r-cran-gmodels 2.16.2-2.1 / usr / lib / R / site-library / gmodels / ChangeLog

2015-07-19  warnes

	* [r2058] 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  warnes

	* [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge

2015-04-06  warnes

	* [r1916] Add ChangeLog files to repository

2014-07-24  warnes

	* [r1869] Update NEWS for gmodels 2.16.0
	* [r1868] - Estimable now adds the class 'estimable' to returned
	  objects.
	  - New ci() method for estimable objects.
	  - Minor improvemets to man page formatting.

2013-07-18  warnes

	* [r1710] Looks like Brian Ripley repackaged for R 3.0.0 and bumped
	  version number, so change it to 2.15.5
	* [r1709] Update for gmodels 2.15.4
	* [r1708] Update to current Rd syntax
	* [r1707] Correct bug in estimable.mlm

2013-07-15  warnes

	* [r1706] Remove unused argument to ci.mer

2012-06-28  warnes

	* [r1577] Update for gmodels version 2.15.3.
	* [r1576] Move percentile() function to a separate file.
	* [r1575] Update est.mer() to support new S4 "mer" class.
	* [r1574] Make lme4 example executable.

2012-06-27  warnes

	* [r1573] Add test code submitted by Ariel.Muldoon@oregonstate.edu.

2012-04-19  warnes

	* [r1528] Update for release 2.15.2
	* [r1527] Update version and date.
	* [r1526] The 'Design' package has been replaced my 'rms', so
	  update man page references.
	* [r1525] More fixes for support of S4 'mer' class from lme4
	  package.
	* [r1524] Split long line.
	* [r1523] Changes to pass R CMD check

2011-12-14  warnes

	* [r1521] Improve formatting of ci.mer().
	* [r1520] Modify est.mer to work with recent lme4 'mer' S4 objects.

2011-01-16  warnes

	* [r1466] Fix warnings reported by R CMD check. Update version
	  number to 2.15.1.

2009-05-09  warnes

	* [r1337] Add tests for lme4 'mer' objects
	* [r1336] Update for 2.15.0
	* [r1335] Update description for 2.15.0
	* [r1334] Add support for lme4's 'mer' objects
	* [r1333] Add support for lme4's 'mer' objects
	* [r1332] Fix .Rd syntax error
	* [r1331] Add softlinks for ChangeLog and NEWS to top level dir for
	  convenience
	* [r1330] Move ChangeLog and NEWS files into inst directory
	* [r1329] Update Greg's email address

2008-04-10  warnes

	* [r1255] Improve languages a bit

2008-01-02  warnes

	* [r1236] Update Marc's email address

2007-12-12  warnes

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

2007-12-07  warnes

	* [r1232] Update DESCRIPTION and NEWS for release 2.14.1
	* [r1231] Correct minor typos in man page for estimable()
	* [r1230] Add support for lme models to estimable()
	* [r1229] Replace non-ascii characters in Soren's name with
	  (equivalent?) ascii character to avoid character encoding issues.

2007-10-22  warnes

	* [r1196] Clarify GPL version

2007-07-26  warnes

	* [r1105] Add support for mlm to estimable().
	* [r1104] Add estimable method for mlm objects

2007-03-09  warnes

	* [r1079] Remove stray character
	* [r1078] Update NEWS file.
	* [r1077] Update version number
	* [r1076] Minor code formatting changes
	* [r1075] Flip lower and upper interval in ci.lmer(). Add example
	  to man page.
	* [r1074] Fix some old email addressses that got missed

2006-11-29  warnes

	* [r1029] Update for 2.13.1
	* [r1028] Correct declartion of S3 methods for estimable()
	* [r1027] Add additional suggested packages
	* [r1026] - Add generic
	  - Fix code vs. doc inconsistiencies

2006-11-28  warnes

	* [r1025] Remove extraneous comma that causes errors in R 2.5.0

2006-11-27  warnes

	* [r1016] Update for 2.13.1
	* [r1015] Add missing export of methods for estimable()

2006-11-14  ggorjan

	* [r1012] Removed executable property

2006-08-02  warnes

	* [r977] Update my email address

2006-06-06  nj7w

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

2006-06-05  nj7w

	* [r965] Additions as per Randall C Johnson
	* [r964] Additions as per Randall C Johnson
	* [r963] - New function to estimate CI's and p-values using
	  mcmcsamp() from the
	  Matrix package

2006-05-05  nj7w

	* [r959] 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  nj7w

	* [r808] Removed ChangeLog
	* [r807] Updated NEWS

2005-12-12  nj7w

	* [r796] Updated version number for CRAN

2005-12-04  warnes

	* [r781] Update for 2.11.0
	* [r780] 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  nj7w

	* [r776] Updated Greg's email address

2005-10-27  warnes

	* [r709] Update version number. Bump minor version since we added
	  functionality.
	* [r708] Add ci.binom() to NAMESPACE, bump version

2005-10-26  warnes

	* [r707] Add ci.binom

2005-10-25  warnes

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

2005-09-12  nj7w

	* [r671] Updated Greg's email

2005-09-07  nj7w

	* [r667] Fixed man page

2005-09-06  nj7w

	* [r664] Updated DESCRIPTION
	* [r663] Added NEWS
	* [r662] Fixed the Package name

2005-09-02  nj7w

	* [r655] Added ChangeLog

2005-08-31  nj7w

	* [r644] Added DESCRIPTION file
	* [r643] removed DESCRIPTION.in

2005-07-11  nj7w

	* [r627] 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  nj7w

	* [r625] Updating the version number, and various help files to
	  synchronize splitting of gregmisc bundle in 4 individual
	  components.
	* [r623] 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  nj7w

	* [r621] 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  warnes

	* [r620] Add dependency on gdata::frameApply.

2005-03-31  warnes

	* [r593] Add ceofFrame function to NAMESPACE
	* [r592] coefFrame example needs to properly load ELISA data from
	  gtools package
	* [r588] Ensure that each file has $Id$ header, and no $Log$
	* [r587] Add coefFrame() function contributed by Jim Rogers

2005-01-18  warnes

	* [r521] Removed Windows Line Endings

2005-01-14  nj7w

	* [r518] Updated the manual to reflect prop.chisq change in its R
	  file.

2005-01-14  warnes

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

2005-01-12  warnes

	* [r515] 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  nj7w

	* [r507] 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  warnes

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

2004-09-30  warneg

	* [r464] Fix typos.

2004-09-27  warneg

	* [r461] Updated to pass R CMD check.

2004-09-03  warneg

	* [r450] Add explicit package to call to quantcut in example.
	* [r446] initial bundle checkin

2004-09-02  warneg

	* [r442] Initial revision

2004-05-25  warnes

	* [r327] Updates from Mark Schwartz.

2004-04-13  warnes

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

2004-03-26  warnes

	* [r306] Reflect movement of code from 'mva' package to 'stats' in
	  R 1.9.0.

2004-03-25  warnes

	* [r296] - 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
	* [r295] 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  warnes

	* [r221] - 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  warnes

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

2003-04-22  warnes

	* [r190] - the variable 'df' was used within the lme code section
	  overwriting
	  the argument 'df'.

2003-03-12  warnes

	* [r173] - Fixed a typo in the example
	  - Added to lme example

2003-03-07  warnes

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

2003-01-30  warnes

	* [r160] - 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.
	* [r158] - 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.
	* [r157] - 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  warnes

	* [r142] - 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  warnes

	* [r138] - Fixes to fast.svd to make it actually work.
	  - Updates to man page to fix mistmatches between code and docs
	  and to
	  fix warnings.
	* [r137] - 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.
	* [r136] Initial checkin for fast.prcomp() and fast.svd().

2002-09-26  warnes

	* [r127] - Added note and example code to illustrate how to
	  properly compute
	  contrasts for the first factor in the model.

2002-09-24  warnes

	* [r124] - Fixed a typo.

2002-09-23  warnes

	* [r119] - Fixed syntax errors in barplot2.Rd and CrossTable.Rd
	  - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
	  glh.test.Rd
	* [r117] - Modified all files to include CVS Id and Log tags.
	* [r116] - 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  warnes

	* [r114] - 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  warneg

	* [r109] Checkin for version 0.5.3

2002-03-26  warneg

	* [r104] - Changed methods to include '...' to match the generic.
	  - Updated for version 0.5.1
	* [r99] Removed incorrect link to 'contrast' from seealso.

2002-02-20  warneg

	* [r81] Minor changes, typo and formatting fixes.

2002-01-17  warneg

	* [r70] - Fixed errror in last example by adding 'conf.int'
	  parameter to
	  'estimable' call.
	* [r69] - Fixed typo in code that resulted in an syntax error.

2002-01-10  warneg

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

2001-12-19  warneg

	* [r66] - Fixed display of formulae.
	  - Added description of return value
	* [r65] - Removed extra element of return object.

2001-12-18  warneg

	* [r64] - Updated documentation to reflect change of parameters
	  from 'alpha'
	  to 'conf.int', including the new optional status of the
	  confidence
	  intervals.
	* [r63] - Modified to make confidence intervals optional. Changed
	  'alpha'
	  parameter giving significance level to 'conf.int' giving
	  confidence
	  level.
	* [r62] - Added summary.glh.test to alias, usage, and example
	  sections.
	* [r61] - 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'
	* [r60] - 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.
	* [r59] Initial checkin.

2001-12-17  warneg

	* [r56] - Fixed spelling errors.
	* [r55] - Fixed the link to contrasts.lm.
	  - Rephrased title/description to be more clear.

2001-12-10  warneg

	* [r49] Renamed 'contrsts.coeff.Rd' to 'estimable.Rd' corresponding
	  to function rename.
	* [r48] renamed from contrast.coeff.R to estimable.R (incorrectly
	  via contrast.lm.R)

2001-12-07  warneg

	* [r37] - Added text noting that lme is now supported.
	* [r36] - Fixed typo: DF column was being filled in with p-value.
	* [r35] - Added ci.lme method to handle lme objects.

2001-10-16  warneg

	* [r27] Fixed unbalanced brace.

2001-08-25  warneg

	* [r12] - Added CVS header.
	  - Added my email address.

2001-05-30  warneg

	* [r2] Initial revision