ChangeLog

2018-06-25 14:53  warnes

	* ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Move NEWS and
	  ChangeLog to top level.

2018-06-25 14:52  warnes

	* ChangeLog, NEWS: Remove NEWS and ChangeLog soft links

2018-06-20 21:06  warnes

	* inst/ChangeLog: Update ChangeLog for gmodels 2.18.0.

2018-06-20 21:04  warnes

	* DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for gmodels
	  2.18.0.

2018-06-20 21:02  warnes

	* NAMESPACE: Add imports from stats package.

2018-06-20 20:51  warnes

	* DESCRIPTION, inst/ChangeLog: Update DESCRIPTION and ChangeLog for
	  gmodels 2.16.1

2018-06-20 20:50  warnes

	* NAMESPACE: Remove obsolete functions.

2018-06-20 20:46  warnes

	* R/fit.contrast.R, man/ci.Rd, man/estimable.Rd,
	  man/fit.contrast.Rd: Fix R CMD check issues.

2018-06-20 20:42  warnes

	* R/ci.R: Remove trailing whitespace

2018-06-20 20:40  warnes

	* R/est_p_ci.R: Use base::trimws() instead of gdata::trim()

2018-06-20 20:35  warnes

	* test: Remove duplicated/incorrect 'test' directory.

2017-06-12 23:53  warnes

	* DESCRIPTION: Update imports

2017-06-12 23:53  warnes

	* NAMESPACE: Add imports for base R packages to NAMESPACE

2017-06-05 21:27  warnes

	* inst/NEWS: Update NEWS and ChangeLog files for 2.18.0.

2016-08-15 19:11  warnes

	* test, test/lme-test.R, test/test_estimable_mlm.R: Add tests for
	  mlm and (obsolete) lme

2016-08-15 19:05  warnes

	* R/est_p_ci.R: Add est_p_ci generic and lm method

2016-08-12 17:15  warnes

	* DESCRIPTION, NAMESPACE, R/ci.R, R/fit.contrast.R, inst/ChangeLog,
	  inst/NEWS, man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd:
	  Updates...

2015-07-22 00:53  warnes

	* DESCRIPTION: Update gmodels DESCRIPTION

2015-07-22 00:48  warnes

	* test, tests, tests/lme-test.R: Renamed 'test' directory to
	  'tests', commented out tests for lme4 which has a changed API

2015-07-20 23:38  warnes

	* DESCRIPTION, NAMESPACE: Changs to squash new R CMD check warnings

2015-07-19 03:22  warnes

	* DESCRIPTION, NAMESPACE, R/ci.R, R/est.mer.R, R/estimable.R,
	  R/fit.contrast.R, R/to.est.R, inst/NEWS, man/ci.Rd,
	  man/estimable.Rd, man/fit.contrast.Rd: - Removed references to
	  'mer' objects, sincel the nlme4 update is not backwards
	  compatible with my code.
	  - Removed 'require' calls.

2015-07-19 02:34  warnes

	* DESCRIPTION, inst/ChangeLog, inst/NEWS: Update DESCRIPTION,
	  ChangeLog, and NEWS for gmodels 2.16.1

2015-07-19 02:30  warnes

	* R/ci.R, man/ci.Rd: ci.binom() was using an incorrect method for
	  calculating binomial confidence interval. The revised code
	  calculates the Clopper-Pearson 'exect' interval, which is
	  *conservative* due to the discrete nature of the binomial
	  distribution.

2015-05-02 17:38  warnes

	* Rename 'trunk' to 'pkg' for compatibility with R-forge

2015-04-06 21:52  warnes

	* Add ChangeLog files to repository

2014-07-24 15:18  warnes

	* Update NEWS for gmodels 2.16.0

2014-07-24 15:14  warnes

	* - Estimable now adds the class 'estimable' to returned objects.
	  - New ci() method for estimable objects.
	  - Minor improvemets to man page formatting.

2013-07-18 14:09  warnes

	* Looks like Brian Ripley repackaged for R 3.0.0 and bumped version
	  number, so change it to 2.15.5

2013-07-18 13:57  warnes

	* Update for gmodels 2.15.4

2013-07-18 13:54  warnes

	* Update to current Rd syntax

2013-07-18 13:46  warnes

	* Correct bug in estimable.mlm

2013-07-15 18:13  warnes

	* Remove unused argument to ci.mer

2012-06-28 00:49  warnes

	* Update for gmodels version 2.15.3.

2012-06-28 00:47  warnes

	* Move percentile() function to a separate file.

2012-06-28 00:41  warnes

	* Update est.mer() to support new S4 "mer" class.

2012-06-28 00:40  warnes

	* Make lme4 example executable.

2012-06-27 22:42  warnes

	* Add test code submitted by Ariel.Muldoon@oregonstate.edu.

2012-04-19 22:09  warnes

	* Update for release 2.15.2

2012-04-19 22:07  warnes

	* Update version and date.

2012-04-19 22:06  warnes

	* The 'Design' package has been replaced my 'rms', so update man
	  page references.

2012-04-19 22:05  warnes

	* More fixes for support of S4 'mer' class from lme4 package.

2012-04-19 21:13  warnes

	* Split long line.

2012-04-19 17:50  warnes

	* Changes to pass R CMD check

2011-12-14 18:17  warnes

	* Improve formatting of ci.mer().

2011-12-14 18:14  warnes

	* Modify est.mer to work with recent lme4 'mer' S4 objects.

2011-01-16 22:17  warnes

	* Fix warnings reported by R CMD check. Update version number to
	  2.15.1.

2009-05-09 05:29  warnes

	* Add tests for lme4 'mer' objects

2009-05-09 05:04  warnes

	* Update for 2.15.0

2009-05-09 05:02  warnes

	* Update description for 2.15.0

2009-05-09 05:01  warnes

	* Add support for lme4's 'mer' objects

2009-05-09 05:00  warnes

	* Add support for lme4's 'mer' objects

2009-05-09 04:53  warnes

	* Fix .Rd syntax error

2009-05-09 04:37  warnes

	* Add softlinks for ChangeLog and NEWS to top level dir for
	  convenience

2009-05-09 04:36  warnes

	* Move ChangeLog and NEWS files into inst directory

2009-05-09 04:00  warnes

	* Update Greg's email address

2008-04-10 14:05  warnes

	* Improve languages a bit

2008-01-02 16:56  warnes

	* Update Marc's email address

2007-12-12 21:16  warnes

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

2007-12-07 22:21  warnes

	* Update DESCRIPTION and NEWS for release 2.14.1

2007-12-07 22:10  warnes

	* Correct minor typos in man page for estimable()

2007-12-07 22:09  warnes

	* Add support for lme models to estimable()

2007-12-07 22:07  warnes

	* Replace non-ascii characters in Soren's name with (equivalent?)
	  ascii character to avoid character encoding issues.

2007-10-22 02:24  warnes

	* Clarify GPL version

2007-07-26 00:20  warnes

	* Add support for mlm to estimable().

2007-07-26 00:10  warnes

	* Add estimable method for mlm objects

2007-03-09 22:35  warnes

	* Remove stray character

2007-03-09 20:10  warnes

	* Update NEWS file.

2007-03-09 20:07  warnes

	* Update version number

2007-03-09 20:06  warnes

	* Minor code formatting changes

2007-03-09 20:06  warnes

	* Flip lower and upper interval in ci.lmer(). Add example to man
	  page.

2007-03-09 19:43  warnes

	* Fix some old email addressses that got missed

2006-11-29 00:11  warnes

	* Update for 2.13.1

2006-11-29 00:05  warnes

	* Correct declartion of S3 methods for estimable()

2006-11-29 00:05  warnes

	* Add additional suggested packages

2006-11-29 00:04  warnes

	* - Add generic
	  - Fix code vs. doc inconsistiencies

2006-11-28 22:38  warnes

	* Remove extraneous comma that causes errors in R 2.5.0

2006-11-27 20:45  warnes

	* Update for 2.13.1

2006-11-27 20:36  warnes

	* Add missing export of methods for estimable()

2006-11-14 22:25  ggorjan

	* Removed executable property

2006-08-02 22:21  warnes

	* Update my email address

2006-06-06 19:17  nj7w

	* Updated ci, estimable and fit.contrast as per Randall Johnson

2006-06-05 21:00  nj7w

	* Additions as per Randall C Johnson

2006-06-05 20:59  nj7w

	* Additions as per Randall C Johnson

2006-06-05 20:57  nj7w

	* - New function to estimate CI's and p-values using mcmcsamp()
	  from the
	  Matrix package

2006-05-05 18:29  nj7w

	* 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

	* Removed ChangeLog

2005-12-13 16:02  nj7w

	* Updated NEWS

2005-12-12 21:57  nj7w

	* Updated version number for CRAN

2005-12-04 06:27  warnes

	* Update for 2.11.0

2005-12-04 06:12  warnes

	* 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

	* Updated Greg's email address

2005-10-27 11:21  warnes

	* Update version number. Bump minor version since we added
	  functionality.

2005-10-27 10:33  warnes

	* Add ci.binom() to NAMESPACE, bump version

2005-10-26 13:39  warnes

	* Add ci.binom

2005-10-25 21:18  warnes

	* Add gdata::nobs to import list. Needed by ci()

2005-09-12 15:44  nj7w

	* Updated Greg's email

2005-09-07 15:31  nj7w

	* Fixed man page

2005-09-06 21:34  nj7w

	* Updated DESCRIPTION

2005-09-06 21:34  nj7w

	* Added NEWS

2005-09-06 16:21  nj7w

	* Fixed the Package name

2005-09-02 23:10  nj7w

	* Added ChangeLog

2005-08-31 16:28  nj7w

	* Added DESCRIPTION file

2005-08-31 16:27  nj7w

	* removed DESCRIPTION.in

2005-07-11 21:35  nj7w

	* 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

	* Updating the version number, and various help files to
	  synchronize splitting of gregmisc bundle in 4 individual
	  components.

2005-06-09 14:13  nj7w

	* 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

	* 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

	* Add dependency on gdata::frameApply.

2005-03-31 20:32  warnes

	* Add ceofFrame function to NAMESPACE

2005-03-31 19:05  warnes

	* coefFrame example needs to properly load ELISA data from gtools
	  package

2005-03-31 18:31  warnes

	* Ensure that each file has $Id$ header, and no $Log$

2005-03-31 18:30  warnes

	* Add coefFrame() function contributed by Jim Rogers

2005-01-18 19:53  warnes

	* Removed Windows Line Endings

2005-01-14 21:40  nj7w

	* Updated the manual to reflect prop.chisq change in its R file.

2005-01-14 19:14  warnes

	* Nitin added display of the Chisquare contribution of each cell,
	  as suggested
	  by Greg Snow.

2005-01-12 20:50  warnes

	* 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

	* 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

	* 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

	* Fix typos.

2004-09-27 21:01  warneg

	* Updated to pass R CMD check.

2004-09-03 22:44  warneg

	* Add explicit package to call to quantcut in example.

2004-09-03 17:27  warneg

	* initial bundle checkin

2004-09-02 17:14  warneg

	* Initial revision

2004-05-25 02:57  warnes

	* Updates from Mark Schwartz.

2004-04-13 11:41  warnes

	* Fix latex warning: it doesn't like double subscripts.

2004-03-26 22:28  warnes

	* Reflect movement of code from 'mva' package to 'stats' in R
	  1.9.0.

2004-03-25 20:09  warnes

	* - 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

	* 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

	* - 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

	* - Fixed incorrect denominator in standard error for mean in
	  ci.default.

2003-04-22 17:24  warnes

	* - the variable 'df' was used within the lme code section
	  overwriting
	  the argument 'df'.

2003-03-12 17:58  warnes

	* - Fixed a typo in the example
	  - Added to lme example

2003-03-07 15:48  warnes

	* - Minor changes to code to allow the package to be provided as an
	  S-Plus chapter.

2003-01-30 21:53  warnes

	* - 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

	* - 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

	* - 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

	* - 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

	* - 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

	* - 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

	* Initial checkin for fast.prcomp() and fast.svd().

2002-09-26 12:11  warnes

	* - 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

	* - Fixed a typo.

2002-09-23 14:27  warnes

	* - 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

	* - Modified all files to include CVS Id and Log tags.

2002-09-23 13:38  warnes

	* - 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

	* - 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

	* Checkin for version 0.5.3

2002-03-26 21:22  warneg

	* - Changed methods to include '...' to match the generic.
	  - Updated for version 0.5.1

2002-03-26 15:30  warneg

	* Removed incorrect link to 'contrast' from seealso.

2002-02-20 20:09  warneg

	* Minor changes, typo and formatting fixes.

2002-01-17 23:51  warneg

	* - Fixed errror in last example by adding 'conf.int' parameter to
	  'estimable' call.

2002-01-17 23:42  warneg

	* - Fixed typo in code that resulted in an syntax error.

2002-01-10 17:35  warneg

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

2001-12-19 20:06  warneg

	* - Fixed display of formulae.
	  - Added description of return value

2001-12-19 20:05  warneg

	* - Removed extra element of return object.

2001-12-18 22:14  warneg

	* - 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

	* - Modified to make confidence intervals optional. Changed 'alpha'
	  parameter giving significance level to 'conf.int' giving
	  confidence
	  level.

2001-12-18 21:36  warneg

	* - Added summary.glh.test to alias, usage, and example sections.

2001-12-18 21:34  warneg

	* - 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

	* - 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

	* Initial checkin.

2001-12-17 18:59  warneg

	* - Fixed spelling errors.

2001-12-17 18:52  warneg

	* - Fixed the link to contrasts.lm.
	  - Rephrased title/description to be more clear.

2001-12-10 19:35  warneg

	* Renamed 'contrsts.coeff.Rd' to 'estimable.Rd' corresponding to
	  function rename.

2001-12-10 19:26  warneg

	* renamed from contrast.coeff.R to estimable.R (incorrectly via
	  contrast.lm.R)

2001-12-07 19:50  warneg

	* - Added text noting that lme is now supported.

2001-12-07 19:19  warneg

	* - Fixed typo: DF column was being filled in with p-value.

2001-12-07 18:49  warneg

	* - Added ci.lme method to handle lme objects.

2001-10-16 23:15  warneg

	* Fixed unbalanced brace.

2001-08-25 05:52  warneg

	* - Added CVS header.
	  - Added my email address.

2001-05-30 13:23  warneg

	* Initial revision