]);
	27	}
	28	}
	29
	30	void roman2int(char** str,
	31	int* nchar,
	32	int* retval)
	33	{
	34	if (*nchar < 1)
	35	{
	36	*retval = NA_INTEGER;
	37	return;
	38	}
	39
	40	int* values = (int) R_alloc(nchar, sizeof(int));
	41	convert(str, nchar, values);
	42
	43	int total=0;
	44	if (*nchar > 1)
	45	{
	46	for(int n=0; n<*nchar-1; n++)
	47	{
	48	if(values[n]<values[n+1])
	49	{
	50	total-=values[n];
	51	}
	52	else
	53	{
	54	total+=values[n];
	55	}
	56	}
	57	}
	58	total += values[*nchar-1];
	59
	60	retval[0] = total;
	61	}

+15

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tests/test_ddirichlet.R less more

	0	## Regression test for bug reported by John Nolan:
	1	##
	2	## Whenever the pair (x[i], a[i]) == (0,1), NA would be returned, due
	3	## to an internal computation of ( 0 * -Inf ) => NaN
	4	##
	5	## The code now checks for this particular issue and sets the value of
	6	## ( 0 * -Inf ) to 0, which is correct for this calculation.
	7	##
	8	library(gtools)
	9
	10	x = c(0,0,1)
	11	alpha = c(1,2,3)
	12
	13	stopifnot( ddirichlet(x=x, alpha=alpha) == 0 )
	14