r-cran-gmodels 2.15.4.1-1 / usr / lib / R / site-library / gmodels / ChangeLog

2012-06-28 00:41  warnes

	* [r1575] R/est.lmer.R, R/est.mer.R: Update est.mer() to support
	  new S4 "mer" class.

2012-06-28 00:40  warnes

	* [r1574] man/ci.Rd: Make lme4 example executable.

2012-06-27 22:42  warnes

	* [r1573] test/lme-test.R: Add test code submitted by
	  Ariel.Muldoon@oregonstate.edu.

2012-04-19 22:09  warnes

	* [r1528] inst/NEWS: Update for release 2.15.2

2012-04-19 22:07  warnes

	* [r1527] DESCRIPTION: Update version and date.

2012-04-19 22:06  warnes

	* [r1526] man/estimable.Rd: The 'Design' package has been replaced
	  my 'rms', so update man page references.

2012-04-19 22:05  warnes

	* [r1525] R/ci.R, R/est.mer.R: More fixes for support of S4 'mer'
	  class from lme4 package.

2012-04-19 21:13  warnes

	* [r1524] man/coefFrame.Rd: Split long line.

2012-04-19 17:50  warnes

	* [r1523] man/ci.Rd, man/glh.test.Rd: Changes to pass R CMD check

2011-12-14 18:17  warnes

	* [r1521] R/ci.R: Improve formatting of ci.mer().

2011-12-14 18:14  warnes

	* [r1520] R/est.mer.R: Modify est.mer to work with recent lme4
	  'mer' S4 objects.

2011-01-16 22:17  warnes

	* [r1466] DESCRIPTION, inst/NEWS, man/ci.Rd, man/estimable.Rd,
	  man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
	  man/make.contrasts.Rd: Fix warnings reported by R CMD check.
	  Update version number to 2.15.1.

2009-05-09 05:29  warnes

	* [r1337] test, test/lme-test.R: Add tests for lme4 'mer' objects

2009-05-09 05:04  warnes

	* [r1336] inst/NEWS: Update for 2.15.0

2009-05-09 05:02  warnes

	* [r1335] DESCRIPTION: Update description for 2.15.0

2009-05-09 05:01  warnes

	* [r1334] R/est.mer.R: Add support for lme4's 'mer' objects

2009-05-09 05:00  warnes

	* [r1333] NAMESPACE, R/ci.R, R/est.lmer.R, R/estimable.R,
	  R/fit.contrast.R, R/to.est.R: Add support for lme4's 'mer'
	  objects

2009-05-09 04:53  warnes

	* [r1332] man/glh.test.Rd: Fix .Rd syntax error

2009-05-09 04:37  warnes

	* [r1331] NEWS: Add softlinks for ChangeLog and NEWS to top level
	  dir for convenience

2009-05-09 04:36  warnes

	* [r1330] ChangeLog, NEWS, inst, inst/NEWS: Move ChangeLog and NEWS
	  files into inst directory

2009-05-09 04:00  warnes

	* [r1329] DESCRIPTION, man/ci.Rd, man/estimable.Rd,
	  man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
	  man/make.contrasts.Rd: Update Greg's email address

2008-04-10 14:05  warnes

	* [r1255] man/ci.Rd: Improve languages a bit

2008-01-02 16:56  warnes

	* [r1236] man/CrossTable.Rd: Update Marc's email address

2007-12-12 21:16  warnes

	* [r1233] DESCRIPTION: Move copyright notice for Randall's
	  contributions from License section to Author section of the
	  DESCRIPTION file.

2007-12-07 22:21  warnes

	* [r1232] DESCRIPTION, NEWS: Update DESCRIPTION and NEWS for
	  release 2.14.1

2007-12-07 22:10  warnes

	* [r1231] man/estimable.Rd: Correct minor typos in man page for
	  estimable()

2007-12-07 22:09  warnes

	* [r1230] R/estimable.R: Add support for lme models to estimable()

2007-12-07 22:07  warnes

	* [r1229] man/estimable.Rd: Replace non-ascii characters in Soren's
	  name with (equivalent?) ascii character to avoid character
	  encoding issues.

2007-10-22 02:24  warnes

	* [r1196] DESCRIPTION: Clarify GPL version

2007-07-26 00:20  warnes

	* [r1105] DESCRIPTION, NAMESPACE, NEWS, R/estimable.mlm.R,
	  man/estimable.Rd: Add support for mlm to estimable().

2007-07-26 00:10  warnes

	* [r1104] R/estimable.R, R/estimable.mlm.R: Add estimable method
	  for mlm objects

2007-03-09 22:35  warnes

	* [r1079] R/ci.R: Remove stray character

2007-03-09 20:10  warnes

	* [r1078] NEWS: Update NEWS file.

2007-03-09 20:07  warnes

	* [r1077] DESCRIPTION: Update version number

2007-03-09 20:06  warnes

	* [r1076] R/ci.R: Minor code formatting changes

2007-03-09 20:06  warnes

	* [r1075] R/est.lmer.R, man/ci.Rd: Flip lower and upper interval in
	  ci.lmer(). Add example to man page.

2007-03-09 19:43  warnes

	* [r1074] man/ci.Rd, man/estimable.Rd: Fix some old email
	  addressses that got missed

2006-11-29 00:11  warnes

	* [r1029] NEWS: Update for 2.13.1

2006-11-29 00:05  warnes

	* [r1028] NAMESPACE: Correct declartion of S3 methods for
	  estimable()

2006-11-29 00:05  warnes

	* [r1027] DESCRIPTION: Add additional suggested packages

2006-11-29 00:04  warnes

	* [r1026] R/estimable.R, man/estimable.Rd: - Add generic
	  - Fix code vs. doc inconsistiencies

2006-11-28 22:38  warnes

	* [r1025] R/ci.R, R/estimable.R, R/fast.prcomp.R: Remove extraneous
	  comma that causes errors in R 2.5.0

2006-11-27 20:45  warnes

	* [r1016] DESCRIPTION, NEWS: Update for 2.13.1

2006-11-27 20:36  warnes

	* [r1015] DESCRIPTION, NAMESPACE: Add missing export of methods for
	  estimable()

2006-11-14 22:25  ggorjan

	* [r1012] R/ci.R, R/fast.prcomp.R, man/ci.Rd: Removed executable
	  property

2006-08-02 22:21  warnes

	* [r977] man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
	  man/make.contrasts.Rd: Update my email address

2006-06-06 19:17  nj7w

	* [r966] man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: Updated
	  ci, estimable and fit.contrast as per Randall Johnson

2006-06-05 21:00  nj7w

	* [r965] DESCRIPTION: Additions as per Randall C Johnson

2006-06-05 20:59  nj7w

	* [r964] R/ci.R, R/estimable.R, R/fit.contrast.R, R/to.est.R:
	  Additions as per Randall C Johnson

2006-06-05 20:57  nj7w

	* [r963] R/est.lmer.R: - New function to estimate CI's and p-values
	  using mcmcsamp() from the
	  Matrix package

2006-05-05 18:29  nj7w

	* [r959] R/CrossTable.R, man/CrossTable.Rd: Fixed an error:
	  According to Marc Schwartz - there was an error when a matrix
	  without dimnames(or names(dimnames)) was passed as x argument

2005-12-13 16:03  nj7w

	* [r808] ChangeLog: Removed ChangeLog

2005-12-13 16:02  nj7w

	* [r807] NEWS: Updated NEWS

2005-12-12 21:57  nj7w

	* [r796] DESCRIPTION: Updated version number for CRAN

2005-12-04 06:27  warnes

	* [r781] NEWS: Update for 2.11.0

2005-12-04 06:12  warnes

	* [r780] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R,
	  R/fit.contrast.R, R/to.est.R, man/ci.Rd, man/estimable.Rd:
	  Integration of code changes suggested by Randall C Johnson to add
	  support for lmer (lme version 4) objects to ci(), estimable(),
	  and
	  fit.contrast().
	  
	  Addition of simplified coefficient specificaiton for estimable()
	  based on a function provided by Randall C Johnson. It is now
	  possible to do things like:
	  estimable(reg, c("xB"=1,"xD"=-1) )
	  instead of:
	  estimable(reg, c( 0, 1, 0, -1) )
	  which should make estimable much easier to use for large models.

2005-12-01 16:54  nj7w

	* [r776] man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
	  man/fit.contrast.Rd, man/make.contrasts.Rd: Updated Greg's email
	  address

2005-10-27 11:21  warnes

	* [r709] DESCRIPTION: Update version number. Bump minor version
	  since we added functionality.

2005-10-27 10:33  warnes

	* [r708] DESCRIPTION, NAMESPACE: Add ci.binom() to NAMESPACE, bump
	  version

2005-10-26 13:39  warnes

	* [r707] R/ci.R, man/ci.Rd: Add ci.binom

2005-10-25 21:18  warnes

	* [r706] NAMESPACE: Add gdata::nobs to import list. Needed by ci()

2005-09-12 15:44  nj7w

	* [r671] man/fast.prcomp.Rd, man/glh.test.Rd: Updated Greg's email

2005-09-07 15:31  nj7w

	* [r667] man/CrossTable.Rd: Fixed man page

2005-09-06 21:34  nj7w

	* [r664] DESCRIPTION: Updated DESCRIPTION

2005-09-06 21:34  nj7w

	* [r663] NEWS: Added NEWS

2005-09-06 16:21  nj7w

	* [r662] DESCRIPTION: Fixed the Package name

2005-09-02 23:10  nj7w

	* [r655] ChangeLog: Added ChangeLog

2005-08-31 16:28  nj7w

	* [r644] DESCRIPTION: Added DESCRIPTION file

2005-08-31 16:27  nj7w

	* [r643] DESCRIPTION.in: removed DESCRIPTION.in

2005-07-11 21:35  nj7w

	* [r627] R/CrossTable.R, man/CrossTable.Rd: Revision based on Marc
	  Schwartz's suggestions:
	  1) Added 'dnn' argument to enable specification of dimnames as
	  per table()
	  2) Corrected bug in SPSS output for 1d table, where proportions
	  were being printed and not percentages ('%' output)

2005-06-09 14:20  nj7w

	* [r625] R/ci.R, R/coefFrame.R, R/estimable.R, R/fast.prcomp.R,
	  R/fit.contrast.R, R/glh.test.R, R/make.contrasts.R,
	  man/CrossTable.Rd, man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
	  man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
	  man/make.contrasts.Rd: Updating the version number, and various
	  help files to synchronize splitting of gregmisc bundle in 4
	  individual components.

2005-06-09 14:13  nj7w

	* [r623] R/CrossTable.R: Updates by Marc Schwartz:
	  CrossTable:
	  
	  # Revision 2.0 2005/04/27
	  # Added 'format = "d"' to all table count output
	  # so that large integers do not print in
	  # scientific notation

2005-05-13 18:59  nj7w

	* [r621] man/CrossTable.Rd: 1) Using dQuote.ascii function in
	  read.xls as the new version of dQuote doesn't work proprly with
	  UTF-8 locale.
	  2) Modified CrossTable.Rd usage in gmodels
	  3) Modified heatmap.2 usage in gplots.

2005-05-11 13:51  warnes

	* [r620] DESCRIPTION.in, NAMESPACE: Add dependency on
	  gdata::frameApply.

2005-03-31 20:32  warnes

	* [r593] NAMESPACE: Add ceofFrame function to NAMESPACE

2005-03-31 19:05  warnes

	* [r592] man/coefFrame.Rd: coefFrame example needs to properly load
	  ELISA data from gtools package

2005-03-31 18:31  warnes

	* [r588] R/CrossTable.R, man/CrossTable.Rd, man/ci.Rd,
	  man/estimable.Rd, man/fast.prcomp.Rd, man/fit.contrast.Rd,
	  man/glh.test.Rd, man/make.contrasts.Rd: Ensure that each file has
	  $Id$ header, and no $Log$

2005-03-31 18:30  warnes

	* [r587] R/coefFrame.R, man/coefFrame.Rd: Add coefFrame() function
	  contributed by Jim Rogers

2005-01-18 19:53  warnes

	* [r521] R/CrossTable.R: Removed Windows Line Endings

2005-01-14 21:40  nj7w

	* [r518] man/CrossTable.Rd: Updated the manual to reflect
	  prop.chisq change in its R file.

2005-01-14 19:14  warnes

	* [r517] R/CrossTable.R: Nitin added display of the Chisquare
	  contribution of each cell, as suggested
	  by Greg Snow.

2005-01-12 20:50  warnes

	* [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
	  poeple from installing on old
	  versions of R which don't support namespaces.

2004-12-23 19:32  nj7w

	* [r507] R/CrossTable.R, man/CrossTable.Rd: Split the function
	  print.CrossTable.vector in two parts - for SAS behaiour and SPSS
	  behaviour. Also put the code of printing statistics in a function
	  'print.statistics'

2004-12-21 22:38  warnes

	* [r502] R/CrossTable.R: Added & extended changes made by Nitin to
	  implement 'SPSS' format, as suggested by
	  Dirk Enzmann <dirk.enzmann@jura.uni-hamburg.de>.

2004-09-30 21:03  warneg

	* [r464] man/glh.test.Rd: Fix typos.

2004-09-27 21:01  warneg

	* [r461] DESCRIPTION, DESCRIPTION.in: Updated to pass R CMD check.

2004-09-03 22:44  warneg

	* [r450] man/fit.contrast.Rd: Add explicit package to call to
	  quantcut in example.

2004-09-03 17:27  warneg

	* [r446] DESCRIPTION, NAMESPACE, R/CrossTable.R, R/ci.R,
	  R/estimable.R, R/fast.prcomp.R, R/fit.contrast.R, R/glh.test.R,
	  R/make.contrasts.R, man/estimable.Rd, man/fit.contrast.Rd,
	  man/glh.test.Rd, man/make.contrasts.Rd: initial bundle checkin

2004-09-02 17:14  warneg

	* [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision

2004-05-25 02:57  warnes

	* [r327] R/CrossTable.R, man/CrossTable.Rd: Updates from Mark
	  Schwartz.

2004-04-13 11:41  warnes

	* [r314] man/estimable.Rd: Fix latex warning: it doesn't like
	  double subscripts.

2004-03-26 22:28  warnes

	* [r306] man/fast.prcomp.Rd: Reflect movement of code from 'mva'
	  package to 'stats' in R 1.9.0.

2004-03-25 20:09  warnes

	* [r296] R/estimable.R, man/estimable.Rd: - Estimable was reporting
	  sqrt(X^2) rather than X^2 in the output.
	  - Provide latex math markup for linear algebra expressions in
	  help text.
	  - Other clarifications in help text

2004-03-25 18:17  warnes

	* [r295] R/estimable.R, man/estimable.Rd: Add enhancements to
	  estimable() provided by S�ren H�jsgaard
	  \email{sorenh@agrsci.dk}:
	  
	  I have made a modified version of the function [..] which
	  1) also works on geese and gee objects and
	  2) can test hypotheses af the forb L * beta = beta0 both as a
	  single Wald test and row-wise for each row in L.

2003-11-17 21:40  warnes

	* [r221] R/fit.contrast.R: - Fix incorrect handling of glm objects
	  by fit.contrast, as reported
	  by Ulrich Halekoh, Phd <ulrich.halekoh@agrsci.dk>.
	  
	  - Add regression test code to for this bug.

2003-08-07 03:49  warnes

	* [r217] R/ci.R: - Fixed incorrect denominator in standard error
	  for mean in ci.default.

2003-04-22 17:24  warnes

	* [r190] R/fit.contrast.R: - the variable 'df' was used within the
	  lme code section overwriting
	  the argument 'df'.

2003-03-12 17:58  warnes

	* [r173] man/fit.contrast.Rd: - Fixed a typo in the example
	  - Added to lme example

2003-03-07 15:48  warnes

	* [r168] R/fast.prcomp.R: - Minor changes to code to allow the
	  package to be provided as an
	  S-Plus chapter.

2003-01-30 21:53  warnes

	* [r160] R/fit.contrast.R, man/fit.contrast.Rd: - Renamed
	  'contrast.lm' to 'fit.contrast'. This new name is more
	  descriptive and makes it easier to create and use methods for
	  other
	  classes, eg lme.
	  
	  - Enabled fit.contrast for lme object now that Doug Bates has
	  provided
	  the necessary support for contrasts in the nlme package.
	  
	  - New contrast.lm function which generates a 'depreciated'
	  warning and
	  calls fit.contrast
	  
	  - Updated help text to match changes.

2003-01-30 21:41  warnes

	* [r158] R/CrossTable.R, man/CrossTable.Rd: - Removed argument
	  'correct' and now print separate corrected values
	  for 2 x 2 tables.
	  - Added arguments 'prop.r', 'prop.c' and 'prop.t' to toggle
	  printing
	  of row, col and table percentages. Default is TRUE.
	  - Added argument 'fisher' to toggle fisher exact test. Default is
	  FALSE.
	  - Added McNemar test to statistics and argument 'mcnemar' to
	  toggle
	  test. Default is FALSE.
	  - Added code to generate an invisible return list containing
	  table
	  counts, proportions and the results of the appropriate
	  statistical tests.

2003-01-30 14:58  warnes

	* [r157] R/make.contrasts.R: - Added explicit check to ensure that
	  the number of specified
	  contrasts is less than or equal to the ncol - 1. Previously, this
	  failed with an obtuse error message when the contrast matrix had
	  row
	  names, and silently dropped contrasts over ncol-1.

2002-11-04 14:13  warnes

	* [r142] R/CrossTable.R: - Moved fisher.test() to after table is
	  printed, so that table is
	  still printed in the event that fisher.test() results in errors.

2002-10-29 23:06  warnes

	* [r138] R/fast.prcomp.R, man/fast.prcomp.Rd: - Fixes to fast.svd
	  to make it actually work.
	  - Updates to man page to fix mistmatches between code and docs
	  and to
	  fix warnings.

2002-10-29 23:00  warnes

	* [r137] R/make.contrasts.R, man/make.contrasts.Rd: - Moved
	  make.contrasts to a separate file.
	  - Enhanced make contrasts to better label contrast matrix, to
	  give
	  how.many a default value, and to coerce vectors into row
	  matrixes.
	  - Added help page for make.contrasts.
	  - Added link from contrasts.lm seealso to make.contrasts.

2002-10-29 19:29  warnes

	* [r136] R/fast.prcomp.R, man/fast.prcomp.Rd: Initial checkin for
	  fast.prcomp() and fast.svd().

2002-09-26 12:11  warnes

	* [r127] man/glh.test.Rd: - Added note and example code to
	  illustrate how to properly compute
	  contrasts for the first factor in the model.

2002-09-24 19:12  warnes

	* [r124] R/glh.test.R: - Fixed a typo.

2002-09-23 14:27  warnes

	* [r119] man/CrossTable.Rd, man/glh.test.Rd: - Fixed syntax errors
	  in barplot2.Rd and CrossTable.Rd
	  - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
	  glh.test.Rd

2002-09-23 13:59  warnes

	* [r117] R/ci.R, man/estimable.Rd, man/glh.test.Rd: - Modified all
	  files to include CVS Id and Log tags.

2002-09-23 13:38  warnes

	* [r116] R/CrossTable.R, man/CrossTable.Rd: - Added CrossTable()
	  and barplot2() code and docs contributed by Marc Schwartz.
	  - Permit combinations() to be used when r>n provided
	  repeat.allowed=TRUE
	  - Bumped up version number

2002-08-01 19:37  warnes

	* [r114] R/ci.R, man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: -
	  Corrected documentation mismatch for ci, ci.default.
	  
	  - Replaced all occurences of '_' for assignment with '<-'.
	  
	  - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE'
	  with
	  the spelled out version.
	  
	  - Updaded version number and date.

2002-04-09 00:51  warneg

	* [r109] R/ci.R, R/estimable.R, R/glh.test.R, man/glh.test.Rd:
	  Checkin for version 0.5.3

2002-03-26 21:22  warneg

	* [r104] R/ci.R, R/glh.test.R, man/ci.Rd, man/glh.test.Rd: -
	  Changed methods to include '...' to match the generic.
	  - Updated for version 0.5.1

2002-03-26 15:30  warneg

	* [r99] man/glh.test.Rd: Removed incorrect link to 'contrast' from
	  seealso.

2002-02-20 20:09  warneg

	* [r81] man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: Minor
	  changes, typo and formatting fixes.

2002-01-17 23:51  warneg

	* [r70] man/estimable.Rd: - Fixed errror in last example by adding
	  'conf.int' parameter to
	  'estimable' call.

2002-01-17 23:42  warneg

	* [r69] R/glh.test.R: - Fixed typo in code that resulted in an
	  syntax error.

2002-01-10 17:35  warneg

	* [r68] R/glh.test.R: - print.glh.test() was using cat() to
	  printing the call. This didn't work and
	  generated an error.

2001-12-19 20:06  warneg

	* [r66] man/glh.test.Rd: - Fixed display of formulae.
	  - Added description of return value

2001-12-19 20:05  warneg

	* [r65] R/glh.test.R: - Removed extra element of return object.

2001-12-18 22:14  warneg

	* [r64] man/estimable.Rd: - Updated documentation to reflect change
	  of parameters from 'alpha'
	  to 'conf.int', including the new optional status of the
	  confidence
	  intervals.

2001-12-18 22:12  warneg

	* [r63] R/estimable.R: - Modified to make confidence intervals
	  optional. Changed 'alpha'
	  parameter giving significance level to 'conf.int' giving
	  confidence
	  level.

2001-12-18 21:36  warneg

	* [r62] man/glh.test.Rd: - Added summary.glh.test to alias, usage,
	  and example sections.

2001-12-18 21:34  warneg

	* [r61] R/glh.test.R: - Modified to work correctly when obj is of
	  class 'aov' by specifying
	  summary.lm instead of summary. This ensures that the summary
	  object
	  has the fields we need.
	  
	  - Moved detailed reporting of results from 'print' to 'summary'
	  function and added a simpler report to 'print'

2001-12-18 21:27  warneg

	* [r60] R/estimable.R: - Modified to work correctly when obj is of
	  class 'aov' by specifying
	  summary.lm instead of summary. This ensures that the summary
	  object
	  has the fields we need.

2001-12-18 00:45  warneg

	* [r59] R/glh.test.R, man/glh.test.Rd: Initial checkin.

2001-12-17 18:59  warneg

	* [r56] man/estimable.Rd: - Fixed spelling errors.

2001-12-17 18:52  warneg

	* [r55] man/estimable.Rd: - Fixed the link to contrasts.lm.
	  - Rephrased title/description to be more clear.

2001-12-10 19:35  warneg

	* [r49] man/estimable.Rd: Renamed 'contrsts.coeff.Rd' to
	  'estimable.Rd' corresponding to function rename.

2001-12-10 19:26  warneg

	* [r48] R/estimable.R: renamed from contrast.coeff.R to estimable.R
	  (incorrectly via contrast.lm.R)

2001-12-07 19:50  warneg

	* [r37] man/ci.Rd: - Added text noting that lme is now supported.

2001-12-07 19:19  warneg

	* [r36] R/ci.R: - Fixed typo: DF column was being filled in with
	  p-value.

2001-12-07 18:49  warneg

	* [r35] R/ci.R: - Added ci.lme method to handle lme objects.

2001-10-16 23:15  warneg

	* [r27] man/ci.Rd: Fixed unbalanced brace.

2001-08-25 05:52  warneg

	* [r12] man/ci.Rd: - Added CVS header.
	  - Added my email address.

2001-05-30 13:23  warneg

	* [r2] ., R, R/ci.R, man, man/ci.Rd: Initial revision