[R-gregmisc-commits] r2195 - in pkg/gmodels: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 25 16:53:15 CEST 2018
Author: warnes
Date: 2018-06-25 16:53:14 +0200 (Mon, 25 Jun 2018)
New Revision: 2195
Added:
pkg/gmodels/ChangeLog
pkg/gmodels/NEWS
Removed:
pkg/gmodels/inst/ChangeLog
pkg/gmodels/inst/NEWS
Log:
Move NEWS and ChangeLog to top level.
Copied: pkg/gmodels/ChangeLog (from rev 2194, pkg/gmodels/inst/ChangeLog)
===================================================================
--- pkg/gmodels/ChangeLog (rev 0)
+++ pkg/gmodels/ChangeLog 2018-06-25 14:53:14 UTC (rev 2195)
@@ -0,0 +1,834 @@
+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 at 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 at 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 at 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 at 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
+
Copied: pkg/gmodels/NEWS (from rev 2194, pkg/gmodels/inst/NEWS)
===================================================================
--- pkg/gmodels/NEWS (rev 0)
+++ pkg/gmodels/NEWS 2018-06-25 14:53:14 UTC (rev 2195)
@@ -0,0 +1,168 @@
+Version 2.18.0 - 2018-06-19
+---------------------------
+
+Bug fixes:
+
+- ci.binom() was using an incorrect method for calcuating binomial
+ conficence intervals. It now calculates the Clopper-Pearson 'exect'
+ interval, which is *conservative* due to the discrete nature of the
+ binomial distribution.
+
+Other Changes:
+
+- Support for lme4 objects has been removed due to incompatible
+ changes to the lme4 package.
+
+Version 2.16.0 - 2014-07-24
+---------------------------
+
+New features:
+
+- The estimable() function now returns objects that are of class
+ 'estimable'.
+
+- The confidence interval function ci() now has a method for
+ 'estimable' objects, with the same layout as for 'lm' objects,
+ making it easier to combine confidence information about model
+ parameters and estimable functions into a single table.
+
+
+Version 2.15.5 - 2013-07-18
+---------------------------
+
+Bug fixes:
+
+- Correct error in estimable.mlm() that caused it to always fail. Added
+ test code to prevent future issues.
+
+Other Changes:
+
+- Update man page file for ci() to current Rd syntax.
+- Remove unused argument to ci.mer()
+
+
+Version 2.15.3 - 2012-06-27
+---------------------------
+
+Bug fixes:
+
+- Update est.mer() to work with "mer" object changes introduced in
+ lme4 version 0.999999-0.
+
+
+Version 2.15.2 - 2012-04-19
+---------------------------
+
+Bug fixes:
+
+- Update est.mer() to work with recent versions of lme4 which changed
+ 'mer' objects from S3 to S4 class
+
+- Changes to pass new R CMD check tests
+
+- The 'Design' package has been replaced my 'rms', so update man page
+ references.
+
+
+Version 2.15.1 - 2011-01-16
+---------------------------
+
+Bug fixes:
+
+- Fix warnings reported by new versions of R CMD check.
+
+
+Version 2.15.0
+--------------
+
+New features:
+
+- Add support for 'mer' model from lme4.
+
+Bug fixes:
+
+- Correct several minor .Rd syntax errors
+
+- Move extra copyright text to Author field instead of License field.
+
+
+Version 2.14.1
+--------------
+
+New features:
+
+- Add support for 'lme' objects to estimable().
+
+Other:
+
+- Fix minor typos in manual page for estimable().
+
+Version 2.14.0
+--------------
+
+New Features:
+
+- Add support for 'mlm' objects to estimable
+
+
+Version 2.13.2
+--------------
+
+Bug Fixes:
+
+- Lower and upper end of confidence interval for lmer objects were
+ reversed in est.lmer().
+
+- Correct Greg's email address in two help files.
+
+
+Version 2.13.1
+--------------
+
+Bug Fixes:
+
+- Problem: R CMD check errors under development version of R 2.5.0
+ Solution:
+ - Add additional packages to 'Suggests' list in DESCRIPTION
+ - Remove extra trailing comma in function calls
+ - fix various code/doc inconsistencies
+
+- Problem: estimable() was failing for lmer objects.
+ Solution:
+ - Create a generic estimable()
+ - Move old function to estimable.default()
+ - Add estimable.lmer() to the exported methods list in NAMESPACE
+
+
+Version 2.13.0
+--------------
+
+
+Version 2.12.0
+--------------
+
+- Updated Greg's email address.
+
+- Add support for lmer (lme version 4) objects to ci(), estimable(),
+ and fit.contrast() via code contributed by Randall C Johnson.
+
+- Add simplfied coefficient specification to 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.
+
+Version 2.1.0
+-------------
+
+Version 2.0.8
+-------------
+
+ - Added DESCRIPTION and removed DESCRIPTION.in
+
+ - Updated CrossTable.R
+
+ - Updated NAMESPACE file
+
Deleted: pkg/gmodels/inst/ChangeLog
===================================================================
--- pkg/gmodels/inst/ChangeLog 2018-06-25 14:52:45 UTC (rev 2194)
+++ pkg/gmodels/inst/ChangeLog 2018-06-25 14:53:14 UTC (rev 2195)
@@ -1,834 +0,0 @@
-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 at 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 at jura.uni-hamburg.de>.
-
-2004-09-30 21:03 warneg
-
- * Fix typos.
-
[TRUNCATED]
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